From b520b2e84bdfd88bc8c4b1f2d23e66227f3a29f2 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 22 Sep 2022 14:23:35 +0100
Subject: [PATCH 001/134] Working EasyBlock for newer versions of GAMESS-US,
 based on PR #1925

---
 easybuild/easyblocks/g/gamess_us.py | 237 ++++++++++++++++++++++------
 1 file changed, 185 insertions(+), 52 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 4d658a7c0e..35a92812b4 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2022 Ghent University
+# Copyright 2009-2020 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -37,17 +37,20 @@
 import fileinput
 import glob
 import os
+import random
 import re
 import shutil
 import sys
 import tempfile
+import fnmatch
 
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import read_file, write_file
+from easybuild.tools.filetools import change_dir, read_file, write_file
 from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.py2vs3 import ascii_letters
 from easybuild.tools.run import run_cmd, run_cmd_qa
 from easybuild.tools.systemtools import get_platform_name
 from easybuild.tools import toolchain
@@ -64,6 +67,7 @@ def extra_options():
             'maxcpus': [None, "Maximum number of cores per node", MANDATORY],
             'maxnodes': [None, "Maximum number of nodes", MANDATORY],
             'runtest': [True, "Run GAMESS-US tests", CUSTOM],
+            'omp': [False, "Enabling OpenMP", CUSTOM],
             'scratch_dir': ['$TMPDIR', "Scratch dir to be used in rungms script", CUSTOM],
         }
         return EasyBlock.extra_options(extra_vars)
@@ -77,8 +81,10 @@ def __init__(self, *args, **kwargs):
             self.testdir = tempfile.mkdtemp()
             # make sure test dir doesn't contain [ or ], rungms csh script doesn't handle that well ("set: No match")
             if re.search(r'[\[\]]', self.testdir):
-                error_msg = "Temporary dir for tests '%s' will cause problems with rungms csh script"
-                raise EasyBuildError(error_msg, self.testdir)
+                raise EasyBuildError("Temporary dir for tests '%s' will cause problems with rungms csh script",
+                                     self.testdir)
+
+        self.scratch_dir = self.cfg['scratch_dir']
 
     def extract_step(self):
         """Extract sources."""
@@ -88,12 +94,17 @@ def extract_step(self):
 
     def configure_step(self):
         """Configure GAMESS-US build via provided interactive 'config' script."""
-
+        """Opening install.info file as append"""
+        f = open(self.builddir + "/install.info", "a")
+        f.writelines(["setenv GMS_PATH " + self.builddir + "\n"
+            "setenv GMS_BUILD_DIR " + self.installdir + "\n"])
         # machine type
         platform_name = get_platform_name()
         x86_64_linux_re = re.compile('^x86_64-.*$')
         if x86_64_linux_re.match(platform_name):
             machinetype = "linux64"
+            f.writelines(["setenv GMS_TARGET " + machinetype + "\n" +
+                "setenv GMS_HPC_SYSTEM_TARGET generic" + "\n"])
         else:
             raise EasyBuildError("Build target %s currently unsupported", platform_name)
 
@@ -114,6 +125,9 @@ def configure_step(self):
         else:
             raise EasyBuildError("Compiler family '%s' currently unsupported.", comp_fam)
 
+        f.writelines(["setenv GMS_FORTRAN " + fortran_comp + "\n" + 
+            "setenv GMS_GFORTRAN_VERNO " + fortran_ver + "\n"])
+
         # math library config
         known_mathlibs = ['imkl', 'OpenBLAS', 'ATLAS', 'ACML']
         mathlib, mathlib_root = None, None
@@ -125,15 +139,38 @@ def configure_step(self):
             raise EasyBuildError("None of the known math libraries (%s) available, giving up.", known_mathlibs)
         if mathlib == 'imkl':
             mathlib = 'mkl'
-            mathlib_root = os.path.join(mathlib_root, 'mkl')
+            mathlib_vers_res = '.'.join(get_software_version('imkl').split('.')[:1])
+            if int(mathlib_vers_res) == 2020:
+                mathlib_root = os.path.join(mathlib_root, 'mkl/lib/intel64')
+            elif int(mathlib_vers_res) == 2021:
+                mathlib_root = os.path.join(mathlib_root, 'mkl/latest/lib/intel64')
+
+            if int(mathlib_vers_res) >= 2020:
+                # For some GAMESS-US versions oneapi is not in lked, so we use 12-so instead
+                if self.version == "20200630-R1" or self.version == "20200930-R2":
+                    mathlib_vers = "12-so"
+                elif self.version == "20210620-R1":
+                    mathlib_vers = "12-so"
+                else:
+                    mathlib_vers = "oneapi-so"
+            else:
+                mathlib_vers = "12"
+
         else:
             mathlib = mathlib.lower()
 
+        f.writelines(["setenv GMS_MATHLIB " + mathlib + "\n" +
+            "setenv GMS_MATHLIB_PATH " + mathlib_root + "\n" +
+            "setenv GMS_MKL_VERNO " + mathlib_vers + "\n" +
+            "setenv GMS_LAPACK_LINK_LINE" + "" + "\n"])
+
         # verify selected DDI communication layer
         known_ddi_comms = ['mpi', 'mixed', 'shmem', 'sockets']
         if not self.cfg['ddi_comm'] in known_ddi_comms:
             raise EasyBuildError("Unsupported DDI communication layer specified (known: %s): %s",
                                  known_ddi_comms, self.cfg['ddi_comm'])
+        
+        f.writelines(["setenv GMS_DDI_COMM " + self.cfg['ddi_comm'] + "\n" ])
 
         # MPI library config
         mpilib, mpilib_root, mpilib_path = None, None, None
@@ -154,38 +191,32 @@ def configure_step(self):
         else:
             mpilib, mpilib_root = '', ''
 
-        # run interactive 'config' script to generate install.info file
-        cmd = "%(preconfigopts)s ./config %(configopts)s" % {
-            'preconfigopts': self.cfg['preconfigopts'],
-            'configopts': self.cfg['configopts'],
-        }
-        qa = {
-            "After the new window is open, please hit <return> to go on.": '',
-            "please enter your target machine name: ": machinetype,
-            "Version? [00] ": self.version,
-            "Please enter your choice of FORTRAN: ": fortran_comp,
-            "hit <return> to continue to the math library setup.": '',
-            "MKL pathname? ": mathlib_root,
-            "MKL version (or 'skip')? ": 'skip',
-            "MKL version (or 'proceed')? ": 'proceed',  # changed in gamess-20170420R1
-            "please hit <return> to compile the GAMESS source code activator": '',
-            "please hit <return> to set up your network for Linux clusters.": '',
-            "communication library ('sockets' or 'mpi')? ": self.cfg['ddi_comm'],
-            "Enter MPI library (impi, mvapich2, mpt, sockets):": mpilib,
-            "Enter MPI library (impi, mpich, mpich2, mvapich2, mpt, sockets):": mpilib,  # changed in gamess-20170420R1
-            "Please enter your %s's location: " % mpilib: mpilib_root,
-            "Do you want to try LIBCCHEM?  (yes/no): ": 'no',
-            "Enter full path to OpenBLAS libraries (without 'lib' subdirectory):": mathlib_root,
-            "Optional: Build Michigan State University CCT3 & CCSD3A methods?  (yes/no): ": 'no',
-        }
-        stdqa = {
-            r"GAMESS directory\? \[.*\] ": self.builddir,
-            r"GAMESS build directory\? \[.*\] ": self.installdir,  # building in install directory
-            r"Enter only the main version number, such as .*\nVersion\? ": fortran_ver,
-            r".+gfortran version.\n( \n)?Please enter only the first decimal place, such as .*:": fortran_ver,
-            "Enter your choice of 'mkl' or .* 'none': ": mathlib,
-        }
-        run_cmd_qa(cmd, qa=qa, std_qa=stdqa, log_all=True, simple=True)
+        f.writelines(["setenv GMS_MPI_LIB " + mpilib + "\n" + 
+            "setenv GMS_MPI_PATH " + mpilib_root + "\n"])
+
+        # These are extra programs which for now we simply set all to FALSE
+        f. writelines(["setenv GMS_MSUCC false " + "\n"])
+        f. writelines(["setenv GMS_LIBCCHEM false" + "\n"])
+        f. writelines(["setenv GMS_PHI none " + "\n"])
+        f. writelines(["setenv GMS_SHMTYPE sysv " + "\n"])
+
+        if self.cfg['omp'] == 'True':
+            f. writelines(["setenv GMS_OPENMP true" + "\n"])
+        else:
+            f. writelines(["setenv GMS_OPENMP false" + "\n"])
+        
+        f. writelines(["setenv GMS_LIBXC false " + "\n"])
+        f. writelines(["setenv GMS_MDI false " + "\n"])
+        f. writelines(["setenv GMS_VM2 false " + "\n"])
+        f. writelines(["setenv TINKER false " + "\n"])
+        f. writelines(["setenv VB2000 false " + "\n"])
+        f. writelines(["setenv XMVB false " + "\n"])
+        f. writelines(["setenv NEO false " + "\n"])
+        f. writelines(["setenv NBO false " + "\n"])
+        f. writelines(["setenv GMS_FPE_FLAGS " + "\n"]) 
+        #f. writelines(["setenv GMS_FPE_FLAGS '-ffpe-trap=invalid,zero,overflow' " + "\n"]) # This seems to be useful for debugging 
+
+        f.close()
 
         self.log.debug("Contents of install.info:\n%s" % read_file(os.path.join(self.builddir, 'install.info')))
 
@@ -209,6 +240,107 @@ def configure_step(self):
         except IOError as err:
             raise EasyBuildError("Failed to patch %s: %s", rungms, err)
 
+        # Replacing the MAXCPUS and MAXNODES in compddi to a value from the EasyConfig file
+        compddi = os.path.join(self.builddir, 'ddi/compddi')
+        try:
+            for line in fileinput.input(compddi, inplace=1, backup='.orig'):
+                line = re.sub(r"^(\s*set MAXCPUS)=.*", r"\1=%s" % self.cfg['maxcpus'], line, 1)
+                line = re.sub(r"^(\s*set MAXNODES)=.*", r"\1=%s" % self.cfg['maxnodes'], line, 1)
+                sys.stdout.write(line)
+        except IOError as err:
+                raise EasyBuildError("Failed to patch compddi", compddi, err)
+
+        # for GAMESS-US 20200630-R1 we need to build the actvte.x program
+        if self.version == "20200630-R1":
+            actvte = os.path.join(self.builddir, 'tools/actvte.code')
+            try:
+                for line in fileinput.input(actvte, inplace=1, backup='.orig'):
+                    line = re.sub("\*UNX", "    ", line)
+                    sys.stdout.write(line)
+            except IOError as err:
+                raise EasyBuildError("Failed to patch actvte.code", actvte, err)
+            # compiling
+            run_cmd("mv %s/tools/actvte.code" % self.builddir + " %s/tools/actvte.f" % self.builddir)
+            run_cmd("%s -o " % fortran_comp + " %s/tools/actvte.x" % self.builddir + " %s/tools/actvte.f" % self.builddir)
+
+    def build_step(self):
+        """Custom build procedure for GAMESS-US: using compddi, compall and lked scripts."""
+        compddi = os.path.join(self.cfg['start_dir'], 'ddi', 'compddi')
+        run_cmd(compddi, log_all=True, simple=True)
+
+        # make sure the libddi.a library is present
+        libddi = os.path.join(self.cfg['start_dir'], 'ddi', 'libddi.a')
+        if not os.path.isfile(libddi):
+            raise EasyBuildError("The libddi.a library (%s) was never built", libddi)
+        else:
+            self.log.info("The libddi.a library (%s) was successfully built." % libddi)
+
+        ddikick = os.path.join(self.cfg['start_dir'], 'ddi', 'ddikick.x')
+        if os.path.isfile(ddikick):
+            self.log.info("The ddikick.x executable (%s) was successfully built." % ddikick)
+
+            if self.cfg['ddi_comm'] == 'sockets':
+                src = ddikick
+                dst = os.path.join(self.cfg['start_dir'], 'ddikick.x')
+                self.log.info("Moving ddikick.x executable from %s to %s." % (src, dst))
+                os.rename(src, dst)
+
+        compall_cmd = os.path.join(self.cfg['start_dir'], 'compall')
+        compall = "%s %s %s" % (self.cfg['prebuildopts'], compall_cmd, self.cfg['buildopts'])
+        run_cmd(compall, log_all=True, simple=True)
+
+        cmd = "%s gamess %s" % (os.path.join(self.cfg['start_dir'], 'lked'), self.version)
+        run_cmd(cmd, log_all=True, simple=True)
+
+        # Done up to here
+        quit()
+
+        if self.scratch_dir:
+            # FIXME: resolve environment variables used in scratch_dir values
+
+            # use unique subdirectory in specified scratch dir;
+            # we should use a shell command to create this directory,
+            # since scratch_dir may include names of environment variables
+            salt = ''.join(random.choice(ascii_letters) for i in range(10))
+            self.scratch_dir = os.path.join(self.scratch_dir, self.name + '-' + salt)
+
+            # make sure that specified directory is accessible via 'ssh', since rungms relies on that;
+            # touch a file, and then use "ssh localhost ls" to see if it's accessible;
+            # we must use shell commands for this, since scratch_dir may contain names of environment variables
+            test_file = os.path.join(self.scratch_dir, 'test.txt')
+            run_cmd("mkdir -p %s" % self.scratch_dir)
+            run_cmd("touch %s" % test_file)
+            test_cmd = 'ssh localhost "ls %s"' % test_file
+            (out, ec) = run_cmd(test_cmd, simple=False, log_ok=False, log_all=False)
+            if ec:
+                error_msg = "Scratch directory %s is not accessible via 'ssh'!\n" % self.scratch_dir
+                error_msg += "Specify a different path using the 'scratch_dir' easyconfig parameter.\n"
+                error_msg += "Output of test command '%s': %s" % (test_cmd, out)
+                raise EasyBuildError(error_msg)
+            else:
+                self.log.info("Using %s as scratch directory", self.scratch_dir)
+
+        # patch hardcoded settings in rungms to use values specified in easyconfig file
+        rungms = os.path.join(self.builddir, 'rungms')
+        extra_gmspath_lines = "set ERICFMT=$GMSPATH/auxdata/ericfmt.dat\nset MCPPATH=$GMSPATH/auxdata/MCP\n"
+        try:
+            for line in fileinput.input(rungms, inplace=1, backup='.orig'):
+                line = re.sub(r"^(\s*set\s*TARGET)=.*", r"\1=%s" % self.cfg['ddi_comm'], line)
+                line = re.sub(r"^(\s*set\s*GMSPATH)=.*", r"\1=%s\n%s" % (self.installdir, extra_gmspath_lines), line)
+                line = re.sub(r"^(\s*set\s*GMS_OPENMP)=.*", r"\1=%s" % "true", line) # changed in gamess-20190930-R2 for OpenBLAS support
+                line = re.sub(r"(null\) set VERNO)=.*", r"\1=%s" % self.version, line)
+                line = re.sub(r"^(\s*set DDI_MPI_CHOICE)=.*", r"\1=%s" % mpilib, line)
+                line = re.sub(r"^(\s*set DDI_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)
+                line = re.sub(r"^(\s*set GA_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)
+                # comment out all adjustments to $LD_LIBRARY_PATH that involves hardcoded paths
+                line = re.sub(r"^(\s*)(setenv\s*LD_LIBRARY_PATH\s*/.*)", r"\1#\2", line)
+                if self.scratch_dir:
+                    line = re.sub(r"^(\s*set\s*SCR)=.*", r"\1=%s" % self.scratch_dir, line)
+                    line = re.sub(r"^(\s*set\s*USERSCR)=.*", r"\1=%s" % self.scratch_dir, line)
+                sys.stdout.write(line)
+        except IOError as err:
+            raise EasyBuildError("Failed to patch %s: %s", rungms, err)
+
     def build_step(self):
         """Custom build procedure for GAMESS-US: using compddi, compall and lked scripts."""
         compddi = os.path.join(self.cfg['start_dir'], 'ddi', 'compddi')
@@ -247,11 +379,7 @@ def test_step(self):
                 self.log.info("Skipping testing of GAMESS-US since MPI testing is disabled")
                 return
 
-            try:
-                cwd = os.getcwd()
-                os.chdir(self.testdir)
-            except OSError as err:
-                raise EasyBuildError("Failed to move to temporary directory for running tests: %s", err)
+            cwd = change_dir(self.testdir)
 
             # copy input files for exam<id> standard tests
             for test_input in glob.glob(os.path.join(self.installdir, 'tests', 'standard', 'exam*.inp')):
@@ -261,7 +389,7 @@ def test_step(self):
                     raise EasyBuildError("Failed to copy %s to %s: %s", test_input, os.getcwd(), err)
 
             rungms = os.path.join(self.installdir, 'rungms')
-            test_env_vars = ['TMPDIR=%s' % self.testdir]
+            test_env_vars = ['export OMP_NUM_THREADS=1; TMPDIR=%s' % self.testdir ]
             if self.toolchain.mpi_family() == toolchain.INTELMPI:
                 test_env_vars.extend([
                     'I_MPI_FALLBACK=enable',  # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)
@@ -269,8 +397,10 @@ def test_step(self):
                 ])
 
             # run all exam<id> tests, dump output to exam<id>.log
-            n_tests = 47
-            for i in range(1, n_tests + 1):
+            # we let Python count the number of *.inp files as that changes
+            tests_path = os.path.join(self.installdir, 'tests', 'standard')
+            n_tests = len(fnmatch.filter(os.listdir(tests_path), '*.inp'))
+            for i in range(1, n_tests+1):
                 test_cmd = ' '.join(test_env_vars + [rungms, 'exam%02d' % i, self.version, '1', '2'])
                 (out, _) = run_cmd(test_cmd, log_all=True, simple=False)
                 write_file('exam%02d.log' % i, out)
@@ -284,12 +414,7 @@ def test_step(self):
             else:
                 raise EasyBuildError("Not all tests ran successfully...")
 
-            # cleanup
-            os.chdir(cwd)
-            try:
-                shutil.rmtree(self.testdir)
-            except OSError as err:
-                raise EasyBuildError("Failed to remove test directory %s: %s", self.testdir, err)
+            change_dir(cwd)
 
     def install_step(self):
         """Skip install step, since we're building in the install directory."""
@@ -309,3 +434,11 @@ def make_module_extra(self):
         txt += self.module_generator.set_environment('GAMESSUSROOT', self.installdir)
         txt += self.module_generator.prepend_paths("PATH", [''])
         return txt
+
+    def cleanup_step(self):
+        """Cleanup set."""
+        # remove dedicated scratch directory (if any);
+        # we must use a shell command for this, since the path may contain environment variables
+        super(EB_GAMESS_minus_US, self).cleanup_step()
+
+        # FIXME

From e1691ad3f71594a7b454ea23f0e07853a73780a9 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 22 Sep 2022 16:34:10 +0100
Subject: [PATCH 002/134] Whitespace deleted

---
 easybuild/easyblocks/g/gamess_us.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 35a92812b4..04b9abae28 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -389,7 +389,7 @@ def test_step(self):
                     raise EasyBuildError("Failed to copy %s to %s: %s", test_input, os.getcwd(), err)
 
             rungms = os.path.join(self.installdir, 'rungms')
-            test_env_vars = ['export OMP_NUM_THREADS=1; TMPDIR=%s' % self.testdir ]
+            test_env_vars = ['export OMP_NUM_THREADS=1; TMPDIR=%s' % self.testdir]
             if self.toolchain.mpi_family() == toolchain.INTELMPI:
                 test_env_vars.extend([
                     'I_MPI_FALLBACK=enable',  # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)

From 1b03f22c81a2414af083c476d661d4a246db78b2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 7 Mar 2023 11:20:07 +0100
Subject: [PATCH 003/134] revert error message format change in gamess-us
 easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 04b9abae28..2ffe4414a2 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -81,8 +81,8 @@ def __init__(self, *args, **kwargs):
             self.testdir = tempfile.mkdtemp()
             # make sure test dir doesn't contain [ or ], rungms csh script doesn't handle that well ("set: No match")
             if re.search(r'[\[\]]', self.testdir):
-                raise EasyBuildError("Temporary dir for tests '%s' will cause problems with rungms csh script",
-                                     self.testdir)
+                error_msg = "Temporary dir for tests '%s' will cause problems with rungms csh script"
+                raise EasyBuildError(error_msg, self.testdir)
 
         self.scratch_dir = self.cfg['scratch_dir']
 

From 1fe8e0aba57c7e1287955352f652e5670bbdfdaa Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 7 Mar 2023 11:27:47 +0100
Subject: [PATCH 004/134] remove duplicate build step in gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 78 -----------------------------
 1 file changed, 78 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 2ffe4414a2..a450ab9387 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -263,84 +263,6 @@ def configure_step(self):
             run_cmd("mv %s/tools/actvte.code" % self.builddir + " %s/tools/actvte.f" % self.builddir)
             run_cmd("%s -o " % fortran_comp + " %s/tools/actvte.x" % self.builddir + " %s/tools/actvte.f" % self.builddir)
 
-    def build_step(self):
-        """Custom build procedure for GAMESS-US: using compddi, compall and lked scripts."""
-        compddi = os.path.join(self.cfg['start_dir'], 'ddi', 'compddi')
-        run_cmd(compddi, log_all=True, simple=True)
-
-        # make sure the libddi.a library is present
-        libddi = os.path.join(self.cfg['start_dir'], 'ddi', 'libddi.a')
-        if not os.path.isfile(libddi):
-            raise EasyBuildError("The libddi.a library (%s) was never built", libddi)
-        else:
-            self.log.info("The libddi.a library (%s) was successfully built." % libddi)
-
-        ddikick = os.path.join(self.cfg['start_dir'], 'ddi', 'ddikick.x')
-        if os.path.isfile(ddikick):
-            self.log.info("The ddikick.x executable (%s) was successfully built." % ddikick)
-
-            if self.cfg['ddi_comm'] == 'sockets':
-                src = ddikick
-                dst = os.path.join(self.cfg['start_dir'], 'ddikick.x')
-                self.log.info("Moving ddikick.x executable from %s to %s." % (src, dst))
-                os.rename(src, dst)
-
-        compall_cmd = os.path.join(self.cfg['start_dir'], 'compall')
-        compall = "%s %s %s" % (self.cfg['prebuildopts'], compall_cmd, self.cfg['buildopts'])
-        run_cmd(compall, log_all=True, simple=True)
-
-        cmd = "%s gamess %s" % (os.path.join(self.cfg['start_dir'], 'lked'), self.version)
-        run_cmd(cmd, log_all=True, simple=True)
-
-        # Done up to here
-        quit()
-
-        if self.scratch_dir:
-            # FIXME: resolve environment variables used in scratch_dir values
-
-            # use unique subdirectory in specified scratch dir;
-            # we should use a shell command to create this directory,
-            # since scratch_dir may include names of environment variables
-            salt = ''.join(random.choice(ascii_letters) for i in range(10))
-            self.scratch_dir = os.path.join(self.scratch_dir, self.name + '-' + salt)
-
-            # make sure that specified directory is accessible via 'ssh', since rungms relies on that;
-            # touch a file, and then use "ssh localhost ls" to see if it's accessible;
-            # we must use shell commands for this, since scratch_dir may contain names of environment variables
-            test_file = os.path.join(self.scratch_dir, 'test.txt')
-            run_cmd("mkdir -p %s" % self.scratch_dir)
-            run_cmd("touch %s" % test_file)
-            test_cmd = 'ssh localhost "ls %s"' % test_file
-            (out, ec) = run_cmd(test_cmd, simple=False, log_ok=False, log_all=False)
-            if ec:
-                error_msg = "Scratch directory %s is not accessible via 'ssh'!\n" % self.scratch_dir
-                error_msg += "Specify a different path using the 'scratch_dir' easyconfig parameter.\n"
-                error_msg += "Output of test command '%s': %s" % (test_cmd, out)
-                raise EasyBuildError(error_msg)
-            else:
-                self.log.info("Using %s as scratch directory", self.scratch_dir)
-
-        # patch hardcoded settings in rungms to use values specified in easyconfig file
-        rungms = os.path.join(self.builddir, 'rungms')
-        extra_gmspath_lines = "set ERICFMT=$GMSPATH/auxdata/ericfmt.dat\nset MCPPATH=$GMSPATH/auxdata/MCP\n"
-        try:
-            for line in fileinput.input(rungms, inplace=1, backup='.orig'):
-                line = re.sub(r"^(\s*set\s*TARGET)=.*", r"\1=%s" % self.cfg['ddi_comm'], line)
-                line = re.sub(r"^(\s*set\s*GMSPATH)=.*", r"\1=%s\n%s" % (self.installdir, extra_gmspath_lines), line)
-                line = re.sub(r"^(\s*set\s*GMS_OPENMP)=.*", r"\1=%s" % "true", line) # changed in gamess-20190930-R2 for OpenBLAS support
-                line = re.sub(r"(null\) set VERNO)=.*", r"\1=%s" % self.version, line)
-                line = re.sub(r"^(\s*set DDI_MPI_CHOICE)=.*", r"\1=%s" % mpilib, line)
-                line = re.sub(r"^(\s*set DDI_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)
-                line = re.sub(r"^(\s*set GA_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)
-                # comment out all adjustments to $LD_LIBRARY_PATH that involves hardcoded paths
-                line = re.sub(r"^(\s*)(setenv\s*LD_LIBRARY_PATH\s*/.*)", r"\1#\2", line)
-                if self.scratch_dir:
-                    line = re.sub(r"^(\s*set\s*SCR)=.*", r"\1=%s" % self.scratch_dir, line)
-                    line = re.sub(r"^(\s*set\s*USERSCR)=.*", r"\1=%s" % self.scratch_dir, line)
-                sys.stdout.write(line)
-        except IOError as err:
-            raise EasyBuildError("Failed to patch %s: %s", rungms, err)
-
     def build_step(self):
         """Custom build procedure for GAMESS-US: using compddi, compall and lked scripts."""
         compddi = os.path.join(self.cfg['start_dir'], 'ddi', 'compddi')

From bcb9f0fbcca6da8459a35b74833cfd4bc9f4757a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 7 Mar 2023 11:32:52 +0100
Subject: [PATCH 005/134] add user_scratch_dir extra option to gamess-us
 easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index a450ab9387..612b987951 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -68,7 +68,8 @@ def extra_options():
             'maxnodes': [None, "Maximum number of nodes", MANDATORY],
             'runtest': [True, "Run GAMESS-US tests", CUSTOM],
             'omp': [False, "Enabling OpenMP", CUSTOM],
-            'scratch_dir': ['$TMPDIR', "Scratch dir to be used in rungms script", CUSTOM],
+            'scratch_dir': ['$TMPDIR', "dir for temporary binary files", CUSTOM],
+            'user_scratch_dir': ['$TMPDIR', "dir for supplementary output files", CUSTOM],
         }
         return EasyBlock.extra_options(extra_vars)
 
@@ -84,8 +85,6 @@ def __init__(self, *args, **kwargs):
                 error_msg = "Temporary dir for tests '%s' will cause problems with rungms csh script"
                 raise EasyBuildError(error_msg, self.testdir)
 
-        self.scratch_dir = self.cfg['scratch_dir']
-
     def extract_step(self):
         """Extract sources."""
         # strip off 'gamess' part to avoid having everything in a 'gamess' subdirectory
@@ -233,9 +232,10 @@ def configure_step(self):
                 line = re.sub(r"^(\s*set GA_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)
                 # comment out all adjustments to $LD_LIBRARY_PATH that involves hardcoded paths
                 line = re.sub(r"^(\s*)(setenv\s*LD_LIBRARY_PATH\s*/.*)", r"\1#\2", line)
-                if self.cfg['scratch_dir']:
-                    line = re.sub(r"^(\s*set\s*SCR)=.*", r"\1=%s" % self.cfg['scratch_dir'], line)
-                    line = re.sub(r"^(\s*set\s*USERSCR)=.*", r"\1=%s" % self.cfg['scratch_dir'], line)
+                # scratch directory paths
+                line = re.sub(r"^(\s*set\s*SCR)=.*", r"if ( ! $?SCR ) \1=%s" % self.cfg['scratch_dir'], line)
+                line = re.sub(r"^(\s*set\s*USERSCR)=.*", r"if ( ! $?USERSCR ) \1=%s" % self.cfg['user_scratch_dir'], line)
+                line = re.sub(r"^(df -k \$SCR)$", r"mkdir -p $SCR && mkdir -p $USERSCR && \1", line)
                 sys.stdout.write(line)
         except IOError as err:
             raise EasyBuildError("Failed to patch %s: %s", rungms, err)

From bf674ad87f23ae303cd710afbf8a0de6c7d500ad Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 8 Mar 2023 15:26:55 +0100
Subject: [PATCH 006/134] streamline IMKL and fix support for OpenBLAS in
 gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 62 +++++++++++++++--------------
 1 file changed, 33 insertions(+), 29 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 612b987951..4ac5684faf 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -44,6 +44,8 @@
 import tempfile
 import fnmatch
 
+from distutils.version import LooseVersion
+
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
 from easybuild.tools.build_log import EasyBuildError
@@ -129,39 +131,41 @@ def configure_step(self):
 
         # math library config
         known_mathlibs = ['imkl', 'OpenBLAS', 'ATLAS', 'ACML']
-        mathlib, mathlib_root = None, None
-        for mathlib in known_mathlibs:
-            mathlib_root = get_software_root(mathlib)
-            if mathlib_root is not None:
-                break
-        if mathlib_root is None:
+        loaded_mathlib = [mathlib for mathlib in known_mathlibs if get_software_root(mathlib)]
+
+        # math library: default settings
+        try:
+            mathlib = loaded_mathlib[0].lower()
+            mathlib_root = get_software_root(loaded_mathlib[0])
+            mathlib_subfolder = ''
+            mathlib_flags = ''
+        except IndexError:
             raise EasyBuildError("None of the known math libraries (%s) available, giving up.", known_mathlibs)
+
         if mathlib == 'imkl':
             mathlib = 'mkl'
-            mathlib_vers_res = '.'.join(get_software_version('imkl').split('.')[:1])
-            if int(mathlib_vers_res) == 2020:
-                mathlib_root = os.path.join(mathlib_root, 'mkl/lib/intel64')
-            elif int(mathlib_vers_res) == 2021:
-                mathlib_root = os.path.join(mathlib_root, 'mkl/latest/lib/intel64')
-
-            if int(mathlib_vers_res) >= 2020:
-                # For some GAMESS-US versions oneapi is not in lked, so we use 12-so instead
-                if self.version == "20200630-R1" or self.version == "20200930-R2":
-                    mathlib_vers = "12-so"
-                elif self.version == "20210620-R1":
-                    mathlib_vers = "12-so"
-                else:
-                    mathlib_vers = "oneapi-so"
-            else:
-                mathlib_vers = "12"
-
+            mathlib_subfolder = 'mkl'
+            mathlib_flags = '-lmkl_intel_lp64'
+            imkl_ver = get_software_version('imkl')
+            if LooseVersion(imkl_ver) >= LooseVersion("2021"):
+                mathlib_subfolder = 'mkl/latest/lib/intel64'
+            elif LooseVersion(imkl_ver) >= LooseVersion("2020"):
+                mathlib_subfolder = 'mkl/lib/intel64'
+        elif mathlib == 'openblas':
+            mathlib_flags="-lopenblas -lgfortran"
+            if LooseVersion(self.version) >= LooseVersion('20210101'):
+                mathlib_subfolder = 'lib'
+
+        if mathlib_root is not None:
+            mathlib_path = os.path.join(mathlib_root, mathlib_subfolder)
+            self.log.debug("Software root of math libraries set to: %s", mathlib_path)
         else:
-            mathlib = mathlib.lower()
+            raise EasyBuildError("Software root of math libraries (%s) not found", mathlib)
 
-        f.writelines(["setenv GMS_MATHLIB " + mathlib + "\n" +
-            "setenv GMS_MATHLIB_PATH " + mathlib_root + "\n" +
-            "setenv GMS_MKL_VERNO " + mathlib_vers + "\n" +
-            "setenv GMS_LAPACK_LINK_LINE" + "" + "\n"])
+        f.writelines([
+            "setenv GMS_MATHLIB " + mathlib + "\n" + 
+            "setenv GMS_MATHLIB_PATH " + mathlib_path + "\n" +
+            "setenv GMS_LAPACK_LINK_LINE " + '"%s"' % mathlib_flags + "\n"])
 
         # verify selected DDI communication layer
         known_ddi_comms = ['mpi', 'mixed', 'shmem', 'sockets']
@@ -169,7 +173,7 @@ def configure_step(self):
             raise EasyBuildError("Unsupported DDI communication layer specified (known: %s): %s",
                                  known_ddi_comms, self.cfg['ddi_comm'])
         
-        f.writelines(["setenv GMS_DDI_COMM " + self.cfg['ddi_comm'] + "\n" ])
+        f.writelines(["setenv GMS_DDI_COMM " + self.cfg['ddi_comm'] + "\n"])
 
         # MPI library config
         mpilib, mpilib_root, mpilib_path = None, None, None

From 04ef3a9922c3456d5b35114d5a087184b5cd194a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 8 Mar 2023 15:27:27 +0100
Subject: [PATCH 007/134] replace extra omp option with
 toolchain.options.openmp

---
 easybuild/easyblocks/g/gamess_us.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 4ac5684faf..d7b741e6eb 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -69,7 +69,6 @@ def extra_options():
             'maxcpus': [None, "Maximum number of cores per node", MANDATORY],
             'maxnodes': [None, "Maximum number of nodes", MANDATORY],
             'runtest': [True, "Run GAMESS-US tests", CUSTOM],
-            'omp': [False, "Enabling OpenMP", CUSTOM],
             'scratch_dir': ['$TMPDIR', "dir for temporary binary files", CUSTOM],
             'user_scratch_dir': ['$TMPDIR', "dir for supplementary output files", CUSTOM],
         }
@@ -203,7 +202,7 @@ def configure_step(self):
         f. writelines(["setenv GMS_PHI none " + "\n"])
         f. writelines(["setenv GMS_SHMTYPE sysv " + "\n"])
 
-        if self.cfg['omp'] == 'True':
+        if self.toolchain.options.get('openmp', None):
             f. writelines(["setenv GMS_OPENMP true" + "\n"])
         else:
             f. writelines(["setenv GMS_OPENMP false" + "\n"])

From 18db2c552d83c7a6e073b24ee2536f9e0cd7124b Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 8 Mar 2023 15:41:29 +0100
Subject: [PATCH 008/134] check dependency on libxc to enable GMS_LIBXC

---
 easybuild/easyblocks/g/gamess_us.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index d7b741e6eb..11d641ae34 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -206,8 +206,16 @@ def configure_step(self):
             f. writelines(["setenv GMS_OPENMP true" + "\n"])
         else:
             f. writelines(["setenv GMS_OPENMP false" + "\n"])
-        
-        f. writelines(["setenv GMS_LIBXC false " + "\n"])
+
+        external_plugs = dict()
+        if LooseVersion(self.version) >= LooseVersion('2021'):
+            external_plugs['GMS_LIBXC'] = "false"
+            if get_software_root('libxc'):
+                external_plugs['GMS_LIBXC'] = "true"
+
+        for opt in external_plugs.items():
+            f. writelines(["setenv %s %s \n" % opt])
+
         f. writelines(["setenv GMS_MDI false " + "\n"])
         f. writelines(["setenv GMS_VM2 false " + "\n"])
         f. writelines(["setenv TINKER false " + "\n"])

From 3b91897d652791eff2ab0c3c924efaaa4e4126f8 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 9 Mar 2023 14:10:09 +0100
Subject: [PATCH 009/134] set interfaces and plugins through plugs_opts in
 gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 39 +++++++++++++++++++----------
 1 file changed, 26 insertions(+), 13 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 11d641ae34..e369987dc5 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -207,22 +207,35 @@ def configure_step(self):
         else:
             f. writelines(["setenv GMS_OPENMP false" + "\n"])
 
-        external_plugs = dict()
-        if LooseVersion(self.version) >= LooseVersion('2021'):
-            external_plugs['GMS_LIBXC'] = "false"
+        # Optional plug-ins and interfaces
+        # libXC
+        plugs_opt = dict()
+        if LooseVersion(self.version) >= LooseVersion('20210101'):
+            plugs_opt['GMS_LIBXC'] = "false"
             if get_software_root('libxc'):
-                external_plugs['GMS_LIBXC'] = "true"
-
-        for opt in external_plugs.items():
+                plugs_opt['GMS_LIBXC'] = "true"
+        # MDI
+        # needs https://github.com/MolSSI-MDI/MDI_Library
+        plugs_opt['GMS_MDI'] = "false"
+        # VM2
+        plugs_opt['GMS_VM2'] = "false"
+        # NBO
+        plugs_opt['NBO'] = "false"
+        if get_software_root('NBO'):
+            plugs_opt['NBO'] = "true"
+        # NEO
+        plugs_opt['NEO'] = "false"
+        # TINKER
+        plugs_opt['TINKER'] = "false"
+        if get_software_root('TINKER'):
+            plugs_opt['TINKER'] = "true"
+        # VB2000
+        plugs_opt['VB2000'] = "false"
+        # XMVB
+        plugs_opt['XMVB'] = "false"
+        for opt in plugs_opt.items():
             f. writelines(["setenv %s %s \n" % opt])
 
-        f. writelines(["setenv GMS_MDI false " + "\n"])
-        f. writelines(["setenv GMS_VM2 false " + "\n"])
-        f. writelines(["setenv TINKER false " + "\n"])
-        f. writelines(["setenv VB2000 false " + "\n"])
-        f. writelines(["setenv XMVB false " + "\n"])
-        f. writelines(["setenv NEO false " + "\n"])
-        f. writelines(["setenv NBO false " + "\n"])
         f. writelines(["setenv GMS_FPE_FLAGS " + "\n"]) 
         #f. writelines(["setenv GMS_FPE_FLAGS '-ffpe-trap=invalid,zero,overflow' " + "\n"]) # This seems to be useful for debugging 
 

From b85076a7d94afae428a4a02920a65cb0aa6f2c4e Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 9 Mar 2023 21:09:41 +0100
Subject: [PATCH 010/134] fix linking to libxc in gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index e369987dc5..a2d7670c5c 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -214,6 +214,16 @@ def configure_step(self):
             plugs_opt['GMS_LIBXC'] = "false"
             if get_software_root('libxc'):
                 plugs_opt['GMS_LIBXC'] = "true"
+                # the linker needs to be patched to use external libXC
+                lixc_libs = [os.path.join(os.environ['EBROOTLIBXC'], 'lib', l) for l in ['libxcf03.a', 'libxc.a']]
+                libxc_linker_flags = ' '.join(lixc_libs)
+                try:
+                    lked = os.path.join(self.builddir, 'lked')
+                    for line in fileinput.input(lked, inplace=1, backup='.orig'):
+                        line = re.sub(r"^(\s*set\sLIBXC_FLAGS)=.*GMS_PATH.*", r'\1="%s"' % libxc_linker_flags, line)
+                        sys.stdout.write(line)
+                except IOError as err:
+                    raise EasyBuildError("Failed to patch %s: %s", lked, err)
         # MDI
         # needs https://github.com/MolSSI-MDI/MDI_Library
         plugs_opt['GMS_MDI'] = "false"
@@ -236,7 +246,8 @@ def configure_step(self):
         for opt in plugs_opt.items():
             f. writelines(["setenv %s %s \n" % opt])
 
-        f. writelines(["setenv GMS_FPE_FLAGS " + "\n"]) 
+        # add include paths from dependencies
+        f. writelines(['setenv GMS_FPE_FLAGS "%s" \n' % os.environ['CPPFLAGS']]) 
         #f. writelines(["setenv GMS_FPE_FLAGS '-ffpe-trap=invalid,zero,overflow' " + "\n"]) # This seems to be useful for debugging 
 
         f.close()

From 133861ca1c939c041f35160aa45e3ca1cc01c7fb Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 10 Mar 2023 08:55:21 +0100
Subject: [PATCH 011/134] move openmp settings to original position in
 gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index a2d7670c5c..125397d64a 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -196,17 +196,18 @@ def configure_step(self):
         f.writelines(["setenv GMS_MPI_LIB " + mpilib + "\n" + 
             "setenv GMS_MPI_PATH " + mpilib_root + "\n"])
 
+        # OpenMP config
+        if self.toolchain.options.get('openmp', None):
+            f. writelines(["setenv GMS_OPENMP true" + "\n"])
+        else:
+            f. writelines(["setenv GMS_OPENMP false" + "\n"])
+
         # These are extra programs which for now we simply set all to FALSE
         f. writelines(["setenv GMS_MSUCC false " + "\n"])
         f. writelines(["setenv GMS_LIBCCHEM false" + "\n"])
         f. writelines(["setenv GMS_PHI none " + "\n"])
         f. writelines(["setenv GMS_SHMTYPE sysv " + "\n"])
 
-        if self.toolchain.options.get('openmp', None):
-            f. writelines(["setenv GMS_OPENMP true" + "\n"])
-        else:
-            f. writelines(["setenv GMS_OPENMP false" + "\n"])
-
         # Optional plug-ins and interfaces
         # libXC
         plugs_opt = dict()

From b7834736ae54caf448b6b2630cec4a676f2c9a40 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sat, 11 Mar 2023 23:47:42 +0100
Subject: [PATCH 012/134] skip tests in gamess-us with less than 2 cores

---
 easybuild/easyblocks/g/gamess_us.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 125397d64a..9254726298 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -337,6 +337,10 @@ def test_step(self):
                 self.log.info("Skipping testing of GAMESS-US since MPI testing is disabled")
                 return
 
+            if int(self.cfg['parallel']) < 2:
+                self.log.info("Skipping testing of GAMESS-US as MPI tests need at least 2 CPU cores to run")
+                return
+
             cwd = change_dir(self.testdir)
 
             # copy input files for exam<id> standard tests

From d4a6a38f2c81ab82d5a6befbba2791ad556a8152 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sat, 11 Mar 2023 23:58:59 +0100
Subject: [PATCH 013/134] remove unused modules from gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 9254726298..b344f96d76 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -52,8 +52,7 @@
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import change_dir, read_file, write_file
 from easybuild.tools.modules import get_software_root, get_software_version
-from easybuild.tools.py2vs3 import ascii_letters
-from easybuild.tools.run import run_cmd, run_cmd_qa
+from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_platform_name
 from easybuild.tools import toolchain
 

From 29e42e3aca40c93f3ce37c04c65d5d335c31b815 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sun, 12 Mar 2023 00:09:53 +0100
Subject: [PATCH 014/134] cleanup scratch generated by tests of gamess-us

---
 easybuild/easyblocks/g/gamess_us.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index b344f96d76..baad03e504 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -50,7 +50,7 @@
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import change_dir, read_file, write_file
+from easybuild.tools.filetools import change_dir, read_file, write_file, remove_dir
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import get_platform_name
@@ -398,8 +398,12 @@ def make_module_extra(self):
 
     def cleanup_step(self):
         """Cleanup set."""
+        super(EB_GAMESS_minus_US, self).cleanup_step()
+
         # remove dedicated scratch directory (if any);
         # we must use a shell command for this, since the path may contain environment variables
-        super(EB_GAMESS_minus_US, self).cleanup_step()
+        (scratch_path, _) = run_cmd('echo "%s"' % self.cfg['scratch_dir'], simple=False)
+        if os.path.isdir(scratch_path):
+            remove_dir(scratch_path)
+            self.log.info("Removed test scratch: %s", scratch_path)
 
-        # FIXME

From e5bc041287c707214ee1597b4f7fbc9158d2f00e Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sun, 12 Mar 2023 00:44:38 +0100
Subject: [PATCH 015/134] use write_file from easybuild to create install.info
 file in gamess-us

---
 easybuild/easyblocks/g/gamess_us.py | 108 +++++++++++++++-------------
 1 file changed, 59 insertions(+), 49 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index baad03e504..9fc3c64390 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -53,8 +53,10 @@
 from easybuild.tools.filetools import change_dir, read_file, write_file, remove_dir
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import get_platform_name
+from easybuild.tools.systemtools import POWER, X86_64
+from easybuild.tools.systemtools import get_cpu_architecture
 from easybuild.tools import toolchain
+INSTALL_INFO = 'install.info'
 
 
 class EB_GAMESS_minus_US(EasyBlock):
@@ -92,20 +94,24 @@ def extract_step(self):
         super(EB_GAMESS_minus_US, self).extract_step()
 
     def configure_step(self):
-        """Configure GAMESS-US build via provided interactive 'config' script."""
-        """Opening install.info file as append"""
-        f = open(self.builddir + "/install.info", "a")
-        f.writelines(["setenv GMS_PATH " + self.builddir + "\n"
-            "setenv GMS_BUILD_DIR " + self.installdir + "\n"])
+        """Configure GAMESS-US via install.info file"""
+        installinfo_opts = {}
+
+        # installation paths
+        installinfo_opts["GMS_PATH"] = self.installdir
+        installinfo_opts["GMS_BUILD_DIR"] = self.builddir
+
         # machine type
-        platform_name = get_platform_name()
-        x86_64_linux_re = re.compile('^x86_64-.*$')
-        if x86_64_linux_re.match(platform_name):
+        cpu_arch = get_cpu_architecture()
+        if cpu_arch == X86_64:
             machinetype = "linux64"
-            f.writelines(["setenv GMS_TARGET " + machinetype + "\n" +
-                "setenv GMS_HPC_SYSTEM_TARGET generic" + "\n"])
+        elif cpu_arch == POWER:
+            machinetype = "ibm64"
         else:
-            raise EasyBuildError("Build target %s currently unsupported", platform_name)
+            raise EasyBuildError("Build target %s currently unsupported", cpu_arch)
+
+        installinfo_opts["GMS_TARGET"] = machinetype
+        installinfo_opts["GMS_HPC_SYSTEM_TARGET"] = "generic"
 
         # compiler config
         comp_fam = self.toolchain.comp_family()
@@ -124,8 +130,8 @@ def configure_step(self):
         else:
             raise EasyBuildError("Compiler family '%s' currently unsupported.", comp_fam)
 
-        f.writelines(["setenv GMS_FORTRAN " + fortran_comp + "\n" + 
-            "setenv GMS_GFORTRAN_VERNO " + fortran_ver + "\n"])
+        installinfo_opts["GMS_FORTRAN"] = fortran_comp
+        installinfo_opts["GMS_GFORTRAN_VERNO"] = fortran_ver
 
         # math library config
         known_mathlibs = ['imkl', 'OpenBLAS', 'ATLAS', 'ACML']
@@ -140,6 +146,7 @@ def configure_step(self):
         except IndexError:
             raise EasyBuildError("None of the known math libraries (%s) available, giving up.", known_mathlibs)
 
+        # math library: special cases
         if mathlib == 'imkl':
             mathlib = 'mkl'
             mathlib_subfolder = 'mkl'
@@ -160,18 +167,18 @@ def configure_step(self):
         else:
             raise EasyBuildError("Software root of math libraries (%s) not found", mathlib)
 
-        f.writelines([
-            "setenv GMS_MATHLIB " + mathlib + "\n" + 
-            "setenv GMS_MATHLIB_PATH " + mathlib_path + "\n" +
-            "setenv GMS_LAPACK_LINK_LINE " + '"%s"' % mathlib_flags + "\n"])
+        installinfo_opts["GMS_MATHLIB"] = mathlib
+        installinfo_opts["GMS_MATHLIB_PATH"] = mathlib_path
+        installinfo_opts["GMS_LAPACK_LINK_LINE"] = '"%s"' % mathlib_flags
 
         # verify selected DDI communication layer
         known_ddi_comms = ['mpi', 'mixed', 'shmem', 'sockets']
         if not self.cfg['ddi_comm'] in known_ddi_comms:
-            raise EasyBuildError("Unsupported DDI communication layer specified (known: %s): %s",
-                                 known_ddi_comms, self.cfg['ddi_comm'])
+            raise EasyBuildError(
+                "Unsupported DDI communication layer specified (known: %s): %s", known_ddi_comms, self.cfg['ddi_comm']
+            )
         
-        f.writelines(["setenv GMS_DDI_COMM " + self.cfg['ddi_comm'] + "\n"])
+        installinfo_opts["GMS_DDI_COMM"] = self.cfg['ddi_comm']
 
         # MPI library config
         mpilib, mpilib_root, mpilib_path = None, None, None
@@ -192,28 +199,29 @@ def configure_step(self):
         else:
             mpilib, mpilib_root = '', ''
 
-        f.writelines(["setenv GMS_MPI_LIB " + mpilib + "\n" + 
-            "setenv GMS_MPI_PATH " + mpilib_root + "\n"])
+        installinfo_opts["GMS_MPI_LIB"] = mpilib
+        installinfo_opts["GMS_MPI_PATH"] = mpilib_root
 
         # OpenMP config
         if self.toolchain.options.get('openmp', None):
-            f. writelines(["setenv GMS_OPENMP true" + "\n"])
+            omp_enabled = "true"
         else:
-            f. writelines(["setenv GMS_OPENMP false" + "\n"])
+            omp_enabled = "false"
+
+        installinfo_opts["GMS_OPENMP"] = omp_enabled
 
         # These are extra programs which for now we simply set all to FALSE
-        f. writelines(["setenv GMS_MSUCC false " + "\n"])
-        f. writelines(["setenv GMS_LIBCCHEM false" + "\n"])
-        f. writelines(["setenv GMS_PHI none " + "\n"])
-        f. writelines(["setenv GMS_SHMTYPE sysv " + "\n"])
+        installinfo_opts["GMS_MSUCC"] = "false"
+        installinfo_opts["GMS_LIBCCHEM"] = "false"
+        installinfo_opts["GMS_PHI"] = "none"
+        installinfo_opts["GMS_SHMTYPE"] = "sysv"
 
         # Optional plug-ins and interfaces
         # libXC
-        plugs_opt = dict()
         if LooseVersion(self.version) >= LooseVersion('20210101'):
-            plugs_opt['GMS_LIBXC'] = "false"
+            installinfo_opts['GMS_LIBXC'] = "false"
             if get_software_root('libxc'):
-                plugs_opt['GMS_LIBXC'] = "true"
+                installinfo_opts['GMS_LIBXC'] = "true"
                 # the linker needs to be patched to use external libXC
                 lixc_libs = [os.path.join(os.environ['EBROOTLIBXC'], 'lib', l) for l in ['libxcf03.a', 'libxc.a']]
                 libxc_linker_flags = ' '.join(lixc_libs)
@@ -226,33 +234,35 @@ def configure_step(self):
                     raise EasyBuildError("Failed to patch %s: %s", lked, err)
         # MDI
         # needs https://github.com/MolSSI-MDI/MDI_Library
-        plugs_opt['GMS_MDI'] = "false"
+        installinfo_opts['GMS_MDI'] = "false"
         # VM2
-        plugs_opt['GMS_VM2'] = "false"
+        installinfo_opts['GMS_VM2'] = "false"
         # NBO
-        plugs_opt['NBO'] = "false"
+        installinfo_opts['NBO'] = "false"
         if get_software_root('NBO'):
-            plugs_opt['NBO'] = "true"
+            installinfo_opts['NBO'] = "true"
         # NEO
-        plugs_opt['NEO'] = "false"
+        installinfo_opts['NEO'] = "false"
         # TINKER
-        plugs_opt['TINKER'] = "false"
+        installinfo_opts['TINKER'] = "false"
         if get_software_root('TINKER'):
-            plugs_opt['TINKER'] = "true"
+            installinfo_opts['TINKER'] = "true"
         # VB2000
-        plugs_opt['VB2000'] = "false"
+        installinfo_opts['VB2000'] = "false"
         # XMVB
-        plugs_opt['XMVB'] = "false"
-        for opt in plugs_opt.items():
-            f. writelines(["setenv %s %s \n" % opt])
+        installinfo_opts['XMVB'] = "false"
 
         # add include paths from dependencies
-        f. writelines(['setenv GMS_FPE_FLAGS "%s" \n' % os.environ['CPPFLAGS']]) 
-        #f. writelines(["setenv GMS_FPE_FLAGS '-ffpe-trap=invalid,zero,overflow' " + "\n"]) # This seems to be useful for debugging 
-
-        f.close()
+        installinfo_opts["GMS_FPE_FLAGS"] = '"%s"' % os.environ['CPPFLAGS']
+        # might be useful for debugging 
+        # installinfo_opts["GMS_FPE_FLAGS"] = '"%s"' % os.environ['CPPFLAGS'] + "-ffpe-trap=invalid,zero,overflow"
 
-        self.log.debug("Contents of install.info:\n%s" % read_file(os.path.join(self.builddir, 'install.info')))
+        # write install.info file with configuration settings
+        # format: setenv KEY VALUE
+        installinfo_file = os.path.join(self.builddir, INSTALL_INFO)
+        txt = '\n'.join(["setenv %s %s" % (k, installinfo_opts[k]) for k in installinfo_opts])
+        write_file(installinfo_file, txt)
+        self.log.debug("Contents of install.info:\n%s" % read_file(installinfo_file))
 
         # patch hardcoded settings in rungms to use values specified in easyconfig file
         rungms = os.path.join(self.builddir, 'rungms')
@@ -402,7 +412,7 @@ def cleanup_step(self):
 
         # remove dedicated scratch directory (if any);
         # we must use a shell command for this, since the path may contain environment variables
-        (scratch_path, _) = run_cmd('echo "%s"' % self.cfg['scratch_dir'], simple=False)
+        (scratch_path, _) = run_cmd('printf "%%s" "%s"' % self.cfg['scratch_dir'], simple=False)
         if os.path.isdir(scratch_path):
             remove_dir(scratch_path)
             self.log.info("Removed test scratch: %s", scratch_path)

From 6dc3248b4136121736014455e82164351ace7325 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sun, 12 Mar 2023 02:18:22 +0100
Subject: [PATCH 016/134] use specific version setting for each fortran
 compiler in gamess-us

---
 easybuild/easyblocks/g/gamess_us.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 9fc3c64390..a069f271f5 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -120,18 +120,20 @@ def configure_step(self):
             fortran_comp = 'ifort'
             (out, _) = run_cmd("ifort -v", simple=False)
             res = re.search(r"^ifort version ([0-9]+)\.[0-9.]+$", out)
-            if res:
-                fortran_ver = res.group(1)
-            else:
+            try:
+                version_num = res.group(1)
+            except (AttributeError, IndexError):
                 raise EasyBuildError("Failed to determine ifort major version number")
+            fortran_version = {"GMS_IFORT_VERNO": version_num}
         elif comp_fam == toolchain.GCC:
             fortran_comp = 'gfortran'
-            fortran_ver = '.'.join(get_software_version('GCC').split('.')[:2])
+            version_num = '.'.join(get_software_version('GCC').split('.')[:2])
+            fortran_version = {"GMS_GFORTRAN_VERNO": version_num}
         else:
             raise EasyBuildError("Compiler family '%s' currently unsupported.", comp_fam)
 
         installinfo_opts["GMS_FORTRAN"] = fortran_comp
-        installinfo_opts["GMS_GFORTRAN_VERNO"] = fortran_ver
+        installinfo_opts.update(fortran_version)
 
         # math library config
         known_mathlibs = ['imkl', 'OpenBLAS', 'ATLAS', 'ACML']

From fa047dcd7cd0f26ab5728b11661ec623ef411d15 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sun, 12 Mar 2023 02:43:13 +0100
Subject: [PATCH 017/134] add support for impi v2021+ to gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index a069f271f5..221ba1ff0d 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -183,9 +183,8 @@ def configure_step(self):
         installinfo_opts["GMS_DDI_COMM"] = self.cfg['ddi_comm']
 
         # MPI library config
-        mpilib, mpilib_root, mpilib_path = None, None, None
+        mpilib, mpilib_path = '', ''
         if self.cfg['ddi_comm'] == 'mpi':
-
             known_mpilibs = ['impi', 'OpenMPI', 'MVAPICH2', 'MPICH2']
             for mpilib in known_mpilibs:
                 mpilib_root = get_software_root(mpilib)
@@ -195,14 +194,16 @@ def configure_step(self):
                 raise EasyBuildError("None of the known MPI libraries (%s) available, giving up.", known_mpilibs)
             mpilib_path = mpilib_root
             if mpilib == 'impi':
-                mpilib_path = os.path.join(mpilib_root, 'intel64')
+                impi_ver = get_software_version('impi')
+                if LooseVersion(impi_ver) >= LooseVersion("2021.0.0"):
+                    mpilib_path = os.path.join(mpilib_root, 'mpi', 'latest')
+                else:
+                    mpilib_path = os.path.join(mpilib_root, 'intel64')
             else:
                 mpilib = mpilib.lower()
-        else:
-            mpilib, mpilib_root = '', ''
 
         installinfo_opts["GMS_MPI_LIB"] = mpilib
-        installinfo_opts["GMS_MPI_PATH"] = mpilib_root
+        installinfo_opts["GMS_MPI_PATH"] = mpilib_path
 
         # OpenMP config
         if self.toolchain.options.get('openmp', None):

From c04d19d794b49a24db668649e142755e003605d0 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sun, 12 Mar 2023 01:52:13 +0100
Subject: [PATCH 018/134] add extra option to gamess-us easyblock to disable
 hyperthreading

---
 easybuild/easyblocks/g/gamess_us.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 221ba1ff0d..0d254ebfbb 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -69,6 +69,7 @@ def extra_options():
             'ddi_comm': ['mpi', "DDI communication layer to use", CUSTOM],
             'maxcpus': [None, "Maximum number of cores per node", MANDATORY],
             'maxnodes': [None, "Maximum number of nodes", MANDATORY],
+            'hyperthreading': [True, "Enable support for hyperthreading (2 threads per core)", CUSTOM],
             'runtest': [True, "Run GAMESS-US tests", CUSTOM],
             'scratch_dir': ['$TMPDIR', "dir for temporary binary files", CUSTOM],
             'user_scratch_dir': ['$TMPDIR', "dir for supplementary output files", CUSTOM],
@@ -284,6 +285,10 @@ def configure_step(self):
                 line = re.sub(r"^(\s*set\s*SCR)=.*", r"if ( ! $?SCR ) \1=%s" % self.cfg['scratch_dir'], line)
                 line = re.sub(r"^(\s*set\s*USERSCR)=.*", r"if ( ! $?USERSCR ) \1=%s" % self.cfg['user_scratch_dir'], line)
                 line = re.sub(r"^(df -k \$SCR)$", r"mkdir -p $SCR && mkdir -p $USERSCR && \1", line)
+                if self.cfg['hyperthreading'] is False:
+                    # disable hyperthreading (1 thread per core)
+                    line = re.sub(r"\$PPN \+ \$PPN", r"$PPN", line)
+                    line = re.sub(r"\$NCPUS \+ \$NCPUS", r"$NCPUS", line)
                 sys.stdout.write(line)
         except IOError as err:
             raise EasyBuildError("Failed to patch %s: %s", rungms, err)

From 440f9600fdab92d9aa41e33195a58dc5c56a8528 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 13 Mar 2023 00:32:41 +0100
Subject: [PATCH 019/134] set version of MKL in gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 0d254ebfbb..dc56010716 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -152,13 +152,15 @@ def configure_step(self):
         # math library: special cases
         if mathlib == 'imkl':
             mathlib = 'mkl'
-            mathlib_subfolder = 'mkl'
-            mathlib_flags = '-lmkl_intel_lp64'
+            mathlib_subfolder = 'mkl/lib/intel64'
+            mkl_version = '12'
             imkl_ver = get_software_version('imkl')
             if LooseVersion(imkl_ver) >= LooseVersion("2021"):
+                # OneAPI version
                 mathlib_subfolder = 'mkl/latest/lib/intel64'
-            elif LooseVersion(imkl_ver) >= LooseVersion("2020"):
-                mathlib_subfolder = 'mkl/lib/intel64'
+                mkl_version = 'oneapi'
+            installinfo_opts["GMS_MKL_VERNO"] = mkl_version
+
         elif mathlib == 'openblas':
             mathlib_flags="-lopenblas -lgfortran"
             if LooseVersion(self.version) >= LooseVersion('20210101'):

From 45e9a3e48310e6fb4509453de48fbce4ebb6d4c0 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 13 Mar 2023 11:59:29 +0100
Subject: [PATCH 020/134] set parallelization of tests in gamess-us to 2
 processes

---
 easybuild/easyblocks/g/gamess_us.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index dc56010716..567a6c98ca 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -56,7 +56,9 @@
 from easybuild.tools.systemtools import POWER, X86_64
 from easybuild.tools.systemtools import get_cpu_architecture
 from easybuild.tools import toolchain
-INSTALL_INFO = 'install.info'
+
+GAMESS_INSTALL_INFO = 'install.info'
+GAMESS_TEST_TASKS = 2
 
 
 class EB_GAMESS_minus_US(EasyBlock):
@@ -265,10 +267,10 @@ def configure_step(self):
 
         # write install.info file with configuration settings
         # format: setenv KEY VALUE
-        installinfo_file = os.path.join(self.builddir, INSTALL_INFO)
+        installinfo_file = os.path.join(self.builddir, GAMESS_INSTALL_INFO)
         txt = '\n'.join(["setenv %s %s" % (k, installinfo_opts[k]) for k in installinfo_opts])
         write_file(installinfo_file, txt)
-        self.log.debug("Contents of install.info:\n%s" % read_file(installinfo_file))
+        self.log.debug("Contents of %s:\n%s" % (installinfo_file, read_file(installinfo_file)))
 
         # patch hardcoded settings in rungms to use values specified in easyconfig file
         rungms = os.path.join(self.builddir, 'rungms')
@@ -382,7 +384,8 @@ def test_step(self):
             tests_path = os.path.join(self.installdir, 'tests', 'standard')
             n_tests = len(fnmatch.filter(os.listdir(tests_path), '*.inp'))
             for i in range(1, n_tests+1):
-                test_cmd = ' '.join(test_env_vars + [rungms, 'exam%02d' % i, self.version, '1', '2'])
+                rungms_cmd = [rungms, 'exam%02d' % i, self.version, str(GAMESS_TEST_TASKS), str(GAMESS_TEST_TASKS)]
+                test_cmd = ' '.join(test_env_vars + rungms_cmd)
                 (out, _) = run_cmd(test_cmd, log_all=True, simple=False)
                 write_file('exam%02d.log' % i, out)
 

From a9de2fdf0a316ca70db760b8ad8154fd4d95a199 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 13 Mar 2023 15:19:16 +0100
Subject: [PATCH 021/134] fix gamess-us configuration for Intel MPI v2019+

---
 easybuild/easyblocks/g/gamess_us.py | 39 +++++++++++++++++++++--------
 1 file changed, 29 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 567a6c98ca..7bbf77d906 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -191,21 +191,40 @@ def configure_step(self):
         mpilib, mpilib_path = '', ''
         if self.cfg['ddi_comm'] == 'mpi':
             known_mpilibs = ['impi', 'OpenMPI', 'MVAPICH2', 'MPICH2']
-            for mpilib in known_mpilibs:
-                mpilib_root = get_software_root(mpilib)
-                if mpilib_root is not None:
-                    break
-            if mpilib_root is None:
+            loaded_mpilib = [mpilib for mpilib in known_mpilibs if get_software_root(mpilib)]
+
+            # mpi library: default settings
+            try:
+                mpilib = loaded_mpilib[0].lower()
+                mpilib_root = get_software_root(loaded_mpilib[0])
+                mpilib_subfolder = ''
+            except IndexError:
                 raise EasyBuildError("None of the known MPI libraries (%s) available, giving up.", known_mpilibs)
-            mpilib_path = mpilib_root
+
             if mpilib == 'impi':
                 impi_ver = get_software_version('impi')
-                if LooseVersion(impi_ver) >= LooseVersion("2021.0.0"):
-                    mpilib_path = os.path.join(mpilib_root, 'mpi', 'latest')
+                if LooseVersion(impi_ver) >= LooseVersion("2021"):
+                    mpilib_subfolder = "mpi/latest"
                 else:
-                    mpilib_path = os.path.join(mpilib_root, 'intel64')
+                    mpilib_subfolder = "intel64"
+
+                if LooseVersion(impi_ver) >= LooseVersion("2019"):
+                    # fix rungms settings for newer versions of Intel MPI
+                    print("PATCH IMPI")
+                    rungms = os.path.join(self.builddir, 'rungms')
+                    try:
+                        for line in fileinput.input(rungms, inplace=1, backup='.orig'):
+                            line = re.sub(r"^(\s*setenv\s*I_MPI_STATS).*", r"# \1", line)
+                            line = re.sub(r"^(\s*setenv\s*I_MPI_WAIT_MODE)\s*enable.*", r"\1 1", line)
+                            sys.stdout.write(line)
+                    except IOError as err:
+                        raise EasyBuildError("Failed to patch Intel MPI settings in %s: %s", rungms, err)
+
+            if mpilib_root is not None:
+                mpilib_path = os.path.join(mpilib_root, mpilib_subfolder)
+                self.log.debug("Software root of MPI libraries set to: %s", mpilib_path)
             else:
-                mpilib = mpilib.lower()
+                raise EasyBuildError("Software root of MPI libraries (%s) not found", mpilib)
 
         installinfo_opts["GMS_MPI_LIB"] = mpilib
         installinfo_opts["GMS_MPI_PATH"] = mpilib_path

From b009762a6e9a40c2660da772cfc26b9762108dfc Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 20 Mar 2023 16:06:57 +0100
Subject: [PATCH 022/134] reduce minimum version for libxc support in gamess-us
 to 20200101

---
 easybuild/easyblocks/g/gamess_us.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 7bbf77d906..9b9149cb74 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -245,7 +245,7 @@ def configure_step(self):
 
         # Optional plug-ins and interfaces
         # libXC
-        if LooseVersion(self.version) >= LooseVersion('20210101'):
+        if LooseVersion(self.version) >= LooseVersion('20200101'):
             installinfo_opts['GMS_LIBXC'] = "false"
             if get_software_root('libxc'):
                 installinfo_opts['GMS_LIBXC'] = "true"

From c4f0baec11cbb45831d83b0f21197204be817954 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 20 Mar 2023 16:07:36 +0100
Subject: [PATCH 023/134] add Alex Domingo as author of gamess-us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 9b9149cb74..aff9753f4e 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -33,6 +33,7 @@
 @author: Toon Willems (Ghent University)
 @author: Pablo Escobar (sciCORE, SIB, University of Basel)
 @author: Benjamin Roberts (The University of Auckland)
+@author: Alex Domingo (Vrije Universiteit Brussel)
 """
 import fileinput
 import glob

From 1505dc54499e85e45af4db1938aea55f8d145e8c Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 6 Dec 2023 18:18:06 +0100
Subject: [PATCH 024/134] fix code formatting in gamess_us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index ea8f10da33..cf8bdd00d9 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -38,7 +38,6 @@
 import fileinput
 import glob
 import os
-import random
 import re
 import shutil
 import sys
@@ -165,7 +164,7 @@ def configure_step(self):
             installinfo_opts["GMS_MKL_VERNO"] = mkl_version
 
         elif mathlib == 'openblas':
-            mathlib_flags="-lopenblas -lgfortran"
+            mathlib_flags = "-lopenblas -lgfortran"
             if LooseVersion(self.version) >= LooseVersion('20210101'):
                 mathlib_subfolder = 'lib'
 
@@ -185,7 +184,7 @@ def configure_step(self):
             raise EasyBuildError(
                 "Unsupported DDI communication layer specified (known: %s): %s", known_ddi_comms, self.cfg['ddi_comm']
             )
-        
+
         installinfo_opts["GMS_DDI_COMM"] = self.cfg['ddi_comm']
 
         # MPI library config
@@ -282,7 +281,7 @@ def configure_step(self):
 
         # add include paths from dependencies
         installinfo_opts["GMS_FPE_FLAGS"] = '"%s"' % os.environ['CPPFLAGS']
-        # might be useful for debugging 
+        # might be useful for debugging
         # installinfo_opts["GMS_FPE_FLAGS"] = '"%s"' % os.environ['CPPFLAGS'] + "-ffpe-trap=invalid,zero,overflow"
 
         # write install.info file with configuration settings
@@ -307,7 +306,9 @@ def configure_step(self):
                 line = re.sub(r"^(\s*)(setenv\s*LD_LIBRARY_PATH\s*/.*)", r"\1#\2", line)
                 # scratch directory paths
                 line = re.sub(r"^(\s*set\s*SCR)=.*", r"if ( ! $?SCR ) \1=%s" % self.cfg['scratch_dir'], line)
-                line = re.sub(r"^(\s*set\s*USERSCR)=.*", r"if ( ! $?USERSCR ) \1=%s" % self.cfg['user_scratch_dir'], line)
+                line = re.sub(
+                    r"^(\s*set\s*USERSCR)=.*", r"if ( ! $?USERSCR ) \1=%s" % self.cfg['user_scratch_dir'], line
+                )
                 line = re.sub(r"^(df -k \$SCR)$", r"mkdir -p $SCR && mkdir -p $USERSCR && \1", line)
                 if self.cfg['hyperthreading'] is False:
                     # disable hyperthreading (1 thread per core)
@@ -325,20 +326,22 @@ def configure_step(self):
                 line = re.sub(r"^(\s*set MAXNODES)=.*", r"\1=%s" % self.cfg['maxnodes'], line, 1)
                 sys.stdout.write(line)
         except IOError as err:
-                raise EasyBuildError("Failed to patch compddi", compddi, err)
+            raise EasyBuildError("Failed to patch compddi", compddi, err)
 
         # for GAMESS-US 20200630-R1 we need to build the actvte.x program
         if self.version == "20200630-R1":
             actvte = os.path.join(self.builddir, 'tools/actvte.code')
             try:
                 for line in fileinput.input(actvte, inplace=1, backup='.orig'):
-                    line = re.sub("\*UNX", "    ", line)
+                    line = re.sub("[*]UNX", "    ", line)
                     sys.stdout.write(line)
             except IOError as err:
                 raise EasyBuildError("Failed to patch actvte.code", actvte, err)
             # compiling
             run_cmd("mv %s/tools/actvte.code" % self.builddir + " %s/tools/actvte.f" % self.builddir)
-            run_cmd("%s -o " % fortran_comp + " %s/tools/actvte.x" % self.builddir + " %s/tools/actvte.f" % self.builddir)
+            run_cmd(
+                "%s -o " % fortran_comp + " %s/tools/actvte.x" % self.builddir + " %s/tools/actvte.f" % self.builddir
+            )
 
     def build_step(self):
         """Custom build procedure for GAMESS-US: using compddi, compall and lked scripts."""
@@ -449,4 +452,3 @@ def cleanup_step(self):
         if os.path.isdir(scratch_path):
             remove_dir(scratch_path)
             self.log.info("Removed test scratch: %s", scratch_path)
-

From 9fd5be5e4a6b5d67084c87829fd25a439a1038d6 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 6 Dec 2023 18:20:39 +0100
Subject: [PATCH 025/134] fix variable names in gamess_us easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index cf8bdd00d9..02a073fc4c 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -118,7 +118,7 @@ def configure_step(self):
 
         # compiler config
         comp_fam = self.toolchain.comp_family()
-        fortran_comp, fortran_ver = None, None
+        fortran_comp, fortran_version = None, None
         if comp_fam == toolchain.INTELCOMP:
             fortran_comp = 'ifort'
             (out, _) = run_cmd("ifort -v", simple=False)
@@ -250,7 +250,7 @@ def configure_step(self):
             if get_software_root('libxc'):
                 installinfo_opts['GMS_LIBXC'] = "true"
                 # the linker needs to be patched to use external libXC
-                lixc_libs = [os.path.join(os.environ['EBROOTLIBXC'], 'lib', l) for l in ['libxcf03.a', 'libxc.a']]
+                lixc_libs = [os.path.join(os.environ['EBROOTLIBXC'], 'lib', lib) for lib in ['libxcf03.a', 'libxc.a']]
                 libxc_linker_flags = ' '.join(lixc_libs)
                 try:
                     lked = os.path.join(self.builddir, 'lked')

From 2bd1871e9fc3bfac327036740f0ba0a897cf1088 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 11 Dec 2023 15:29:20 +0100
Subject: [PATCH 026/134] disable libcchem2 support in GAMESS-US v20230601+

---
 easybuild/easyblocks/g/gamess_us.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 02a073fc4c..d9c98da3c2 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -239,9 +239,13 @@ def configure_step(self):
 
         # These are extra programs which for now we simply set all to FALSE
         installinfo_opts["GMS_MSUCC"] = "false"
-        installinfo_opts["GMS_LIBCCHEM"] = "false"
         installinfo_opts["GMS_PHI"] = "none"
         installinfo_opts["GMS_SHMTYPE"] = "sysv"
+        installinfo_opts["GMS_LIBCCHEM"] = "false"  # libcchem
+        if LooseVersion(self.version) >= LooseVersion('20230601'):
+            # install options for libcchem2
+            installinfo_opts["GMS_HPCCHEM"] = "false"
+            installinfo_opts["GMS_HPCCHEM_USE_DATA_SERVERS"] = "false"
 
         # Optional plug-ins and interfaces
         # libXC

From d46d5a12ed74810772e35399ec2508080f287a80 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 12 Dec 2023 09:22:01 +0100
Subject: [PATCH 027/134] disable OpenMP offloading on Intel GPUs in GAMESS-US

---
 easybuild/easyblocks/g/gamess_us.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index d9c98da3c2..318a84594d 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -237,6 +237,12 @@ def configure_step(self):
 
         installinfo_opts["GMS_OPENMP"] = omp_enabled
 
+        # Accelerators (disabled)
+        # TODO: add support for GPUs
+        if LooseVersion(self.version) >= LooseVersion('20230601'):
+            # offloading onto Intel GPUs
+            installinfo_opts["GMS_OPENMP_OFFLOAD"] = "false"
+
         # These are extra programs which for now we simply set all to FALSE
         installinfo_opts["GMS_MSUCC"] = "false"
         installinfo_opts["GMS_PHI"] = "none"

From c0c0e5e7a85489a1b73baa9bb598633176fdbcb1 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 12 Dec 2023 09:22:20 +0100
Subject: [PATCH 028/134] disable Michigan State University code in GAMESS-US

---
 easybuild/easyblocks/g/gamess_us.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 318a84594d..f3f0d1da17 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -252,6 +252,8 @@ def configure_step(self):
             # install options for libcchem2
             installinfo_opts["GMS_HPCCHEM"] = "false"
             installinfo_opts["GMS_HPCCHEM_USE_DATA_SERVERS"] = "false"
+            # build Michigan State University code
+            installinfo_opts["GMS_MSUAUTO"] = "false"
 
         # Optional plug-ins and interfaces
         # libXC

From df5cfd1c04c29fe927c1aa1bec53b542f49ee137 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 12 Dec 2023 14:02:11 +0100
Subject: [PATCH 029/134] disable RISM plugin in GAMESS-US v20230601+

---
 easybuild/easyblocks/g/gamess_us.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index f3f0d1da17..5a45ddc9ba 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -274,20 +274,23 @@ def configure_step(self):
         # MDI
         # needs https://github.com/MolSSI-MDI/MDI_Library
         installinfo_opts['GMS_MDI'] = "false"
-        # VM2
-        installinfo_opts['GMS_VM2'] = "false"
         # NBO
         installinfo_opts['NBO'] = "false"
         if get_software_root('NBO'):
             installinfo_opts['NBO'] = "true"
         # NEO
         installinfo_opts['NEO'] = "false"
+        # RISM
+        if LooseVersion(self.version) >= LooseVersion('20230601'):
+            installinfo_opts['RISM'] = "false"
         # TINKER
         installinfo_opts['TINKER'] = "false"
         if get_software_root('TINKER'):
             installinfo_opts['TINKER'] = "true"
         # VB2000
         installinfo_opts['VB2000'] = "false"
+        # VM2
+        installinfo_opts['GMS_VM2'] = "false"
         # XMVB
         installinfo_opts['XMVB'] = "false"
 

From b4b7479553c5e89bc3b7fff2f99cb939659bab19 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 15 Dec 2023 11:40:05 +0100
Subject: [PATCH 030/134] run GAMESS-US tests following the parallelism set in
 parallel setting

---
 easybuild/easyblocks/g/gamess_us.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 5a45ddc9ba..28614e4b0f 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -58,7 +58,6 @@
 from easybuild.tools import toolchain
 
 GAMESS_INSTALL_INFO = 'install.info'
-GAMESS_TEST_TASKS = 2
 
 
 class EB_GAMESS_minus_US(EasyBlock):
@@ -420,9 +419,10 @@ def test_step(self):
             # run all exam<id> tests, dump output to exam<id>.log
             # we let Python count the number of *.inp files as that changes
             tests_path = os.path.join(self.installdir, 'tests', 'standard')
-            n_tests = len(fnmatch.filter(os.listdir(tests_path), '*.inp'))
-            for i in range(1, n_tests+1):
-                rungms_cmd = [rungms, 'exam%02d' % i, self.version, str(GAMESS_TEST_TASKS), str(GAMESS_TEST_TASKS)]
+            tests_num = len(fnmatch.filter(os.listdir(tests_path), '*.inp'))
+            tests_procs = str(self.cfg['parallel'])
+            for i in range(1, tests_num+1):
+                rungms_cmd = [rungms, 'exam%02d' % i, self.version, tests_procs, tests_procs]
                 test_cmd = ' '.join(test_env_vars + rungms_cmd)
                 (out, _) = run_cmd(test_cmd, log_all=True, simple=False)
                 write_file('exam%02d.log' % i, out)
@@ -430,7 +430,7 @@ def test_step(self):
             # verify output of tests
             check_cmd = os.path.join(self.installdir, 'tests', 'standard', 'checktst')
             (out, _) = run_cmd(check_cmd, log_all=True, simple=False)
-            success_regex = re.compile("^All %d test results are correct" % n_tests, re.M)
+            success_regex = re.compile("^All %d test results are correct" % tests_num, re.M)
             if success_regex.search(out):
                 self.log.info("All tests ran successfully!")
             else:

From a017f26b9391cdf4494a112a2893b31cb0018262 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sat, 16 Dec 2023 00:39:31 +0100
Subject: [PATCH 031/134] blacklist GAMESS-US tests not compatible with
 parallel execution

---
 easybuild/easyblocks/g/gamess_us.py | 47 ++++++++++++++++++-----------
 1 file changed, 29 insertions(+), 18 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 28614e4b0f..4eb717c836 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -42,7 +42,6 @@
 import shutil
 import sys
 import tempfile
-import fnmatch
 
 from distutils.version import LooseVersion
 
@@ -58,7 +57,14 @@
 from easybuild.tools import toolchain
 
 GAMESS_INSTALL_INFO = 'install.info'
-
+GAMESS_MPI_TEST_BLACKLIST = [
+    'exam05',  # only the gradients for CITYP=CIS run in parallel
+    'exam32',  # only CCTYP=CCSD or CCTYP=CCSD(T) can run in parallel
+    'exam42',  # ROHF'S CCTYP must be CCSD or CR-CCL, with serial execution
+    'exam45',  # only CCTYP=CCSD or CCTYP=CCSD(T) can run in parallel
+    'exam46',  # ROHF'S CCTYP must be CCSD or CR-CCL, with serial execution
+    'exam47',  # ROHF'S CCTYP must be CCSD or CR-CCL, with serial execution
+]
 
 class EB_GAMESS_minus_US(EasyBlock):
     """Support for building/installing GAMESS-US."""
@@ -402,11 +408,16 @@ def test_step(self):
             cwd = change_dir(self.testdir)
 
             # copy input files for exam<id> standard tests
+            target_tests = []
             for test_input in glob.glob(os.path.join(self.installdir, 'tests', 'standard', 'exam*.inp')):
-                try:
-                    shutil.copy2(test_input, os.getcwd())
-                except OSError as err:
-                    raise EasyBuildError("Failed to copy %s to %s: %s", test_input, os.getcwd(), err)
+                test_name = os.path.splitext(os.path.basename(test_input))[0]
+                if test_name not in GAMESS_MPI_TEST_BLACKLIST:
+                    try:
+                        shutil.copy2(test_input, os.getcwd())
+                    except OSError as err:
+                        raise EasyBuildError("Failed to copy %s to %s: %s", test_input, os.getcwd(), err)
+                    else:
+                        target_tests.append(test_name)
 
             rungms = os.path.join(self.installdir, 'rungms')
             test_env_vars = ['export OMP_NUM_THREADS=1; TMPDIR=%s' % self.testdir]
@@ -416,25 +427,25 @@ def test_step(self):
                     'I_MPI_HYDRA_BOOTSTRAP=fork',  # tests are only run locally (2 processes), so no SSH required
                 ])
 
-            # run all exam<id> tests, dump output to exam<id>.log
-            # we let Python count the number of *.inp files as that changes
-            tests_path = os.path.join(self.installdir, 'tests', 'standard')
-            tests_num = len(fnmatch.filter(os.listdir(tests_path), '*.inp'))
+            # run target exam<id> tests, dump output to exam<id>.log
             tests_procs = str(self.cfg['parallel'])
-            for i in range(1, tests_num+1):
-                rungms_cmd = [rungms, 'exam%02d' % i, self.version, tests_procs, tests_procs]
+            for test_exam in target_tests:
+                rungms_cmd = [rungms, test_exam, self.version, tests_procs, tests_procs]
                 test_cmd = ' '.join(test_env_vars + rungms_cmd)
                 (out, _) = run_cmd(test_cmd, log_all=True, simple=False)
-                write_file('exam%02d.log' % i, out)
+                write_file('%s.log' % test_exam, out)
 
-            # verify output of tests
             check_cmd = os.path.join(self.installdir, 'tests', 'standard', 'checktst')
             (out, _) = run_cmd(check_cmd, log_all=True, simple=False)
-            success_regex = re.compile("^All %d test results are correct" % tests_num, re.M)
-            if success_regex.search(out):
-                self.log.info("All tests ran successfully!")
+
+            # verify output of tests
+            failed_regex = re.compile(r"^.*!!FAILED\.$", re.M)
+            failed_tests = [exam[0:6] for exam in failed_regex.findall(out)]
+            if set(failed_tests) == set(GAMESS_MPI_TEST_BLACKLIST):
+                blacklisted_msg = "(blacklisted: %s)" % ", ".join(GAMESS_MPI_TEST_BLACKLIST)
+                self.log.info("All target tests ran successfully! %s", blacklisted_msg)
             else:
-                raise EasyBuildError("Not all tests ran successfully...")
+                raise EasyBuildError("ERROR: Not all target tests ran successfully")
 
             change_dir(cwd)
 

From a9d1ef0f43c247e3e1e6041061935f0317a3729e Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 18 Dec 2023 10:32:19 +0100
Subject: [PATCH 032/134] run GAMESS-US tests in the scratch directory

---
 easybuild/easyblocks/g/gamess_us.py | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 4eb717c836..dcdc5728d9 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -49,7 +49,7 @@
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import change_dir, read_file, write_file, remove_dir
+from easybuild.tools.filetools import change_dir, mkdir, read_file, write_file, remove_dir
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import POWER, X86_64
@@ -87,9 +87,20 @@ def __init__(self, *args, **kwargs):
         """Easyblock constructor, enable building in installation directory."""
         super(EB_GAMESS_minus_US, self).__init__(*args, **kwargs)
         self.build_in_installdir = True
+
+        # resolve path to scratch dir and make it
+        scratch_dir_resolved = os.path.expandvars(self.cfg['scratch_dir'])
+        if "$" in scratch_dir_resolved:
+            error_msg = "Provided scratch directory '%s' does not resolve into a path."
+            raise EasyBuildError(error_msg, self.cfg['scratch_dir'])
+
+        mkdir(scratch_dir_resolved, parents=True)
+
         self.testdir = None
         if self.cfg['runtest']:
-            self.testdir = tempfile.mkdtemp()
+            # run tests in scratch dir
+            self.testdir = tempfile.mkdtemp(dir=scratch_dir_resolved)
+
             # make sure test dir doesn't contain [ or ], rungms csh script doesn't handle that well ("set: No match")
             if re.search(r'[\[\]]', self.testdir):
                 error_msg = "Temporary dir for tests '%s' will cause problems with rungms csh script"
@@ -420,7 +431,7 @@ def test_step(self):
                         target_tests.append(test_name)
 
             rungms = os.path.join(self.installdir, 'rungms')
-            test_env_vars = ['export OMP_NUM_THREADS=1; TMPDIR=%s' % self.testdir]
+            test_env_vars = ['export OMP_NUM_THREADS=1; SCR=%s' % self.testdir]
             if self.toolchain.mpi_family() == toolchain.INTELMPI:
                 test_env_vars.extend([
                     'I_MPI_FALLBACK=enable',  # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)
@@ -472,9 +483,7 @@ def cleanup_step(self):
         """Cleanup set."""
         super(EB_GAMESS_minus_US, self).cleanup_step()
 
-        # remove dedicated scratch directory (if any);
-        # we must use a shell command for this, since the path may contain environment variables
-        (scratch_path, _) = run_cmd('printf "%%s" "%s"' % self.cfg['scratch_dir'], simple=False)
-        if os.path.isdir(scratch_path):
-            remove_dir(scratch_path)
-            self.log.info("Removed test scratch: %s", scratch_path)
+        # remove test directory
+        if os.path.isdir(self.testdir):
+            remove_dir(self.testdir)
+            self.log.info("Removed test scratch: %s", self.testdir)

From da4b7770252ffa37cfe29c6c589440b84b48cab2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 18 Dec 2023 11:12:46 +0100
Subject: [PATCH 033/134] fix code formatting in GAMESS-US easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index dcdc5728d9..f1f941ca98 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -66,6 +66,7 @@
     'exam47',  # ROHF'S CCTYP must be CCSD or CR-CCL, with serial execution
 ]
 
+
 class EB_GAMESS_minus_US(EasyBlock):
     """Support for building/installing GAMESS-US."""
 

From b839b5dd1e09c7191304046fe79c9434a068b2c1 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 18 Dec 2023 14:05:55 +0100
Subject: [PATCH 034/134] move cleanup of test dir back to test step of
 GAMESS-US

---
 easybuild/easyblocks/g/gamess_us.py | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index f1f941ca98..22e2d711c4 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -459,7 +459,12 @@ def test_step(self):
             else:
                 raise EasyBuildError("ERROR: Not all target tests ran successfully")
 
+            # cleanup
             change_dir(cwd)
+            try:
+                remove_dir(self.testdir)
+            except OSError as err:
+                raise EasyBuildError("Failed to remove test directory %s: %s", self.testdir, err)
 
     def install_step(self):
         """Skip install step, since we're building in the install directory."""
@@ -479,12 +484,3 @@ def make_module_extra(self):
         txt += self.module_generator.set_environment('GAMESSUSROOT', self.installdir)
         txt += self.module_generator.prepend_paths("PATH", [''])
         return txt
-
-    def cleanup_step(self):
-        """Cleanup set."""
-        super(EB_GAMESS_minus_US, self).cleanup_step()
-
-        # remove test directory
-        if os.path.isdir(self.testdir):
-            remove_dir(self.testdir)
-            self.log.info("Removed test scratch: %s", self.testdir)

From cf206fb485fdcda4344f45c677811ee57550cca3 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 18 Dec 2023 14:07:03 +0100
Subject: [PATCH 035/134] replace shutil.copy2 with filetools.copy_files method
 in GAMESS-US

---
 easybuild/easyblocks/g/gamess_us.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 22e2d711c4..b6e6655e75 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -39,7 +39,6 @@
 import glob
 import os
 import re
-import shutil
 import sys
 import tempfile
 
@@ -49,7 +48,7 @@
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import change_dir, mkdir, read_file, write_file, remove_dir
+from easybuild.tools.filetools import change_dir, copy_file, mkdir, read_file, write_file, remove_dir
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import POWER, X86_64
@@ -417,7 +416,11 @@ def test_step(self):
                 self.log.info("Skipping testing of GAMESS-US as MPI tests need at least 2 CPU cores to run")
                 return
 
-            cwd = change_dir(self.testdir)
+            try:
+                cwd = os.getcwd()
+                change_dir(self.testdir)
+            except OSError as err:
+                raise EasyBuildError("Failed to move to temporary directory for running tests: %s", err)
 
             # copy input files for exam<id> standard tests
             target_tests = []
@@ -425,9 +428,9 @@ def test_step(self):
                 test_name = os.path.splitext(os.path.basename(test_input))[0]
                 if test_name not in GAMESS_MPI_TEST_BLACKLIST:
                     try:
-                        shutil.copy2(test_input, os.getcwd())
+                        copy_file(test_input, self.testdir)
                     except OSError as err:
-                        raise EasyBuildError("Failed to copy %s to %s: %s", test_input, os.getcwd(), err)
+                        raise EasyBuildError("Failed to copy %s to %s: %s", test_input, self.testdir, err)
                     else:
                         target_tests.append(test_name)
 

From 2d513f25aa9d6d1c7ef005678d1dbcffc3898f1a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 18 Dec 2023 14:09:46 +0100
Subject: [PATCH 036/134] replace distutils.LooseVersion with
 easybuild.tools.LooseVersion in GAMESS-US easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index b6e6655e75..e8fd7d8512 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -42,8 +42,6 @@
 import sys
 import tempfile
 
-from distutils.version import LooseVersion
-
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM, MANDATORY
 from easybuild.tools.build_log import EasyBuildError
@@ -53,7 +51,7 @@
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import POWER, X86_64
 from easybuild.tools.systemtools import get_cpu_architecture
-from easybuild.tools import toolchain
+from easybuild.tools import LooseVersion, toolchain
 
 GAMESS_INSTALL_INFO = 'install.info'
 GAMESS_MPI_TEST_BLACKLIST = [

From 9af8f84c87e8d57a5a52f59def57c99f2538ab34 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 21 Dec 2023 09:46:41 +0100
Subject: [PATCH 037/134] add support for GMS_THREADED_BLAS in 2023+ versions
 of GAMESS-US

---
 easybuild/easyblocks/g/gamess_us.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index e8fd7d8512..0c73fc6063 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -130,7 +130,7 @@ def configure_step(self):
         installinfo_opts["GMS_TARGET"] = machinetype
         installinfo_opts["GMS_HPC_SYSTEM_TARGET"] = "generic"
 
-        # compiler config
+        # Compiler config
         comp_fam = self.toolchain.comp_family()
         fortran_comp, fortran_version = None, None
         if comp_fam == toolchain.INTELCOMP:
@@ -152,7 +152,15 @@ def configure_step(self):
         installinfo_opts["GMS_FORTRAN"] = fortran_comp
         installinfo_opts.update(fortran_version)
 
-        # math library config
+        # OpenMP config
+        if self.toolchain.options.get('openmp', None):
+            omp_enabled = "true"
+        else:
+            omp_enabled = "false"
+
+        installinfo_opts["GMS_OPENMP"] = omp_enabled
+
+        # Math library config
         known_mathlibs = ['imkl', 'OpenBLAS', 'ATLAS', 'ACML']
         loaded_mathlib = [mathlib for mathlib in known_mathlibs if get_software_root(mathlib)]
 
@@ -177,6 +185,9 @@ def configure_step(self):
                 mkl_version = 'oneapi'
             installinfo_opts["GMS_MKL_VERNO"] = mkl_version
 
+            if LooseVersion(self.version) >= LooseVersion('20230601'):
+                installinfo_opts["GMS_THREADED_BLAS"] = omp_enabled
+
         elif mathlib == 'openblas':
             mathlib_flags = "-lopenblas -lgfortran"
             if LooseVersion(self.version) >= LooseVersion('20210101'):
@@ -243,14 +254,6 @@ def configure_step(self):
         installinfo_opts["GMS_MPI_LIB"] = mpilib
         installinfo_opts["GMS_MPI_PATH"] = mpilib_path
 
-        # OpenMP config
-        if self.toolchain.options.get('openmp', None):
-            omp_enabled = "true"
-        else:
-            omp_enabled = "false"
-
-        installinfo_opts["GMS_OPENMP"] = omp_enabled
-
         # Accelerators (disabled)
         # TODO: add support for GPUs
         if LooseVersion(self.version) >= LooseVersion('20230601'):

From c79e6e250d03ef6013b7d63677bfd25dd8f65b83 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sat, 3 Feb 2024 10:58:24 +0100
Subject: [PATCH 038/134] execute all tests in serial for non-mpi builds of
 GAMESS-US

---
 easybuild/easyblocks/g/gamess_us.py | 90 ++++++++++++++++-------------
 1 file changed, 51 insertions(+), 39 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 0c73fc6063..d68e96c2db 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -54,7 +54,7 @@
 from easybuild.tools import LooseVersion, toolchain
 
 GAMESS_INSTALL_INFO = 'install.info'
-GAMESS_MPI_TEST_BLACKLIST = [
+GAMESS_SERIAL_TESTS = [
     'exam05',  # only the gradients for CITYP=CIS run in parallel
     'exam32',  # only CCTYP=CCSD or CCTYP=CCSD(T) can run in parallel
     'exam42',  # ROHF'S CCTYP must be CCSD or CR-CCL, with serial execution
@@ -406,60 +406,72 @@ def build_step(self):
 
     def test_step(self):
         """Run GAMESS-US tests (if 'runtest' easyconfig parameter is set to True)."""
-        # don't use provided 'runall' script for tests, since that only runs the tests single-core
         if self.cfg['runtest']:
-
-            if not build_option('mpi_tests'):
-                self.log.info("Skipping testing of GAMESS-US since MPI testing is disabled")
-                return
-
-            if int(self.cfg['parallel']) < 2:
-                self.log.info("Skipping testing of GAMESS-US as MPI tests need at least 2 CPU cores to run")
-                return
-
+            # Avoid provided 'runall' script for tests, since that only runs the tests in serial
+            # Tests must be run in parallel for MPI builds and can be run serial for other build types
+
+            target_tests = [
+                # (test name, path to test input)
+                (os.path.splitext(os.path.basename(exam_file))[0], exam_file)
+                for exam_file in glob.glob(os.path.join(self.installdir, 'tests', 'standard', 'exam*.inp'))
+            ]
+            test_procs = "1"
+            test_env_vars = ['export OMP_NUM_THREADS=1']
+
+            if self.cfg['ddi_comm'] == 'mpi':
+                if not build_option('mpi_tests'):
+                    self.log.info("Skipping tests of MPI build of GAMESS-US by user request ('mpi_tests' is disabled)")
+                    retur
+
+                # MPI builds can only run tests that support parallel execution
+                if int(self.cfg['parallel']) < 2:
+                    self.log.info("Skipping testing of GAMESS-US as MPI tests need at least 2 CPU cores to run")
+                    return
+
+                test_procs = str(self.cfg['parallel'])
+                target_tests = [exam for exam in target_tests if exam[0] not in GAMESS_SERIAL_TESTS]
+
+                if self.toolchain.mpi_family() == toolchain.INTELMPI:
+                    test_env_vars.extend([
+                        'export I_MPI_FALLBACK=enable',  # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)
+                        'export I_MPI_HYDRA_BOOTSTRAP=fork',  # tests are only run locally (2 processes), so no SSH required
+                    ])
+
+            # Prepare test directory to run tests
             try:
                 cwd = os.getcwd()
                 change_dir(self.testdir)
             except OSError as err:
                 raise EasyBuildError("Failed to move to temporary directory for running tests: %s", err)
 
-            # copy input files for exam<id> standard tests
-            target_tests = []
-            for test_input in glob.glob(os.path.join(self.installdir, 'tests', 'standard', 'exam*.inp')):
-                test_name = os.path.splitext(os.path.basename(test_input))[0]
-                if test_name not in GAMESS_MPI_TEST_BLACKLIST:
-                    try:
-                        copy_file(test_input, self.testdir)
-                    except OSError as err:
-                        raise EasyBuildError("Failed to copy %s to %s: %s", test_input, self.testdir, err)
-                    else:
-                        target_tests.append(test_name)
+            for exam, exam_file in target_tests:
+                try:
+                    copy_file(exam_file, self.testdir)
+                except OSError as err:
+                    raise EasyBuildError("Failed to copy test '%s' to %s: %s", exam, self.testdir, err)
 
-            rungms = os.path.join(self.installdir, 'rungms')
-            test_env_vars = ['export OMP_NUM_THREADS=1; SCR=%s' % self.testdir]
-            if self.toolchain.mpi_family() == toolchain.INTELMPI:
-                test_env_vars.extend([
-                    'I_MPI_FALLBACK=enable',  # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)
-                    'I_MPI_HYDRA_BOOTSTRAP=fork',  # tests are only run locally (2 processes), so no SSH required
-                ])
+            test_env_vars.append('SCR=%s' % self.testdir)
 
             # run target exam<id> tests, dump output to exam<id>.log
-            tests_procs = str(self.cfg['parallel'])
-            for test_exam in target_tests:
-                rungms_cmd = [rungms, test_exam, self.version, tests_procs, tests_procs]
-                test_cmd = ' '.join(test_env_vars + rungms_cmd)
-                (out, _) = run_cmd(test_cmd, log_all=True, simple=False)
-                write_file('%s.log' % test_exam, out)
+            rungms = os.path.join(self.installdir, 'rungms')
+            for exam, exam_file in target_tests:
+                rungms_prefix = ' && '.join(test_env_vars)
+                test_cmd = [rungms_prefix, rungms, exam_file, self.version, test_procs, test_procs]
+                (out, _) = run_cmd(' '.join(test_cmd), log_all=True, simple=False)
+                write_file('%s.log' % exam, out)
 
             check_cmd = os.path.join(self.installdir, 'tests', 'standard', 'checktst')
             (out, _) = run_cmd(check_cmd, log_all=True, simple=False)
 
             # verify output of tests
             failed_regex = re.compile(r"^.*!!FAILED\.$", re.M)
-            failed_tests = [exam[0:6] for exam in failed_regex.findall(out)]
-            if set(failed_tests) == set(GAMESS_MPI_TEST_BLACKLIST):
-                blacklisted_msg = "(blacklisted: %s)" % ", ".join(GAMESS_MPI_TEST_BLACKLIST)
-                self.log.info("All target tests ran successfully! %s", blacklisted_msg)
+            failed_tests = set([exam[0:6] for exam in failed_regex.findall(out)])
+            done_tests = set([exam[0] for exam in target_tests])
+            if done_tests - failed_tests == done_tests:
+                info_msg = "All target tests ran successfully!"
+                if self.cfg['ddi_comm'] == 'mpi':
+                    info_msg += " (serial tests ignored: %s)" % ", ".join(GAMESS_SERIAL_TESTS)
+                self.log.info(info_msg)
             else:
                 raise EasyBuildError("ERROR: Not all target tests ran successfully")
 

From 253ef5b522dd3b266278ef25c3220174adf06cdd Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sat, 3 Feb 2024 11:02:26 +0100
Subject: [PATCH 039/134] fix code formatting in GAMESS-US easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index d68e96c2db..60b2b32397 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -421,7 +421,7 @@ def test_step(self):
             if self.cfg['ddi_comm'] == 'mpi':
                 if not build_option('mpi_tests'):
                     self.log.info("Skipping tests of MPI build of GAMESS-US by user request ('mpi_tests' is disabled)")
-                    retur
+                    return
 
                 # MPI builds can only run tests that support parallel execution
                 if int(self.cfg['parallel']) < 2:
@@ -433,8 +433,10 @@ def test_step(self):
 
                 if self.toolchain.mpi_family() == toolchain.INTELMPI:
                     test_env_vars.extend([
-                        'export I_MPI_FALLBACK=enable',  # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)
-                        'export I_MPI_HYDRA_BOOTSTRAP=fork',  # tests are only run locally (2 processes), so no SSH required
+                        # enable fallback in case first fabric fails (see $I_MPI_FABRICS_LIST)
+                        'export I_MPI_FALLBACK=enable',
+                        # tests are only run locally (single node), so no SSH required
+                        'export I_MPI_HYDRA_BOOTSTRAP=fork',
                     ])
 
             # Prepare test directory to run tests

From bf2392926fe6e2f3d3dd86533bbb76a690c1131c Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Thu, 14 Mar 2024 15:45:12 +0100
Subject: [PATCH 040/134] Added easyblock for QE with cmake

---
 .../easyblocks/q/quantumespressocmake.py      | 354 ++++++++++++++++++
 1 file changed, 354 insertions(+)
 create mode 100644 easybuild/easyblocks/q/quantumespressocmake.py

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
new file mode 100644
index 0000000000..2209afed49
--- /dev/null
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -0,0 +1,354 @@
+##
+# Copyright 2009-2023 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for Quantum ESPRESSO, implemented as an easyblock
+
+@author: Davide Grassano (CECAM, EPFL)
+"""
+import os
+import re
+
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.tools import LooseVersion
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
+
+from easybuild.easyblocks.generic.cmakemake import CMakeMake
+
+
+class EB_QuantumESPRESSOcmake(CMakeMake):
+    """Support for building and installing Quantum ESPRESSO."""
+
+    TEST_SUITE_DIR = "test-suite"
+
+    @staticmethod
+    def extra_options():
+        """Custom easyconfig parameters for Quantum ESPRESSO."""
+        extra_vars = {
+            'with_cuda': [False, "Enable CUDA support", CUSTOM],
+            'with_scalapack': [True, "Enable ScaLAPACK support", CUSTOM],
+            'with_fox': [False, "Enable FoX support", CUSTOM],
+            'with_gipaw': [True, "Enable GIPAW support", CUSTOM],
+            'with_d3q': [False, "Enable D3Q support", CUSTOM],
+            'with_qmcpack': [False, "Enable QMCPACK support", CUSTOM],
+            'test_suite_nprocs': [1, "Number of processors to use for the test suite", CUSTOM],
+            'test_suite_allow_failures': [[
+                'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
+                '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+                '--ph_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+                '--epw_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+                '--tddfpt_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
+            ], "List of test suite targets that are allowed to fail (name can partially match)", CUSTOM],
+            'test_suite_threshold': [
+                0.97,
+                "Threshold for test suite success rate (does count also allowed failures)",
+                CUSTOM
+                ],
+            'test_suite_max_failed': [0, "Maximum number of failing tests (does not count allowed failures)", CUSTOM],
+        }
+        return CMakeMake.extra_options(extra_vars)
+
+    def __init__(self, *args, **kwargs):
+        """Add extra config options specific to Quantum ESPRESSO."""
+        super(EB_QuantumESPRESSOcmake, self).__init__(*args, **kwargs)
+
+        self.install_subdir = "qe-%s" % self.version
+
+        self.check_bins = []
+
+    def _add_toolchains_opts(self):
+        """Enable toolchain options for Quantum ESPRESSO."""
+        self._add_mpi()
+        self._add_openmp()
+        self._add_cuda()
+
+    def _add_libraries(self):
+        """Enable external libraries for Quantum ESPRESSO."""
+        self._add_scalapack()
+        self._add_fox()
+        self._add_libxc()
+        self._add_elpa()
+        self._add_hdf5()
+
+    def _add_plugins(self):
+        """Enable plugins for Quantum ESPRESSO."""
+        plugins = []
+        plugins += self._add_gipaw()
+        plugins += self._add_d3q()
+        plugins += self._add_qmcpack()
+        if plugins:
+            self.cfg.update('configopts', '-DQE_ENABLE_PLUGINS="%s"' % ';'.join(plugins))
+
+    def _add_mpi(self):
+        """Enable MPI for Quantum ESPRESSO."""
+        if self.toolchain.options.get('usempi', False):
+            self.cfg.update('configopts', '-DENABLE_MPI=ON')
+
+    def _add_openmp(self):
+        """Enable OpenMP for Quantum ESPRESSO."""
+        if self.toolchain.options.get('openmp', False):
+            self.cfg.update('configopts', '-DENABLE_OPENMP=ON')
+
+    def _add_cuda(self):
+        """Enable CUDA for Quantum ESPRESSO."""
+        if self.cfg.get('with_cuda', False):
+            self.cfg.update('configopts', '-DQE_ENABLE_CUDA=ON')
+            self.cfg.update('configopts', '-DQE_ENABLE_OPENACC=ON')
+
+    def _add_scalapack(self):
+        """Enable ScaLAPACK for Quantum ESPRESSO."""
+        if self.cfg.get('with_scalapack', False):
+            if not self.toolchain.options.get('usempi', False):
+                raise EasyBuildError("ScaLAPACK support requires MPI")
+            self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=ON')
+
+    def _add_fox(self):
+        """Enable FoX for Quantum ESPRESSO."""
+        if self.cfg.get('with_fox', False):
+            self.cfg.update('configopts', '-DQE_ENABLE_FOX=ON')
+
+    def _add_hdf5(self):
+        """Enable HDF5 for Quantum ESPRESSO."""
+        if get_software_root("HDF5"):
+            self.cfg.update('configopts', '-DQE_ENABLE_HDF5=ON')
+
+    def _add_libxc(self):
+        """Enable LibXC for Quantum ESPRESSO."""
+        if get_software_root("libxc"):
+            self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=ON')
+
+    def _add_elpa(self):
+        """Enable ELPA for Quantum ESPRESSO."""
+        if get_software_root("ELPA"):
+            if not self.cfg.get('with_scalapack', False):
+                raise EasyBuildError("ELPA support requires ScaLAPACK")
+            if LooseVersion(self.version) == LooseVersion('7.3') and self.toolchain.options.get('openmp', False):
+                raise EasyBuildError("QE 7.3 with cmake does not support ELPA with OpenMP")
+            self.cfg.update('configopts', '-DQE_ENABLE_ELPA=ON')
+
+    def _add_gipaw(self):
+        """Enable GIPAW for Quantum ESPRESSO."""
+        res = []
+        if self.cfg.get('with_gipaw', False):
+            if LooseVersion(self.version) == LooseVersion('7.3.1'):
+                # See issue: https://github.com/dceresoli/qe-gipaw/issues/19
+                raise EasyBuildError("GIPAW will fail to compile in QE 7.3.1")
+            res = ['gipaw']
+            self.check_bins += ['gipaw.x']
+        return res
+
+    def _add_d3q(self):
+        """Enable D3Q for Quantum ESPRESSO."""
+        res = []
+        if self.cfg.get('with_d3q', False):
+            if LooseVersion(self.version) > LooseVersion('7.0'):
+                # See issues:
+                # https://gitlab.com/QEF/q-e/-/issues/666
+                # https://github.com/anharmonic/d3q/issues/13
+                raise EasyBuildError("D3Q is not supported in QE 7.0+")
+            res = ['d3q']
+            self.check_bins += [
+                'd3_asr3.x', 'd3_lw.x', 'd3_q2r.x', 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x',
+                'd3_sparse.x', 'd3_sqom.x', 'd3_tk.x'
+                ]
+        return res
+
+    def _add_qmcpack(self):
+        """Enable QMCPACK for Quantum ESPRESSO."""
+        res = []
+        if self.cfg.get('with_qmcpack', False):
+            res = ['pw2qmcpack']
+            self.check_bins += ['pw2qmcpack.x']
+        return res
+
+    def configure_step(self):
+        """Custom configuration procedure for Quantum ESPRESSO."""
+
+        if LooseVersion(self.version) < LooseVersion('7.3'):
+            raise EasyBuildError("EB QuantumEspresso cmake is implemented for versions >= 7.3")
+
+        self._add_toolchains_opts()
+        self._add_libraries()
+        self._add_plugins()
+
+        # Enable/configure test suite
+        nprocs = self.cfg.get('test_suite_nprocs', 1)
+        self.cfg.update('configopts', '-DQE_ENABLE_TEST=ON')
+        self.cfg.update('configopts', '-DTESTCODE_NPROCS=%d' % nprocs)
+
+        # Change format of timings to seconds only (from d/h/m/s)
+        self.cfg.update('configopts', '-DQE_CLOCK_SECONDS=ON')
+
+        super(EB_QuantumESPRESSOcmake, self).configure_step()
+
+    def test_step(self):
+        """
+        Test the compilation using Quantum ESPRESSO's test suite.
+        ctest -j NCONCURRENT (NCONCURRENT = max (1, PARALLEL / NPROCS))
+        """
+
+        thr = self.cfg.get('test_suite_threshold', 0.97)
+        nprocs = self.cfg.get('test_suite_nprocs', 1)
+        concurrent = max(1, self.cfg.get('parallel', 1) // nprocs)
+        allow_fail = self.cfg.get('test_suite_allow_failures', [])
+
+        cmd = ' '.join([
+            'ctest',
+            '-j%d' % concurrent,
+            '--output-on-failure',
+        ])
+
+        (out, _) = run_cmd(cmd, log_all=False, log_ok=False, simple=False, regexp=False)
+
+        # Example output:
+        # 74% tests passed, 124 tests failed out of 481
+        rgx = r'^ *(?P<perc>\d+)% tests passed, +(?P<failed>\d+) +tests failed out of +(?P<total>\d+)'
+        mch = re.search(rgx, out, re.MULTILINE)
+        if not mch:
+            raise EasyBuildError("Failed to parse test suite output")
+        
+        perc = int(mch.group('perc')) / 100
+        num_fail = int(mch.group('failed'))
+        total = int(mch.group('total'))
+        passed = total - num_fail
+        failures = []  # list of tests that failed, to be logged at the end
+
+
+        # Example output for reported failures:
+        # 635/635 Test #570: system--epw_wfpt-correctness ......................................***Failed    3.52 sec
+        self.log.debug("Test suite output:")
+        self.log.debug(out)
+        for line in out.splitlines():
+            if '***Failed' in line:
+                for allowed in allow_fail:
+                    if allowed in line:
+                        self.log.info('Ignoring failure: %s' % line)
+                        break
+                else:
+                    failures.append(line)
+                self.log.warning(line)
+
+        # Allow for flaky tests (eg too strict thresholds on results for structure relaxation)
+        num_fail = len(failures)
+        num_fail_thr = self.cfg.get('test_suite_max_failed', 0)
+        # perc = spass / max(stot, 1)
+        self.log.info("Total tests passed %d out of %d  (%.2f%%)" % (passed, total, perc * 100))
+        if perc < thr:
+            raise EasyBuildError(
+                "Test suite failed with less than %.2f %% (%.2f) success rate" % (thr * 100, perc * 100)
+                )
+        if num_fail > num_fail_thr:
+            raise EasyBuildError(
+                "Test suite failed with more than %d failures %d" % (num_fail_thr, num_fail)
+                )
+
+        return out
+
+    def sanity_check_step(self):
+        """Custom sanity check for Quantum ESPRESSO."""
+
+        targets = self.cfg['buildopts'].split()
+
+        # Condition for all targets being build 'make'  or 'make all_currents'
+        all_cond = len(targets) == 0 or 'all_currents' in targets
+        pwall_cond = 'pwall' in targets
+
+
+        # Standard binaries
+        if all_cond or 'cp' in targets :
+            self.check_bins += ["cp.x", "cppp.x", "manycp.x", "wfdd.x"]
+
+        if all_cond or 'epw' in targets:
+            self.check_bins += ["epw.x"]
+
+        if all_cond or 'gwl' in targets:
+            self.check_bins += [
+                "abcoeff_to_eps.x", "bse_main.x", "graph.x", "gww_fit.x", "gww.x", "head.x", "memory_pw4gww.x",
+                "pw4gww.x", "simple_bse.x", "simple_ip.x", "simple.x"
+                ]
+
+        if all_cond or 'hp' in targets:
+            self.check_bins += ["hp.x"]
+
+        if all_cond or 'ld1' in targets:
+            self.check_bins += ["ld1.x"]
+
+        if all_cond or pwall_cond or 'neb' in targets:
+            self.check_bins += ["neb.x", "path_interpolation.x"]
+
+        if all_cond or pwall_cond or 'ph' in targets:
+            self.check_bins += [
+                "alpha2f.x", "dynmat.x", "fd_ef.x", "fd.x", "lambda.x", "phcg.x", "postahc.x", "q2r.x", "dvscf_q2r.x",
+                "epa.x", "fd_ifc.x", "fqha.x", "matdyn.x", "ph.x", "q2qstar.x"
+                ]
+
+        if all_cond or pwall_cond or 'pp' in targets:
+            self.check_bins += [
+                "average.x", "dos_sp.x", "ef.x", "fermi_int_0.x", "fermi_proj.x", "fs.x", "molecularpdos.x",
+                "pawplot.x", "plotband.x", "plotrho.x", "ppacf.x", "pp.x", "pw2bgw.x", "pw2gt.x", "pw2wannier90.x",
+                "wannier_ham.x", "wfck2r.x", "bands.x", "dos.x", "epsilon.x", "fermi_int_1.x", "fermi_velocity.x",
+                "initial_state.x", "open_grid.x", "plan_avg.x", "plotproj.x", "pmw.x", "pprism.x", "projwfc.x",
+                "pw2critic.x", "pw2gw.x", "sumpdos.x", "wannier_plot.x"
+                ]
+
+        if all_cond or pwall_cond or 'pw' in targets:
+            self.check_bins += [
+                "cell2ibrav.x", "ev.x", "ibrav2cell.x", "kpoints.x", "pwi2xsf.x", "pw.x", "scan_ibrav.x"
+                ]
+
+        if all_cond or pwall_cond or 'pwcond' in targets:
+            self.check_bins += ["pwcond.x"]
+
+        if all_cond or 'tddfpt' in targets:
+            self.check_bins += ["turbo_davidson.x", "turbo_eels.x", "turbo_lanczos.x", "turbo_magnon.x", "turbo_spectrum.x"]
+
+        if all_cond or 'upf' in targets:
+            self.check_bins += ["upfconv.x", "virtual_v2.x"]
+
+        if all_cond or 'xspectra' in targets:
+            self.check_bins += ["molecularnexafs.x", "spectra_correction.x", "xspectra.x"]
+
+        # Plugins binaries
+        if (all_cond and self.cfg.get('with_gipaw', False)) or 'gipaw' in targets:
+            self.check_bins += ["gipaw.x"]
+
+        if (all_cond and self.cfg.get('d3q', False)) or 'd3q' in targets:
+            self.check_bins += [
+                'd3_asr3.x', 'd3_lw.x', 'd3_q2r.x', 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x',
+                'd3_sparse.x', 'd3_sqom.x', 'd3_tk.x'
+                ]
+            
+        if (all_cond and self.cfg.get('with_qmcpack', False)) or 'pw2qmcpack' in targets:
+            self.check_bins += ['pw2qmcpack.x']
+
+        self.log.debug("Checking for binaries: %s" % ', '.join(self.check_bins))
+
+        custom_paths = {
+            'files': [os.path.join('bin', x) for x in self.check_bins],
+            'dirs': []
+        }
+
+        super(EB_QuantumESPRESSOcmake, self).sanity_check_step(custom_paths=custom_paths)

From 28bbe87685e94782bd3eb8e62e16b72263e34c95 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Thu, 14 Mar 2024 15:46:13 +0100
Subject: [PATCH 041/134] Plugin binaries already added in the _add_XXX methods

---
 easybuild/easyblocks/q/quantumespressocmake.py | 15 ---------------
 1 file changed, 15 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 2209afed49..d78180be83 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -331,21 +331,6 @@ def sanity_check_step(self):
         if all_cond or 'xspectra' in targets:
             self.check_bins += ["molecularnexafs.x", "spectra_correction.x", "xspectra.x"]
 
-        # Plugins binaries
-        if (all_cond and self.cfg.get('with_gipaw', False)) or 'gipaw' in targets:
-            self.check_bins += ["gipaw.x"]
-
-        if (all_cond and self.cfg.get('d3q', False)) or 'd3q' in targets:
-            self.check_bins += [
-                'd3_asr3.x', 'd3_lw.x', 'd3_q2r.x', 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x',
-                'd3_sparse.x', 'd3_sqom.x', 'd3_tk.x'
-                ]
-            
-        if (all_cond and self.cfg.get('with_qmcpack', False)) or 'pw2qmcpack' in targets:
-            self.check_bins += ['pw2qmcpack.x']
-
-        self.log.debug("Checking for binaries: %s" % ', '.join(self.check_bins))
-
         custom_paths = {
             'files': [os.path.join('bin', x) for x in self.check_bins],
             'dirs': []

From 2a814076b3be4ecc8a157c1ab4193c60ea5b331c Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 15 Mar 2024 14:13:22 +0100
Subject: [PATCH 042/134] Added fix for intel toolchain

---
 easybuild/easyblocks/q/quantumespressocmake.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index d78180be83..265bce17ac 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -30,6 +30,7 @@
 import os
 import re
 
+import easybuild.tools.toolchain as toolchain
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools import LooseVersion
 from easybuild.tools.build_log import EasyBuildError
@@ -189,6 +190,8 @@ def configure_step(self):
 
         if LooseVersion(self.version) < LooseVersion('7.3'):
             raise EasyBuildError("EB QuantumEspresso cmake is implemented for versions >= 7.3")
+        
+        comp_fam = self.toolchain.comp_family()
 
         self._add_toolchains_opts()
         self._add_libraries()
@@ -202,6 +205,13 @@ def configure_step(self):
         # Change format of timings to seconds only (from d/h/m/s)
         self.cfg.update('configopts', '-DQE_CLOCK_SECONDS=ON')
 
+        # Needed to avoid a DSO missing from command line linking error with the Intel toolchain
+        # https://gitlab.com/QEF/q-e/-/issues/667
+        if self.cfg.get('build_shared_libs', False) and comp_fam == toolchain.INTELCOMP:
+            ldflags = os.environ.get('LDFLAGS', '')
+            ldflags += ' -Wl,--copy-dt-needed-entries '
+            os.environ['LDFLAGS'] = ldflags
+ 
         super(EB_QuantumESPRESSOcmake, self).configure_step()
 
     def test_step(self):
@@ -323,7 +333,9 @@ def sanity_check_step(self):
             self.check_bins += ["pwcond.x"]
 
         if all_cond or 'tddfpt' in targets:
-            self.check_bins += ["turbo_davidson.x", "turbo_eels.x", "turbo_lanczos.x", "turbo_magnon.x", "turbo_spectrum.x"]
+            self.check_bins += [
+                "turbo_davidson.x", "turbo_eels.x", "turbo_lanczos.x", "turbo_magnon.x", "turbo_spectrum.x"
+                ]
 
         if all_cond or 'upf' in targets:
             self.check_bins += ["upfconv.x", "virtual_v2.x"]

From 1337fcc368326d9cfa4adc4505aa8330ca7e41eb Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 15 Mar 2024 15:39:40 +0100
Subject: [PATCH 043/134] pre-commit hooks

---
 .../easyblocks/q/quantumespressocmake.py      | 96 +++++++++----------
 1 file changed, 48 insertions(+), 48 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 265bce17ac..4e027b63a6 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -43,32 +43,32 @@
 class EB_QuantumESPRESSOcmake(CMakeMake):
     """Support for building and installing Quantum ESPRESSO."""
 
-    TEST_SUITE_DIR = "test-suite"
+    TEST_SUITE_DIR = 'test-suite'
 
     @staticmethod
     def extra_options():
         """Custom easyconfig parameters for Quantum ESPRESSO."""
         extra_vars = {
-            'with_cuda': [False, "Enable CUDA support", CUSTOM],
-            'with_scalapack': [True, "Enable ScaLAPACK support", CUSTOM],
-            'with_fox': [False, "Enable FoX support", CUSTOM],
-            'with_gipaw': [True, "Enable GIPAW support", CUSTOM],
-            'with_d3q': [False, "Enable D3Q support", CUSTOM],
-            'with_qmcpack': [False, "Enable QMCPACK support", CUSTOM],
-            'test_suite_nprocs': [1, "Number of processors to use for the test suite", CUSTOM],
+            'with_cuda': [False, 'Enable CUDA support', CUSTOM],
+            'with_scalapack': [True, 'Enable ScaLAPACK support', CUSTOM],
+            'with_fox': [False, 'Enable FoX support', CUSTOM],
+            'with_gipaw': [True, 'Enable GIPAW support', CUSTOM],
+            'with_d3q': [False, 'Enable D3Q support', CUSTOM],
+            'with_qmcpack': [False, 'Enable QMCPACK support', CUSTOM],
+            'test_suite_nprocs': [1, 'Number of processors to use for the test suite', CUSTOM],
             'test_suite_allow_failures': [[
                 'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
                 '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
                 '--ph_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
                 '--epw_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
                 '--tddfpt_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-            ], "List of test suite targets that are allowed to fail (name can partially match)", CUSTOM],
+            ], 'List of test suite targets that are allowed to fail (name can partially match)', CUSTOM],
             'test_suite_threshold': [
                 0.97,
-                "Threshold for test suite success rate (does count also allowed failures)",
+                'Threshold for test suite success rate (does count also allowed failures)',
                 CUSTOM
                 ],
-            'test_suite_max_failed': [0, "Maximum number of failing tests (does not count allowed failures)", CUSTOM],
+            'test_suite_max_failed': [0, 'Maximum number of failing tests (does not count allowed failures)', CUSTOM],
         }
         return CMakeMake.extra_options(extra_vars)
 
@@ -76,7 +76,7 @@ def __init__(self, *args, **kwargs):
         """Add extra config options specific to Quantum ESPRESSO."""
         super(EB_QuantumESPRESSOcmake, self).__init__(*args, **kwargs)
 
-        self.install_subdir = "qe-%s" % self.version
+        self.install_subdir = 'qe-%s' % self.version
 
         self.check_bins = []
 
@@ -123,7 +123,7 @@ def _add_scalapack(self):
         """Enable ScaLAPACK for Quantum ESPRESSO."""
         if self.cfg.get('with_scalapack', False):
             if not self.toolchain.options.get('usempi', False):
-                raise EasyBuildError("ScaLAPACK support requires MPI")
+                raise EasyBuildError('ScaLAPACK support requires MPI')
             self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=ON')
 
     def _add_fox(self):
@@ -133,21 +133,21 @@ def _add_fox(self):
 
     def _add_hdf5(self):
         """Enable HDF5 for Quantum ESPRESSO."""
-        if get_software_root("HDF5"):
+        if get_software_root('HDF5'):
             self.cfg.update('configopts', '-DQE_ENABLE_HDF5=ON')
 
     def _add_libxc(self):
         """Enable LibXC for Quantum ESPRESSO."""
-        if get_software_root("libxc"):
+        if get_software_root('libxc'):
             self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=ON')
 
     def _add_elpa(self):
         """Enable ELPA for Quantum ESPRESSO."""
-        if get_software_root("ELPA"):
+        if get_software_root('ELPA'):
             if not self.cfg.get('with_scalapack', False):
-                raise EasyBuildError("ELPA support requires ScaLAPACK")
+                raise EasyBuildError('ELPA support requires ScaLAPACK')
             if LooseVersion(self.version) == LooseVersion('7.3') and self.toolchain.options.get('openmp', False):
-                raise EasyBuildError("QE 7.3 with cmake does not support ELPA with OpenMP")
+                raise EasyBuildError('QE 7.3 with cmake does not support ELPA with OpenMP')
             self.cfg.update('configopts', '-DQE_ENABLE_ELPA=ON')
 
     def _add_gipaw(self):
@@ -156,7 +156,7 @@ def _add_gipaw(self):
         if self.cfg.get('with_gipaw', False):
             if LooseVersion(self.version) == LooseVersion('7.3.1'):
                 # See issue: https://github.com/dceresoli/qe-gipaw/issues/19
-                raise EasyBuildError("GIPAW will fail to compile in QE 7.3.1")
+                raise EasyBuildError('GIPAW will fail to compile in QE 7.3.1')
             res = ['gipaw']
             self.check_bins += ['gipaw.x']
         return res
@@ -169,7 +169,7 @@ def _add_d3q(self):
                 # See issues:
                 # https://gitlab.com/QEF/q-e/-/issues/666
                 # https://github.com/anharmonic/d3q/issues/13
-                raise EasyBuildError("D3Q is not supported in QE 7.0+")
+                raise EasyBuildError('D3Q is not supported in QE 7.0+')
             res = ['d3q']
             self.check_bins += [
                 'd3_asr3.x', 'd3_lw.x', 'd3_q2r.x', 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x',
@@ -189,8 +189,8 @@ def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""
 
         if LooseVersion(self.version) < LooseVersion('7.3'):
-            raise EasyBuildError("EB QuantumEspresso cmake is implemented for versions >= 7.3")
-        
+            raise EasyBuildError('EB QuantumEspresso cmake is implemented for versions >= 7.3')
+
         comp_fam = self.toolchain.comp_family()
 
         self._add_toolchains_opts()
@@ -211,7 +211,7 @@ def configure_step(self):
             ldflags = os.environ.get('LDFLAGS', '')
             ldflags += ' -Wl,--copy-dt-needed-entries '
             os.environ['LDFLAGS'] = ldflags
- 
+
         super(EB_QuantumESPRESSOcmake, self).configure_step()
 
     def test_step(self):
@@ -238,8 +238,8 @@ def test_step(self):
         rgx = r'^ *(?P<perc>\d+)% tests passed, +(?P<failed>\d+) +tests failed out of +(?P<total>\d+)'
         mch = re.search(rgx, out, re.MULTILINE)
         if not mch:
-            raise EasyBuildError("Failed to parse test suite output")
-        
+            raise EasyBuildError('Failed to parse test suite output')
+
         perc = int(mch.group('perc')) / 100
         num_fail = int(mch.group('failed'))
         total = int(mch.group('total'))
@@ -249,7 +249,7 @@ def test_step(self):
 
         # Example output for reported failures:
         # 635/635 Test #570: system--epw_wfpt-correctness ......................................***Failed    3.52 sec
-        self.log.debug("Test suite output:")
+        self.log.debug('Test suite output:')
         self.log.debug(out)
         for line in out.splitlines():
             if '***Failed' in line:
@@ -265,14 +265,14 @@ def test_step(self):
         num_fail = len(failures)
         num_fail_thr = self.cfg.get('test_suite_max_failed', 0)
         # perc = spass / max(stot, 1)
-        self.log.info("Total tests passed %d out of %d  (%.2f%%)" % (passed, total, perc * 100))
+        self.log.info('Total tests passed %d out of %d  (%.2f%%)' % (passed, total, perc * 100))
         if perc < thr:
             raise EasyBuildError(
-                "Test suite failed with less than %.2f %% (%.2f) success rate" % (thr * 100, perc * 100)
+                'Test suite failed with less than %.2f %% (%.2f) success rate' % (thr * 100, perc * 100)
                 )
         if num_fail > num_fail_thr:
             raise EasyBuildError(
-                "Test suite failed with more than %d failures %d" % (num_fail_thr, num_fail)
+                'Test suite failed with more than %d failures %d' % (num_fail_thr, num_fail)
                 )
 
         return out
@@ -289,59 +289,59 @@ def sanity_check_step(self):
 
         # Standard binaries
         if all_cond or 'cp' in targets :
-            self.check_bins += ["cp.x", "cppp.x", "manycp.x", "wfdd.x"]
+            self.check_bins += ['cp.x', 'cppp.x', 'manycp.x', 'wfdd.x']
 
         if all_cond or 'epw' in targets:
-            self.check_bins += ["epw.x"]
+            self.check_bins += ['epw.x']
 
         if all_cond or 'gwl' in targets:
             self.check_bins += [
-                "abcoeff_to_eps.x", "bse_main.x", "graph.x", "gww_fit.x", "gww.x", "head.x", "memory_pw4gww.x",
-                "pw4gww.x", "simple_bse.x", "simple_ip.x", "simple.x"
+                'abcoeff_to_eps.x', 'bse_main.x', 'graph.x', 'gww_fit.x', 'gww.x', 'head.x', 'memory_pw4gww.x',
+                'pw4gww.x', 'simple_bse.x', 'simple_ip.x', 'simple.x'
                 ]
 
         if all_cond or 'hp' in targets:
-            self.check_bins += ["hp.x"]
+            self.check_bins += ['hp.x']
 
         if all_cond or 'ld1' in targets:
-            self.check_bins += ["ld1.x"]
+            self.check_bins += ['ld1.x']
 
         if all_cond or pwall_cond or 'neb' in targets:
-            self.check_bins += ["neb.x", "path_interpolation.x"]
+            self.check_bins += ['neb.x', 'path_interpolation.x']
 
         if all_cond or pwall_cond or 'ph' in targets:
             self.check_bins += [
-                "alpha2f.x", "dynmat.x", "fd_ef.x", "fd.x", "lambda.x", "phcg.x", "postahc.x", "q2r.x", "dvscf_q2r.x",
-                "epa.x", "fd_ifc.x", "fqha.x", "matdyn.x", "ph.x", "q2qstar.x"
+                'alpha2f.x', 'dynmat.x', 'fd_ef.x', 'fd.x', 'lambda.x', 'phcg.x', 'postahc.x', 'q2r.x', 'dvscf_q2r.x',
+                'epa.x', 'fd_ifc.x', 'fqha.x', 'matdyn.x', 'ph.x', 'q2qstar.x'
                 ]
 
         if all_cond or pwall_cond or 'pp' in targets:
             self.check_bins += [
-                "average.x", "dos_sp.x", "ef.x", "fermi_int_0.x", "fermi_proj.x", "fs.x", "molecularpdos.x",
-                "pawplot.x", "plotband.x", "plotrho.x", "ppacf.x", "pp.x", "pw2bgw.x", "pw2gt.x", "pw2wannier90.x",
-                "wannier_ham.x", "wfck2r.x", "bands.x", "dos.x", "epsilon.x", "fermi_int_1.x", "fermi_velocity.x",
-                "initial_state.x", "open_grid.x", "plan_avg.x", "plotproj.x", "pmw.x", "pprism.x", "projwfc.x",
-                "pw2critic.x", "pw2gw.x", "sumpdos.x", "wannier_plot.x"
+                'average.x', 'dos_sp.x', 'ef.x', 'fermi_int_0.x', 'fermi_proj.x', 'fs.x', 'molecularpdos.x',
+                'pawplot.x', 'plotband.x', 'plotrho.x', 'ppacf.x', 'pp.x', 'pw2bgw.x', 'pw2gt.x', 'pw2wannier90.x',
+                'wannier_ham.x', 'wfck2r.x', 'bands.x', 'dos.x', 'epsilon.x', 'fermi_int_1.x', 'fermi_velocity.x',
+                'initial_state.x', 'open_grid.x', 'plan_avg.x', 'plotproj.x', 'pmw.x', 'pprism.x', 'projwfc.x',
+                'pw2critic.x', 'pw2gw.x', 'sumpdos.x', 'wannier_plot.x'
                 ]
 
         if all_cond or pwall_cond or 'pw' in targets:
             self.check_bins += [
-                "cell2ibrav.x", "ev.x", "ibrav2cell.x", "kpoints.x", "pwi2xsf.x", "pw.x", "scan_ibrav.x"
+                'cell2ibrav.x', 'ev.x', 'ibrav2cell.x', 'kpoints.x', 'pwi2xsf.x', 'pw.x', 'scan_ibrav.x'
                 ]
 
         if all_cond or pwall_cond or 'pwcond' in targets:
-            self.check_bins += ["pwcond.x"]
+            self.check_bins += ['pwcond.x']
 
         if all_cond or 'tddfpt' in targets:
             self.check_bins += [
-                "turbo_davidson.x", "turbo_eels.x", "turbo_lanczos.x", "turbo_magnon.x", "turbo_spectrum.x"
+                'turbo_davidson.x', 'turbo_eels.x', 'turbo_lanczos.x', 'turbo_magnon.x', 'turbo_spectrum.x'
                 ]
 
         if all_cond or 'upf' in targets:
-            self.check_bins += ["upfconv.x", "virtual_v2.x"]
+            self.check_bins += ['upfconv.x', 'virtual_v2.x']
 
         if all_cond or 'xspectra' in targets:
-            self.check_bins += ["molecularnexafs.x", "spectra_correction.x", "xspectra.x"]
+            self.check_bins += ['molecularnexafs.x', 'spectra_correction.x', 'xspectra.x']
 
         custom_paths = {
             'files': [os.path.join('bin', x) for x in self.check_bins],

From 4621fb738570e90db26d768fb95429376b9e3c85 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 18 Mar 2024 15:38:06 +0100
Subject: [PATCH 044/134] Linting + moved ignored tests to config files

---
 .../easyblocks/q/quantumespressocmake.py      | 28 ++++++++-----------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 4e027b63a6..dce75d3b50 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -30,7 +30,6 @@
 import os
 import re
 
-import easybuild.tools.toolchain as toolchain
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools import LooseVersion
 from easybuild.tools.build_log import EasyBuildError
@@ -56,13 +55,11 @@ def extra_options():
             'with_d3q': [False, 'Enable D3Q support', CUSTOM],
             'with_qmcpack': [False, 'Enable QMCPACK support', CUSTOM],
             'test_suite_nprocs': [1, 'Number of processors to use for the test suite', CUSTOM],
-            'test_suite_allow_failures': [[
-                'test_qe_xclib_',  # 7.3.1:  https://gitlab.com/QEF/q-e/-/issues/640
-                '--hp_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-                '--ph_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-                '--epw_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-                '--tddfpt_',  # 7.3.1:  Broken testsuite (https://gitlab.com/QEF/q-e/-/issues/665)
-            ], 'List of test suite targets that are allowed to fail (name can partially match)', CUSTOM],
+            'test_suite_allow_failures': [
+                [],
+                'List of test suite targets that are allowed to fail (name can partially match)',
+                CUSTOM
+                ],
             'test_suite_threshold': [
                 0.97,
                 'Threshold for test suite success rate (does count also allowed failures)',
@@ -165,15 +162,16 @@ def _add_d3q(self):
         """Enable D3Q for Quantum ESPRESSO."""
         res = []
         if self.cfg.get('with_d3q', False):
-            if LooseVersion(self.version) > LooseVersion('7.0'):
+            if LooseVersion(self.version) <= LooseVersion('7.3.1'):
                 # See issues:
                 # https://gitlab.com/QEF/q-e/-/issues/666
                 # https://github.com/anharmonic/d3q/issues/13
-                raise EasyBuildError('D3Q is not supported in QE 7.0+')
+                raise EasyBuildError('D3Q compilation will fail for QE 7.3 and 7.3.1')
             res = ['d3q']
             self.check_bins += [
-                'd3_asr3.x', 'd3_lw.x', 'd3_q2r.x', 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x',
-                'd3_sparse.x', 'd3_sqom.x', 'd3_tk.x'
+                'd3_asr3.x', 'd3_db.x', 'd3_import_shengbte.x', 'd3_interpolate2.x', 'd3_lw.x', 'd3_q2r.x',
+                'd3_qha.x','d3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x', 'd3_rmzeu.x', 'd3_sparse.x',
+                'd3_sqom.x', 'd3_tk.x',
                 ]
         return res
 
@@ -191,8 +189,6 @@ def configure_step(self):
         if LooseVersion(self.version) < LooseVersion('7.3'):
             raise EasyBuildError('EB QuantumEspresso cmake is implemented for versions >= 7.3')
 
-        comp_fam = self.toolchain.comp_family()
-
         self._add_toolchains_opts()
         self._add_libraries()
         self._add_plugins()
@@ -205,9 +201,9 @@ def configure_step(self):
         # Change format of timings to seconds only (from d/h/m/s)
         self.cfg.update('configopts', '-DQE_CLOCK_SECONDS=ON')
 
-        # Needed to avoid a DSO missing from command line linking error with the Intel toolchain
+        # Needed to avoid a DSO missing from command line linking error
         # https://gitlab.com/QEF/q-e/-/issues/667
-        if self.cfg.get('build_shared_libs', False) and comp_fam == toolchain.INTELCOMP:
+        if self.cfg.get('build_shared_libs', False) :
             ldflags = os.environ.get('LDFLAGS', '')
             ldflags += ' -Wl,--copy-dt-needed-entries '
             os.environ['LDFLAGS'] = ldflags

From ee3695fafd3273327d43a535afb8ab04f6da5918 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 18 Mar 2024 15:45:30 +0100
Subject: [PATCH 045/134] Reuse message

---
 .../easyblocks/q/quantumespressocmake.py      | 117 +++++++++---------
 1 file changed, 57 insertions(+), 60 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index dce75d3b50..b9f003b37a 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -79,115 +79,112 @@ def __init__(self, *args, **kwargs):
 
     def _add_toolchains_opts(self):
         """Enable toolchain options for Quantum ESPRESSO."""
-        self._add_mpi()
-        self._add_openmp()
-        self._add_cuda()
+        if self.toolchain.options.get('usempi', False):
+            self._add_mpi()
+        if self.toolchain.options.get('openmp', False):
+            self._add_openmp()
+        if self.cfg.get('with_cuda', False):
+            self._add_cuda()
 
     def _add_libraries(self):
         """Enable external libraries for Quantum ESPRESSO."""
-        self._add_scalapack()
-        self._add_fox()
-        self._add_libxc()
-        self._add_elpa()
-        self._add_hdf5()
+        if self.cfg.get('with_scalapack', False):
+            self._add_scalapack()
+        if self.cfg.get('with_fox', False):
+            self._add_fox()
+        if get_software_root('libxc'):
+            self._add_libxc()
+        if get_software_root('ELPA'):
+            self._add_elpa()
+        if get_software_root('HDF5'):
+            self._add_hdf5()
 
     def _add_plugins(self):
         """Enable plugins for Quantum ESPRESSO."""
         plugins = []
-        plugins += self._add_gipaw()
-        plugins += self._add_d3q()
-        plugins += self._add_qmcpack()
+        if self.cfg.get('with_gipaw', False):
+            plugins += self._add_gipaw()
+        if self.cfg.get('with_d3q', False):
+            plugins += self._add_d3q()
+        if self.cfg.get('with_qmcpack', False):
+            plugins += self._add_qmcpack()
         if plugins:
             self.cfg.update('configopts', '-DQE_ENABLE_PLUGINS="%s"' % ';'.join(plugins))
 
     def _add_mpi(self):
         """Enable MPI for Quantum ESPRESSO."""
-        if self.toolchain.options.get('usempi', False):
-            self.cfg.update('configopts', '-DENABLE_MPI=ON')
+        self.cfg.update('configopts', '-DENABLE_MPI=ON')
 
     def _add_openmp(self):
         """Enable OpenMP for Quantum ESPRESSO."""
-        if self.toolchain.options.get('openmp', False):
-            self.cfg.update('configopts', '-DENABLE_OPENMP=ON')
+        self.cfg.update('configopts', '-DENABLE_OPENMP=ON')
 
     def _add_cuda(self):
         """Enable CUDA for Quantum ESPRESSO."""
-        if self.cfg.get('with_cuda', False):
-            self.cfg.update('configopts', '-DQE_ENABLE_CUDA=ON')
-            self.cfg.update('configopts', '-DQE_ENABLE_OPENACC=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_CUDA=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_OPENACC=ON')
 
     def _add_scalapack(self):
         """Enable ScaLAPACK for Quantum ESPRESSO."""
-        if self.cfg.get('with_scalapack', False):
-            if not self.toolchain.options.get('usempi', False):
-                raise EasyBuildError('ScaLAPACK support requires MPI')
-            self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=ON')
+        if not self.toolchain.options.get('usempi', False):
+            raise EasyBuildError('ScaLAPACK support requires MPI')
+        self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=ON')
 
     def _add_fox(self):
         """Enable FoX for Quantum ESPRESSO."""
-        if self.cfg.get('with_fox', False):
-            self.cfg.update('configopts', '-DQE_ENABLE_FOX=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_FOX=ON')
 
     def _add_hdf5(self):
         """Enable HDF5 for Quantum ESPRESSO."""
-        if get_software_root('HDF5'):
-            self.cfg.update('configopts', '-DQE_ENABLE_HDF5=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_HDF5=ON')
 
     def _add_libxc(self):
         """Enable LibXC for Quantum ESPRESSO."""
-        if get_software_root('libxc'):
-            self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=ON')
 
     def _add_elpa(self):
         """Enable ELPA for Quantum ESPRESSO."""
-        if get_software_root('ELPA'):
-            if not self.cfg.get('with_scalapack', False):
-                raise EasyBuildError('ELPA support requires ScaLAPACK')
-            if LooseVersion(self.version) == LooseVersion('7.3') and self.toolchain.options.get('openmp', False):
-                raise EasyBuildError('QE 7.3 with cmake does not support ELPA with OpenMP')
-            self.cfg.update('configopts', '-DQE_ENABLE_ELPA=ON')
+        if not self.cfg.get('with_scalapack', False):
+            raise EasyBuildError('ELPA support requires ScaLAPACK')
+        if LooseVersion(self.version) == LooseVersion('7.3') and self.toolchain.options.get('openmp', False):
+            raise EasyBuildError('QE 7.3 with cmake does not support ELPA with OpenMP')
+        self.cfg.update('configopts', '-DQE_ENABLE_ELPA=ON')
 
     def _add_gipaw(self):
         """Enable GIPAW for Quantum ESPRESSO."""
-        res = []
-        if self.cfg.get('with_gipaw', False):
-            if LooseVersion(self.version) == LooseVersion('7.3.1'):
-                # See issue: https://github.com/dceresoli/qe-gipaw/issues/19
-                raise EasyBuildError('GIPAW will fail to compile in QE 7.3.1')
-            res = ['gipaw']
-            self.check_bins += ['gipaw.x']
+        if LooseVersion(self.version) == LooseVersion('7.3.1'):
+            # See issue: https://github.com/dceresoli/qe-gipaw/issues/19
+            raise EasyBuildError('GIPAW will fail to compile in QE 7.3.1')
+        res = ['gipaw']
+        self.check_bins += ['gipaw.x']
         return res
 
     def _add_d3q(self):
         """Enable D3Q for Quantum ESPRESSO."""
-        res = []
-        if self.cfg.get('with_d3q', False):
-            if LooseVersion(self.version) <= LooseVersion('7.3.1'):
-                # See issues:
-                # https://gitlab.com/QEF/q-e/-/issues/666
-                # https://github.com/anharmonic/d3q/issues/13
-                raise EasyBuildError('D3Q compilation will fail for QE 7.3 and 7.3.1')
-            res = ['d3q']
-            self.check_bins += [
-                'd3_asr3.x', 'd3_db.x', 'd3_import_shengbte.x', 'd3_interpolate2.x', 'd3_lw.x', 'd3_q2r.x',
-                'd3_qha.x','d3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x', 'd3_rmzeu.x', 'd3_sparse.x',
-                'd3_sqom.x', 'd3_tk.x',
-                ]
+        if LooseVersion(self.version) <= LooseVersion('7.3.1'):
+            # See issues:
+            # https://gitlab.com/QEF/q-e/-/issues/666
+            # https://github.com/anharmonic/d3q/issues/13
+            raise EasyBuildError('D3Q compilation will fail for QE 7.3 and 7.3.1')
+        res = ['d3q']
+        self.check_bins += [
+            'd3_asr3.x', 'd3_db.x', 'd3_import_shengbte.x', 'd3_interpolate2.x', 'd3_lw.x', 'd3_q2r.x',
+            'd3_qha.x','d3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x', 'd3_rmzeu.x', 'd3_sparse.x',
+            'd3_sqom.x', 'd3_tk.x',
+            ]
         return res
 
     def _add_qmcpack(self):
         """Enable QMCPACK for Quantum ESPRESSO."""
-        res = []
-        if self.cfg.get('with_qmcpack', False):
-            res = ['pw2qmcpack']
-            self.check_bins += ['pw2qmcpack.x']
+        res = ['pw2qmcpack']
+        self.check_bins += ['pw2qmcpack.x']
         return res
 
     def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""
 
         if LooseVersion(self.version) < LooseVersion('7.3'):
-            raise EasyBuildError('EB QuantumEspresso cmake is implemented for versions >= 7.3')
+            raise EasyBuildError('EB QuantumEspresso with cmake is implemented for versions >= 7.3')
 
         self._add_toolchains_opts()
         self._add_libraries()
@@ -268,7 +265,7 @@ def test_step(self):
                 )
         if num_fail > num_fail_thr:
             raise EasyBuildError(
-                'Test suite failed with more than %d failures %d' % (num_fail_thr, num_fail)
+                'Test suite failed with %d failures (%d failures permitted)' % (num_fail, num_fail_thr)
                 )
 
         return out

From f4b87a696f038dbaf4ad596a149b10d9be906381 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 18 Mar 2024 15:56:59 +0100
Subject: [PATCH 046/134] Linting

---
 easybuild/easyblocks/q/quantumespressocmake.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index b9f003b37a..bb4fd95949 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -169,7 +169,7 @@ def _add_d3q(self):
         res = ['d3q']
         self.check_bins += [
             'd3_asr3.x', 'd3_db.x', 'd3_import_shengbte.x', 'd3_interpolate2.x', 'd3_lw.x', 'd3_q2r.x',
-            'd3_qha.x','d3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x', 'd3_rmzeu.x', 'd3_sparse.x',
+            'd3_qha.x', 'd3_qq2rr.x', 'd3q.x', 'd3_r2q.x', 'd3_recenter.x', 'd3_rmzeu.x', 'd3_sparse.x',
             'd3_sqom.x', 'd3_tk.x',
             ]
         return res
@@ -200,7 +200,7 @@ def configure_step(self):
 
         # Needed to avoid a DSO missing from command line linking error
         # https://gitlab.com/QEF/q-e/-/issues/667
-        if self.cfg.get('build_shared_libs', False) :
+        if self.cfg.get('build_shared_libs', False):
             ldflags = os.environ.get('LDFLAGS', '')
             ldflags += ' -Wl,--copy-dt-needed-entries '
             os.environ['LDFLAGS'] = ldflags
@@ -239,7 +239,6 @@ def test_step(self):
         passed = total - num_fail
         failures = []  # list of tests that failed, to be logged at the end
 
-
         # Example output for reported failures:
         # 635/635 Test #570: system--epw_wfpt-correctness ......................................***Failed    3.52 sec
         self.log.debug('Test suite output:')
@@ -279,9 +278,8 @@ def sanity_check_step(self):
         all_cond = len(targets) == 0 or 'all_currents' in targets
         pwall_cond = 'pwall' in targets
 
-
         # Standard binaries
-        if all_cond or 'cp' in targets :
+        if all_cond or 'cp' in targets:
             self.check_bins += ['cp.x', 'cppp.x', 'manycp.x', 'wfdd.x']
 
         if all_cond or 'epw' in targets:

From ac204f4f1cd4f080ccca811666b717bfa0bbc989 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Thu, 21 Mar 2024 12:49:38 +0100
Subject: [PATCH 047/134] Using `env.setvar` instead of `os.environ`

---
 easybuild/easyblocks/q/quantumespressocmake.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index bb4fd95949..fa6977141e 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -30,6 +30,7 @@
 import os
 import re
 
+import easybuild.tools.environment as env
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools import LooseVersion
 from easybuild.tools.build_log import EasyBuildError
@@ -201,9 +202,9 @@ def configure_step(self):
         # Needed to avoid a DSO missing from command line linking error
         # https://gitlab.com/QEF/q-e/-/issues/667
         if self.cfg.get('build_shared_libs', False):
-            ldflags = os.environ.get('LDFLAGS', '')
+            ldflags = os.getenv('LDFLAGS', '')
             ldflags += ' -Wl,--copy-dt-needed-entries '
-            os.environ['LDFLAGS'] = ldflags
+            env.setvar('LDFLAGS', ldflags)
 
         super(EB_QuantumESPRESSOcmake, self).configure_step()
 

From b3759f5458f20959afb0d6d48bc4995462c52589 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 22 Mar 2024 15:50:33 +0100
Subject: [PATCH 048/134] Added possibility to install with pre-downloaded
 submodules

---
 .../easyblocks/q/quantumespressocmake.py      | 47 +++++++++++++++++--
 1 file changed, 44 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index fa6977141e..2e845ded3d 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -29,6 +29,7 @@
 """
 import os
 import re
+import shutil
 
 import easybuild.tools.environment as env
 from easybuild.framework.easyconfig import CUSTOM
@@ -44,6 +45,16 @@ class EB_QuantumESPRESSOcmake(CMakeMake):
     """Support for building and installing Quantum ESPRESSO."""
 
     TEST_SUITE_DIR = 'test-suite'
+    SUBMODULES = [
+        'lapack',
+        'mbd',
+        'devxlib',
+        'fox',
+        'd3q',
+        'qe-gipaw',
+        'pw2qmcpack',
+        'wannier90'
+    ]
 
     @staticmethod
     def extra_options():
@@ -166,7 +177,10 @@ def _add_d3q(self):
             # See issues:
             # https://gitlab.com/QEF/q-e/-/issues/666
             # https://github.com/anharmonic/d3q/issues/13
-            raise EasyBuildError('D3Q compilation will fail for QE 7.3 and 7.3.1')
+            if not os.path.exists(os.path.join(self.builddir, self.install_subdir, 'external', 'd3q', '.git')):
+                raise EasyBuildError(
+                    'D3Q compilation will fail for QE 7.3 and 7.3.1 without submodule downloaded from easyconfig.'
+                    )
         res = ['d3q']
         self.check_bins += [
             'd3_asr3.x', 'd3_db.x', 'd3_import_shengbte.x', 'd3_interpolate2.x', 'd3_lw.x', 'd3_q2r.x',
@@ -181,12 +195,36 @@ def _add_qmcpack(self):
         self.check_bins += ['pw2qmcpack.x']
         return res
 
+    def _copy_submodule_dirs(self):
+        """Copy submodule dirs downloaded by EB into XXX/external"""
+        for submod in self.SUBMODULES:
+            src = os.path.join(self.builddir, submod)
+            dst = os.path.join(self.builddir, self.install_subdir, 'external', submod)
+            if os.path.exists(src):
+                self.log.info('Copying submodule %s into %s' % (submod, dst))
+                # Remove empty directories and replace them with the downloaded submodule
+                if os.path.exists(dst):
+                    shutil.rmtree(dst)
+                shutil.move(src, dst)
+            else:
+                self.log.warning('Submodule %s not found at %s' % (submod, src))
+
+            # Trick QE to think that the submodule is already installed in case `keep_git_dir` is not used in
+            # the easyconfig file
+            gitf = os.path.join(dst, '.git')
+            if not os.path.exists(gitf):
+                os.mkdir(gitf)
+
     def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""
 
         if LooseVersion(self.version) < LooseVersion('7.3'):
             raise EasyBuildError('EB QuantumEspresso with cmake is implemented for versions >= 7.3')
 
+        # Needs to be before other functions that could check existance of .git for submodules to
+        # make compatibility checks
+        self._copy_submodule_dirs()
+
         self._add_toolchains_opts()
         self._add_libraries()
         self._add_plugins()
@@ -257,15 +295,18 @@ def test_step(self):
         # Allow for flaky tests (eg too strict thresholds on results for structure relaxation)
         num_fail = len(failures)
         num_fail_thr = self.cfg.get('test_suite_max_failed', 0)
-        # perc = spass / max(stot, 1)
         self.log.info('Total tests passed %d out of %d  (%.2f%%)' % (passed, total, perc * 100))
+        if failures:
+            self.log.warning('The following tests failed (and are not ignored):')
+            for failure in failures:
+                self.log.warning('|   ' + failure)
         if perc < thr:
             raise EasyBuildError(
                 'Test suite failed with less than %.2f %% (%.2f) success rate' % (thr * 100, perc * 100)
                 )
         if num_fail > num_fail_thr:
             raise EasyBuildError(
-                'Test suite failed with %d failures (%d failures permitted)' % (num_fail, num_fail_thr)
+                'Test suite failed with %d non-ignored failures (%d failures permitted)' % (num_fail, num_fail_thr)
                 )
 
         return out

From a91fabe30b722eb705d820ee3442bc2cfa3cfffb Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 22 Mar 2024 18:35:23 +0100
Subject: [PATCH 049/134] Fixed flags

---
 easybuild/easyblocks/q/quantumespressocmake.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 2e845ded3d..c3899aaaf8 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -125,11 +125,11 @@ def _add_plugins(self):
 
     def _add_mpi(self):
         """Enable MPI for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DENABLE_MPI=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_MPI=ON')
 
     def _add_openmp(self):
         """Enable OpenMP for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DENABLE_OPENMP=ON')
+        self.cfg.update('configopts', '-DQE_ENABLE_OPENMP=ON')
 
     def _add_cuda(self):
         """Enable CUDA for Quantum ESPRESSO."""

From 7433a5e0abd5edacea855f577a8c4a3948d15971 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 25 Mar 2024 11:24:05 +0100
Subject: [PATCH 050/134] Ensure that options can also be disabled (plus error
 in compilation of d3q without mpi)

---
 .../easyblocks/q/quantumespressocmake.py      | 81 ++++++++++++-------
 1 file changed, 50 insertions(+), 31 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index c3899aaaf8..14c606572d 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -91,25 +91,17 @@ def __init__(self, *args, **kwargs):
 
     def _add_toolchains_opts(self):
         """Enable toolchain options for Quantum ESPRESSO."""
-        if self.toolchain.options.get('usempi', False):
-            self._add_mpi()
-        if self.toolchain.options.get('openmp', False):
-            self._add_openmp()
-        if self.cfg.get('with_cuda', False):
-            self._add_cuda()
+        self._add_mpi()
+        self._add_openmp()
+        self._add_cuda()
 
     def _add_libraries(self):
         """Enable external libraries for Quantum ESPRESSO."""
-        if self.cfg.get('with_scalapack', False):
-            self._add_scalapack()
-        if self.cfg.get('with_fox', False):
-            self._add_fox()
-        if get_software_root('libxc'):
-            self._add_libxc()
-        if get_software_root('ELPA'):
-            self._add_elpa()
-        if get_software_root('HDF5'):
-            self._add_hdf5()
+        self._add_scalapack()
+        self._add_fox()
+        self._add_hdf5()
+        self._add_libxc()
+        self._add_elpa()
 
     def _add_plugins(self):
         """Enable plugins for Quantum ESPRESSO."""
@@ -125,42 +117,67 @@ def _add_plugins(self):
 
     def _add_mpi(self):
         """Enable MPI for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DQE_ENABLE_MPI=ON')
+        if self.toolchain.options.get('usempi', False):
+            self.cfg.update('configopts', '-DQE_ENABLE_MPI=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_MPI=OFF')
 
     def _add_openmp(self):
         """Enable OpenMP for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DQE_ENABLE_OPENMP=ON')
+        if self.toolchain.options.get('openmp', False):
+            self.cfg.update('configopts', '-DQE_ENABLE_OPENMP=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_OPENMP=OFF')
 
     def _add_cuda(self):
         """Enable CUDA for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DQE_ENABLE_CUDA=ON')
-        self.cfg.update('configopts', '-DQE_ENABLE_OPENACC=ON')
+        if self.cfg.get('with_cuda', False):
+            self.cfg.update('configopts', '-DQE_ENABLE_CUDA=ON')
+            self.cfg.update('configopts', '-DQE_ENABLE_OPENACC=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_CUDA=OFF')
+            self.cfg.update('configopts', '-DQE_ENABLE_OPENACC=OFF')
 
     def _add_scalapack(self):
         """Enable ScaLAPACK for Quantum ESPRESSO."""
-        if not self.toolchain.options.get('usempi', False):
-            raise EasyBuildError('ScaLAPACK support requires MPI')
-        self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=ON')
+        if self.cfg.get('with_scalapack', False):
+            if not self.toolchain.options.get('usempi', False):
+                raise EasyBuildError('ScaLAPACK support requires MPI')
+            self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_SCALAPACK=OFF')
 
     def _add_fox(self):
         """Enable FoX for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DQE_ENABLE_FOX=ON')
+        if self.cfg.get('with_fox', False):
+            self.cfg.update('configopts', '-DQE_ENABLE_FOX=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_FOX=OFF')
 
     def _add_hdf5(self):
         """Enable HDF5 for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DQE_ENABLE_HDF5=ON')
+        if get_software_root('HDF5'):
+            self.cfg.update('configopts', '-DQE_ENABLE_HDF5=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_HDF5=OFF')
 
     def _add_libxc(self):
         """Enable LibXC for Quantum ESPRESSO."""
-        self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=ON')
+        if get_software_root('libxc'):
+            self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_LIBXC=OFF')
 
     def _add_elpa(self):
         """Enable ELPA for Quantum ESPRESSO."""
-        if not self.cfg.get('with_scalapack', False):
-            raise EasyBuildError('ELPA support requires ScaLAPACK')
-        if LooseVersion(self.version) == LooseVersion('7.3') and self.toolchain.options.get('openmp', False):
-            raise EasyBuildError('QE 7.3 with cmake does not support ELPA with OpenMP')
-        self.cfg.update('configopts', '-DQE_ENABLE_ELPA=ON')
+        if get_software_root('ELPA'):
+            if not self.cfg.get('with_scalapack', False):
+                raise EasyBuildError('ELPA support requires ScaLAPACK')
+            if LooseVersion(self.version) == LooseVersion('7.3') and self.toolchain.options.get('openmp', False):
+                raise EasyBuildError('QE 7.3 with cmake does not support ELPA with OpenMP')
+            self.cfg.update('configopts', '-DQE_ENABLE_ELPA=ON')
+        else:
+            self.cfg.update('configopts', '-DQE_ENABLE_ELPA=OFF')
 
     def _add_gipaw(self):
         """Enable GIPAW for Quantum ESPRESSO."""
@@ -181,6 +198,8 @@ def _add_d3q(self):
                 raise EasyBuildError(
                     'D3Q compilation will fail for QE 7.3 and 7.3.1 without submodule downloaded from easyconfig.'
                     )
+        if not self.toolchain.options.get('usempi', False):
+            raise EasyBuildError('D3Q support requires MPI enabled')
         res = ['d3q']
         self.check_bins += [
             'd3_asr3.x', 'd3_db.x', 'd3_import_shengbte.x', 'd3_interpolate2.x', 'd3_lw.x', 'd3_q2r.x',

From 2bb7f0bf882b44e665d82ba150a6633469e8f7aa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 Apr 2024 15:30:14 +0000
Subject: [PATCH 051/134] Add ABAQUS license server to generated module

---
 easybuild/easyblocks/a/abaqus.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/easybuild/easyblocks/a/abaqus.py b/easybuild/easyblocks/a/abaqus.py
index fc614ab7e8..000b2f9de3 100644
--- a/easybuild/easyblocks/a/abaqus.py
+++ b/easybuild/easyblocks/a/abaqus.py
@@ -366,3 +366,12 @@ def make_module_req_guess(self):
         })
 
         return guesses
+
+    def make_module_extra(self):
+        """Add LM_LICENSE_FILE path if specified"""
+        txt =  super(EB_ABAQUS, self).make_module_extra()
+        license_file = os.getenv('EB_ABAQUS_LICENSE_FILE', None)
+        if license_file is not None:
+            txt += self.module_generator.prepend_paths('LM_LICENSE_FILE', [license_file], allow_abs=True)
+
+        return txt

From 556445be88a078149e60ca7004ed0f24887c718b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 Apr 2024 16:33:41 +0000
Subject: [PATCH 052/134] Fix style

---
 easybuild/easyblocks/a/abaqus.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/a/abaqus.py b/easybuild/easyblocks/a/abaqus.py
index 000b2f9de3..868a2e52a2 100644
--- a/easybuild/easyblocks/a/abaqus.py
+++ b/easybuild/easyblocks/a/abaqus.py
@@ -369,7 +369,7 @@ def make_module_req_guess(self):
 
     def make_module_extra(self):
         """Add LM_LICENSE_FILE path if specified"""
-        txt =  super(EB_ABAQUS, self).make_module_extra()
+        txt = super(EB_ABAQUS, self).make_module_extra()
         license_file = os.getenv('EB_ABAQUS_LICENSE_FILE', None)
         if license_file is not None:
             txt += self.module_generator.prepend_paths('LM_LICENSE_FILE', [license_file], allow_abs=True)

From e14ec142323960619c2d5ef245a5284a8f35fa50 Mon Sep 17 00:00:00 2001
From: Davide Grassano <34096612+Crivella@users.noreply.github.com>
Date: Fri, 5 Apr 2024 10:32:30 +0200
Subject: [PATCH 053/134] Update easybuild/easyblocks/q/quantumespressocmake.py

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 easybuild/easyblocks/q/quantumespressocmake.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 14c606572d..5b0cffc36c 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -196,7 +196,7 @@ def _add_d3q(self):
             # https://github.com/anharmonic/d3q/issues/13
             if not os.path.exists(os.path.join(self.builddir, self.install_subdir, 'external', 'd3q', '.git')):
                 raise EasyBuildError(
-                    'D3Q compilation will fail for QE 7.3 and 7.3.1 without submodule downloaded from easyconfig.'
+                    'D3Q compilation will fail for QE 7.3 and 7.3.1 without submodule downloaded via sources in easyconfig.'
                     )
         if not self.toolchain.options.get('usempi', False):
             raise EasyBuildError('D3Q support requires MPI enabled')

From 311a819eb2f34fbd472060a4df4a73b34c0abb97 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 10:47:45 +0200
Subject: [PATCH 054/134] Linting and version check

---
 easybuild/easyblocks/q/quantumespressocmake.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 5b0cffc36c..d4bb979682 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -196,7 +196,8 @@ def _add_d3q(self):
             # https://github.com/anharmonic/d3q/issues/13
             if not os.path.exists(os.path.join(self.builddir, self.install_subdir, 'external', 'd3q', '.git')):
                 raise EasyBuildError(
-                    'D3Q compilation will fail for QE 7.3 and 7.3.1 without submodule downloaded via sources in easyconfig.'
+                    'D3Q compilation will fail for QE 7.3 and 7.3.1 without submodule downloaded via' +
+                    'sources in easyconfig.'
                     )
         if not self.toolchain.options.get('usempi', False):
             raise EasyBuildError('D3Q support requires MPI enabled')
@@ -256,12 +257,13 @@ def configure_step(self):
         # Change format of timings to seconds only (from d/h/m/s)
         self.cfg.update('configopts', '-DQE_CLOCK_SECONDS=ON')
 
-        # Needed to avoid a DSO missing from command line linking error
-        # https://gitlab.com/QEF/q-e/-/issues/667
-        if self.cfg.get('build_shared_libs', False):
-            ldflags = os.getenv('LDFLAGS', '')
-            ldflags += ' -Wl,--copy-dt-needed-entries '
-            env.setvar('LDFLAGS', ldflags)
+        if LooseVersion(self.version) <= LooseVersion('7.3.1'):
+            # Needed to avoid a `DSO missing from command line` linking error
+            # https://gitlab.com/QEF/q-e/-/issues/667
+            if self.cfg.get('build_shared_libs', False):
+                ldflags = os.getenv('LDFLAGS', '')
+                ldflags += ' -Wl,--copy-dt-needed-entries '
+                env.setvar('LDFLAGS', ldflags)
 
         super(EB_QuantumESPRESSOcmake, self).configure_step()
 

From c9c8bc23943bab590d21e5ec3bdfbb88d3139841 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 11:45:32 +0200
Subject: [PATCH 055/134] Fixed logic

---
 easybuild/easyblocks/q/quantumespressocmake.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index d4bb979682..48914d36f4 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -220,20 +220,22 @@ def _copy_submodule_dirs(self):
         for submod in self.SUBMODULES:
             src = os.path.join(self.builddir, submod)
             dst = os.path.join(self.builddir, self.install_subdir, 'external', submod)
+
             if os.path.exists(src):
                 self.log.info('Copying submodule %s into %s' % (submod, dst))
                 # Remove empty directories and replace them with the downloaded submodule
                 if os.path.exists(dst):
                     shutil.rmtree(dst)
                 shutil.move(src, dst)
+
+                # Trick QE to think that the submodule is already installed in case `keep_git_dir` is not used in
+                # the easyconfig file
+                gitf = os.path.join(dst, '.git')
+                if not os.path.exists(gitf):
+                    os.mkdir(gitf)
             else:
                 self.log.warning('Submodule %s not found at %s' % (submod, src))
 
-            # Trick QE to think that the submodule is already installed in case `keep_git_dir` is not used in
-            # the easyconfig file
-            gitf = os.path.join(dst, '.git')
-            if not os.path.exists(gitf):
-                os.mkdir(gitf)
 
     def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""

From 0e0f27cd5b5f68f44b775fe94dc9aec3e03a6c58 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 11:46:42 +0200
Subject: [PATCH 056/134] Lint

---
 easybuild/easyblocks/q/quantumespressocmake.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 48914d36f4..74554223ff 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -236,7 +236,6 @@ def _copy_submodule_dirs(self):
             else:
                 self.log.warning('Submodule %s not found at %s' % (submod, src))
 
-
     def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""
 

From 59a981f67897ed1e0a5fbcec08ecfbe346b7630d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 5 Apr 2024 12:19:51 +0000
Subject: [PATCH 057/134] Add ABAQUSLM_LICENSE_FILE as well

---
 easybuild/easyblocks/a/abaqus.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyblocks/a/abaqus.py b/easybuild/easyblocks/a/abaqus.py
index 868a2e52a2..7f6eb0820a 100644
--- a/easybuild/easyblocks/a/abaqus.py
+++ b/easybuild/easyblocks/a/abaqus.py
@@ -373,5 +373,7 @@ def make_module_extra(self):
         license_file = os.getenv('EB_ABAQUS_LICENSE_FILE', None)
         if license_file is not None:
             txt += self.module_generator.prepend_paths('LM_LICENSE_FILE', [license_file], allow_abs=True)
+            # also needed for some versions:
+            txt += self.module_generator.prepend_paths('ABAQUSLM_LICENSE_FILE', [license_file], allow_abs=True)
 
         return txt

From 018142a4b01a99877f4e62554dff3cfe1a580785 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Fri, 5 Apr 2024 13:02:42 +0000
Subject: [PATCH 058/134] adding easyblocks: ansysem.py

---
 easybuild/easyblocks/a/ansysem.py | 98 +++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 easybuild/easyblocks/a/ansysem.py

diff --git a/easybuild/easyblocks/a/ansysem.py b/easybuild/easyblocks/a/ansysem.py
new file mode 100644
index 0000000000..6cb596e2ba
--- /dev/null
+++ b/easybuild/easyblocks/a/ansysem.py
@@ -0,0 +1,98 @@
+##
+# Copyright 2009-2020 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for installing ANSYS Eletromagnetics
+
+@author: Alexi Rivera (Chalmers University of Technology)
+@author: Mikael OEhman (Chalmers University of Technology)
+@author: Chia-Jung Hsu (Chalmers University of Technology)
+"""
+import os
+import glob
+import tempfile
+
+from easybuild.easyblocks.generic.packedbinary import PackedBinary
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.run import run_cmd
+
+
+class EB_ANSYSEM(PackedBinary):
+    """Support for installing Ansys Electromagnetics."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize Ansys Electromagnetics specific variables."""
+        super(EB_ANSYSEM, self).__init__(*args, **kwargs)
+
+    def install_step(self):
+        """Install Ansys Electromagnetics using its setup tool."""
+        licserv = os.getenv('EB_ANSYS_EM_LICENSE_SERVER')
+        licport = os.getenv('EB_ANSYS_EM_LICENSE_SERVER_PORT')
+        licservs = licserv.split(',')
+        licservopt = ["-DLICENSE_SERVER%d=%s" % (i, serv) for i, serv in enumerate(licservs, 1)]
+        redundant = len(licservs) > 1
+        options = " ".join([
+            "-i silent",
+            "-DUSER_INSTALL_DIR=%s" % self.installdir,
+            "-DTMP_DIR=%s" % tempfile.TemporaryDirectory().name,
+            "-DLIBRARY_COMMON_INSTALL=1",
+            "-DSPECIFY_LIC_CFG=1",
+            "-DREDUNDANT_SERVERS=%d" % redundant,
+            *licservopt,
+            "-DSPECIFY_PORT=1",
+            "-DLICENSE_PORT=%s" % licport,
+        ])
+        cmd = "./Linux/AnsysEM/Disk1/InstData/setup.exe %s" % options
+        run_cmd(cmd, log_all=True, simple=True)
+
+    def make_module_extra(self):
+        """Extra module entries for Ansys Electromagnetics."""
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+        else:
+            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
+
+        txt = super(EB_ANSYSEM, self).make_module_extra()
+        txt += self.module_generator.prepend_paths('PATH', subdir)
+        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', subdir)
+        txt += self.module_generator.prepend_paths('LIBRARY_PATH', subdir)
+        return txt
+
+    def sanity_check_step(self):
+        """Custom sanity check for Ansys Electromagnetics."""
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+        else:
+            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
+
+        custom_paths = {
+            'files': [os.path.join(subdir, 'ansysedt')],
+            'dirs': [subdir],
+        }
+
+        custom_commands = ['%s -ng' % os.path.join(subdir, 'ansysedt')]
+
+        super(EB_ANSYSEM, self).sanity_check_step(custom_paths=custom_paths)

From 53b54bfb08f896058a87b0cc54f1f924c5916593 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 15:21:39 +0200
Subject: [PATCH 059/134] Getting `nprocs` for test only in one place

---
 easybuild/easyblocks/q/quantumespressocmake.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/q/quantumespressocmake.py b/easybuild/easyblocks/q/quantumespressocmake.py
index 74554223ff..70a5df031b 100644
--- a/easybuild/easyblocks/q/quantumespressocmake.py
+++ b/easybuild/easyblocks/q/quantumespressocmake.py
@@ -251,9 +251,9 @@ def configure_step(self):
         self._add_plugins()
 
         # Enable/configure test suite
-        nprocs = self.cfg.get('test_suite_nprocs', 1)
+        self._test_nprocs = self.cfg.get('test_suite_nprocs', 1)
         self.cfg.update('configopts', '-DQE_ENABLE_TEST=ON')
-        self.cfg.update('configopts', '-DTESTCODE_NPROCS=%d' % nprocs)
+        self.cfg.update('configopts', '-DTESTCODE_NPROCS=%d' % self._test_nprocs)
 
         # Change format of timings to seconds only (from d/h/m/s)
         self.cfg.update('configopts', '-DQE_CLOCK_SECONDS=ON')
@@ -275,8 +275,7 @@ def test_step(self):
         """
 
         thr = self.cfg.get('test_suite_threshold', 0.97)
-        nprocs = self.cfg.get('test_suite_nprocs', 1)
-        concurrent = max(1, self.cfg.get('parallel', 1) // nprocs)
+        concurrent = max(1, self.cfg.get('parallel', 1) // self._test_nprocs)
         allow_fail = self.cfg.get('test_suite_allow_failures', [])
 
         cmd = ' '.join([

From edcfec4334f7029112213a05784e75f9b644c3f8 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 5 Apr 2024 15:22:35 +0200
Subject: [PATCH 060/134] Check for QE < 7.3.1 on configmake easyblock

---
 easybuild/easyblocks/q/quantumespresso.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyblocks/q/quantumespresso.py b/easybuild/easyblocks/q/quantumespresso.py
index 563890072a..dad09fb4ea 100644
--- a/easybuild/easyblocks/q/quantumespresso.py
+++ b/easybuild/easyblocks/q/quantumespresso.py
@@ -367,6 +367,12 @@ def _adjust_compiler_flags(self, comp_fam):
     def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""
 
+        if LooseVersion(self.version) < LooseVersion("7.3.1"):
+            raise EasyBuildError(
+                "QuantumESPRESSO 7.3.1 and later are not supported with the this easyblock (ConfigureMake), " +
+                "use the EB_QuantumESPRESSOcmake (CMakeMake) easyblock instead."
+                )
+
         # compose list of DFLAGS (flag, value, keep_stuff)
         # for guidelines, see include/defs.h.README in sources
         self.dflags = []

From a1cbcad0fdd0d0868ba80e77e904d637e29e6d05 Mon Sep 17 00:00:00 2001
From: Davide Grassano <34096612+Crivella@users.noreply.github.com>
Date: Fri, 5 Apr 2024 15:28:09 +0200
Subject: [PATCH 061/134] Update easybuild/easyblocks/q/quantumespresso.py

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 easybuild/easyblocks/q/quantumespresso.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/q/quantumespresso.py b/easybuild/easyblocks/q/quantumespresso.py
index dad09fb4ea..7d86dfabeb 100644
--- a/easybuild/easyblocks/q/quantumespresso.py
+++ b/easybuild/easyblocks/q/quantumespresso.py
@@ -367,7 +367,7 @@ def _adjust_compiler_flags(self, comp_fam):
     def configure_step(self):
         """Custom configuration procedure for Quantum ESPRESSO."""
 
-        if LooseVersion(self.version) < LooseVersion("7.3.1"):
+        if LooseVersion(self.version) >= LooseVersion("7.3.1"):
             raise EasyBuildError(
                 "QuantumESPRESSO 7.3.1 and later are not supported with the this easyblock (ConfigureMake), " +
                 "use the EB_QuantumESPRESSOcmake (CMakeMake) easyblock instead."

From 47b7975d5b0115d50acddbbac9ce721d30b2aca0 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Fri, 5 Apr 2024 14:28:43 +0000
Subject: [PATCH 062/134] Fix sanity check command

---
 easybuild/easyblocks/a/ansysem.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/a/ansysem.py b/easybuild/easyblocks/a/ansysem.py
index 6cb596e2ba..8dd9c1feb8 100644
--- a/easybuild/easyblocks/a/ansysem.py
+++ b/easybuild/easyblocks/a/ansysem.py
@@ -93,6 +93,8 @@ def sanity_check_step(self):
             'dirs': [subdir],
         }
 
-        custom_commands = ['%s -ng' % os.path.join(subdir, 'ansysedt')]
+        executable = os.path.join(subdir, 'ansysedt')
+        inpfile = os.path.join(subdir, 'Examples', 'RMxprt', 'lssm', 'sm-1.aedt')
+        custom_commands = ['./%s -ng -BatchSolve -Distributed %s' % (executable, inpfile)]
 
-        super(EB_ANSYSEM, self).sanity_check_step(custom_paths=custom_paths)
+        super(EB_ANSYSEM, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From 3c6b47b0c57ce79594029442cda561f944b717e6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Apr 2024 20:55:53 +0200
Subject: [PATCH 063/134] bump version to 4.9.2dev

---
 easybuild/easyblocks/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/__init__.py b/easybuild/easyblocks/__init__.py
index a1f69a95f6..56d224f3be 100644
--- a/easybuild/easyblocks/__init__.py
+++ b/easybuild/easyblocks/__init__.py
@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.9.1')
+VERSION = LooseVersion('4.9.2.dev0')
 UNKNOWN = 'UNKNOWN'
 
 

From 28101a024f5147a4f6c2c8c4b26df3abbb866e93 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Tue, 9 Apr 2024 09:29:32 +0000
Subject: [PATCH 064/134] adding easyblocks: optislang.py

---
 easybuild/easyblocks/o/optislang.py | 108 ++++++++++++++++++++++++++++
 1 file changed, 108 insertions(+)
 create mode 100644 easybuild/easyblocks/o/optislang.py

diff --git a/easybuild/easyblocks/o/optislang.py b/easybuild/easyblocks/o/optislang.py
new file mode 100644
index 0000000000..0436fc6c42
--- /dev/null
+++ b/easybuild/easyblocks/o/optislang.py
@@ -0,0 +1,108 @@
+##
+# Copyright 2009-2024 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for installing ANSYS optiSLang, implemented as an easyblock
+
+@author: Chia-Jung Hsu (Chalmers University for Technology)
+"""
+import os
+import re
+import stat
+import tempfile
+from easybuild.tools import LooseVersion
+
+from easybuild.easyblocks.generic.packedbinary import PackedBinary
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import adjust_permissions
+from easybuild.tools.run import run_cmd
+
+
+class EB_optiSLang(PackedBinary):
+    """Support for installing ANSYS optiSLang."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize optiSLang-specific variables."""
+        super(EB_optiSLang, self).__init__(*args, **kwargs)
+        self.ansysver = None
+
+    def install_step(self):
+        """Custom install procedure for ANSYS optiSLang."""
+        licservs = self.cfg['license_server']
+        if licservs is None:
+            licservs = os.getenv('EB_ANSYS_LICENSE_SERVER', 'license.example.com')
+        licservs = licservs.split(',')
+        licport = self.cfg['license_server_port']
+        if licport is None:
+            licport = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055')
+        licopts = ['-licserverinfo %s:%s' % (licport, serv) for serv in licservs]
+        licoptsstr = ' '.join(licopts)
+
+        tmpdir = tempfile.mkdtemp()
+
+        # Sources (e.g. iso files) may drop the execute permissions
+        adjust_permissions('INSTALL', stat.S_IXUSR)
+        cmd = "./INSTALL -silent -install_dir %s -usetempdir %s %s" % (self.installdir, tmpdir, licoptsstr)
+        run_cmd(cmd, log_all=True, simple=True)
+
+        adjust_permissions(self.installdir, stat.S_IWOTH, add=False)
+
+    def set_ansysver(self):
+        """Determine name of version subdirectory in installation directory."""
+        entries = os.listdir(self.installdir)
+        version_dir_regex = re.compile('^v[0-9]+')
+        version_dirs = [e for e in entries if version_dir_regex.match(e)]
+        if len(version_dirs) == 1:
+            self.ansysver = version_dirs[0]
+        else:
+            raise EasyBuildError("Failed to isolate version subdirectory in %s: %s", self.installdir, entries)
+
+    def make_module_req_guess(self):
+        """Custom extra module file entries for ANSYS optiSLang."""
+
+        if self.ansysver is None:
+            self.set_ansysver()
+
+        guesses = super(EB_optiSLang, self).make_module_req_guess()
+        dirs = [
+            'aisol/bin/linx64',
+            'dpf/bin/linux64',
+            'optiSLang',
+        ]
+
+        guesses['PATH'] = [os.path.join(self.ansysver, d) for d in dirs]
+
+        return guesses
+
+    def sanity_check_step(self):
+        """Custom sanity check for ANSYS optiSLang."""
+
+        if self.ansysver is None:
+            self.set_ansysver()
+
+        custom_paths = {
+            'files': [os.path.join(self.ansysver, 'optiSLang', x) for x in ['optislang', 'optislang-python']],
+            'dirs': [os.path.join(self.ansysver, x) for x in ['aisol', 'dpf']]
+        }
+        super(EB_optiSLang, self).sanity_check_step(custom_paths=custom_paths)

From 46186d6f68569e389102e54234e879a82c21cb71 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Tue, 9 Apr 2024 15:50:16 +0000
Subject: [PATCH 065/134] Rename to AEDT

---
 easybuild/easyblocks/a/aedt.py | 100 +++++++++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 easybuild/easyblocks/a/aedt.py

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
new file mode 100644
index 0000000000..a7af3e3333
--- /dev/null
+++ b/easybuild/easyblocks/a/aedt.py
@@ -0,0 +1,100 @@
+##
+# Copyright 2009-2020 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for installing Ansys Electronics Desktop
+
+@author: Alexi Rivera (Chalmers University of Technology)
+@author: Mikael OEhman (Chalmers University of Technology)
+@author: Chia-Jung Hsu (Chalmers University of Technology)
+"""
+import os
+import glob
+import tempfile
+
+from easybuild.easyblocks.generic.packedbinary import PackedBinary
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.run import run_cmd
+
+
+class EB_AEDT(PackedBinary):
+    """Support for installing Ansys Electronics Desktop."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize Ansys Electronics Desktop specific variables."""
+        super(EB_AEDT, self).__init__(*args, **kwargs)
+
+    def install_step(self):
+        """Install Ansys Electronics Desktop using its setup tool."""
+        licserv = os.getenv('EB_AEDT_LICENSE_SERVER')
+        licport = os.getenv('EB_AEDT_LICENSE_SERVER_PORT')
+        licservs = licserv.split(',')
+        licservopt = ["-DLICENSE_SERVER%d=%s" % (i, serv) for i, serv in enumerate(licservs, 1)]
+        redundant = len(licservs) > 1
+        options = " ".join([
+            "-i silent",
+            "-DUSER_INSTALL_DIR=%s" % self.installdir,
+            "-DTMP_DIR=%s" % tempfile.TemporaryDirectory().name,
+            "-DLIBRARY_COMMON_INSTALL=1",
+            "-DSPECIFY_LIC_CFG=1",
+            "-DREDUNDANT_SERVERS=%d" % redundant,
+            *licservopt,
+            "-DSPECIFY_PORT=1",
+            "-DLICENSE_PORT=%s" % licport,
+        ])
+        cmd = "./Linux/AnsysEM/Disk1/InstData/setup.exe %s" % options
+        run_cmd(cmd, log_all=True, simple=True)
+
+    def make_module_extra(self):
+        """Extra module entries for Ansys Electronics Desktop."""
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+        else:
+            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
+
+        txt = super(EB_AEDT, self).make_module_extra()
+        txt += self.module_generator.prepend_paths('PATH', subdir)
+        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', subdir)
+        txt += self.module_generator.prepend_paths('LIBRARY_PATH', subdir)
+        return txt
+
+    def sanity_check_step(self):
+        """Custom sanity check for Ansys Electronics Desktop."""
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+        else:
+            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
+
+        custom_paths = {
+            'files': [os.path.join(subdir, 'ansysedt')],
+            'dirs': [subdir],
+        }
+
+        executable = os.path.join(subdir, 'ansysedt')
+        inpfile = os.path.join(subdir, 'Examples', 'RMxprt', 'lssm', 'sm-1.aedt')
+        custom_commands = ['./%s -ng -BatchSolve -Distributed %s' % (executable, inpfile)]
+
+        super(EB_AEDT, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From 8a48908b34f53a22357434fa3a8b441a2f881619 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@users.noreply.github.com>
Date: Tue, 9 Apr 2024 17:53:53 +0200
Subject: [PATCH 066/134] Remove old ansysem.py

---
 easybuild/easyblocks/a/ansysem.py | 100 ------------------------------
 1 file changed, 100 deletions(-)
 delete mode 100644 easybuild/easyblocks/a/ansysem.py

diff --git a/easybuild/easyblocks/a/ansysem.py b/easybuild/easyblocks/a/ansysem.py
deleted file mode 100644
index 8dd9c1feb8..0000000000
--- a/easybuild/easyblocks/a/ansysem.py
+++ /dev/null
@@ -1,100 +0,0 @@
-##
-# Copyright 2009-2020 Ghent University
-#
-# This file is part of EasyBuild,
-# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
-# with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
-# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
-# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
-#
-# https://github.com/easybuilders/easybuild
-#
-# EasyBuild is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation v2.
-#
-# EasyBuild is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
-##
-"""
-EasyBuild support for installing ANSYS Eletromagnetics
-
-@author: Alexi Rivera (Chalmers University of Technology)
-@author: Mikael OEhman (Chalmers University of Technology)
-@author: Chia-Jung Hsu (Chalmers University of Technology)
-"""
-import os
-import glob
-import tempfile
-
-from easybuild.easyblocks.generic.packedbinary import PackedBinary
-from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.run import run_cmd
-
-
-class EB_ANSYSEM(PackedBinary):
-    """Support for installing Ansys Electromagnetics."""
-
-    def __init__(self, *args, **kwargs):
-        """Initialize Ansys Electromagnetics specific variables."""
-        super(EB_ANSYSEM, self).__init__(*args, **kwargs)
-
-    def install_step(self):
-        """Install Ansys Electromagnetics using its setup tool."""
-        licserv = os.getenv('EB_ANSYS_EM_LICENSE_SERVER')
-        licport = os.getenv('EB_ANSYS_EM_LICENSE_SERVER_PORT')
-        licservs = licserv.split(',')
-        licservopt = ["-DLICENSE_SERVER%d=%s" % (i, serv) for i, serv in enumerate(licservs, 1)]
-        redundant = len(licservs) > 1
-        options = " ".join([
-            "-i silent",
-            "-DUSER_INSTALL_DIR=%s" % self.installdir,
-            "-DTMP_DIR=%s" % tempfile.TemporaryDirectory().name,
-            "-DLIBRARY_COMMON_INSTALL=1",
-            "-DSPECIFY_LIC_CFG=1",
-            "-DREDUNDANT_SERVERS=%d" % redundant,
-            *licservopt,
-            "-DSPECIFY_PORT=1",
-            "-DLICENSE_PORT=%s" % licport,
-        ])
-        cmd = "./Linux/AnsysEM/Disk1/InstData/setup.exe %s" % options
-        run_cmd(cmd, log_all=True, simple=True)
-
-    def make_module_extra(self):
-        """Extra module entries for Ansys Electromagnetics."""
-        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
-        if len(idirs) == 1:
-            subdir = os.path.relpath(idirs[0], self.installdir)
-        else:
-            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
-
-        txt = super(EB_ANSYSEM, self).make_module_extra()
-        txt += self.module_generator.prepend_paths('PATH', subdir)
-        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', subdir)
-        txt += self.module_generator.prepend_paths('LIBRARY_PATH', subdir)
-        return txt
-
-    def sanity_check_step(self):
-        """Custom sanity check for Ansys Electromagnetics."""
-        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
-        if len(idirs) == 1:
-            subdir = os.path.relpath(idirs[0], self.installdir)
-        else:
-            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
-
-        custom_paths = {
-            'files': [os.path.join(subdir, 'ansysedt')],
-            'dirs': [subdir],
-        }
-
-        executable = os.path.join(subdir, 'ansysedt')
-        inpfile = os.path.join(subdir, 'Examples', 'RMxprt', 'lssm', 'sm-1.aedt')
-        custom_commands = ['./%s -ng -BatchSolve -Distributed %s' % (executable, inpfile)]
-
-        super(EB_ANSYSEM, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From 87005fbac923565cc0f8f9af1d25fb97bac74703 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Tue, 9 Apr 2024 16:04:25 +0000
Subject: [PATCH 067/134] Remove unused imports

---
 easybuild/easyblocks/o/optislang.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/o/optislang.py b/easybuild/easyblocks/o/optislang.py
index 0436fc6c42..0e345c1310 100644
--- a/easybuild/easyblocks/o/optislang.py
+++ b/easybuild/easyblocks/o/optislang.py
@@ -31,7 +31,6 @@
 import re
 import stat
 import tempfile
-from easybuild.tools import LooseVersion
 
 from easybuild.easyblocks.generic.packedbinary import PackedBinary
 from easybuild.tools.build_log import EasyBuildError

From 4d264a4d1f295cee3b8bc246b66300ca33d9adf1 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Thu, 11 Apr 2024 09:29:43 +0000
Subject: [PATCH 068/134] Add post install step

---
 easybuild/easyblocks/a/aedt.py | 54 +++++++++++++++++++++++-----------
 1 file changed, 37 insertions(+), 17 deletions(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index a7af3e3333..4aa435a8e6 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -44,6 +44,14 @@ class EB_AEDT(PackedBinary):
     def __init__(self, *args, **kwargs):
         """Initialize Ansys Electronics Desktop specific variables."""
         super(EB_AEDT, self).__init__(*args, **kwargs)
+        self.subdir = None
+
+    def _set_subdir(self):
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
+        if len(idirs) == 1:
+            self.subdir = os.path.relpath(idirs[0], self.installdir)
+        else:
+            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
 
     def install_step(self):
         """Install Ansys Electronics Desktop using its setup tool."""
@@ -66,35 +74,47 @@ def install_step(self):
         cmd = "./Linux/AnsysEM/Disk1/InstData/setup.exe %s" % options
         run_cmd(cmd, log_all=True, simple=True)
 
+    def post_install_step(self):
+        """Disable OS check and set LC_ALL/LANG for runtime"""
+        if not self.subdir:
+            self._set_subdir()
+
+        # Clean script file to disable over restrict OS checking
+        with open(os.path.join(self.installdir, self.subdir, "VerifyOS.bash"), "w") as f:
+            f.write("")
+
+        # Set LC_ALL and LANG for runtime
+        for fname in [".setup_runtime", ".setup_runtime_mpi"]:
+            with open(os.path.join(self.installdir, self.subdir, fname), "r") as f:
+                orig = f.read()
+            with open(os.path.join(self.installdir, self.subdir, fname), "w") as f:
+                f.write("export LC_ALL=C\n")
+                f.write("export LANG=C\n")
+                f.write(orig)
+
     def make_module_extra(self):
         """Extra module entries for Ansys Electronics Desktop."""
-        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
-        if len(idirs) == 1:
-            subdir = os.path.relpath(idirs[0], self.installdir)
-        else:
-            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
+        if not self.subdir:
+            self._set_subdir()
 
         txt = super(EB_AEDT, self).make_module_extra()
-        txt += self.module_generator.prepend_paths('PATH', subdir)
-        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', subdir)
-        txt += self.module_generator.prepend_paths('LIBRARY_PATH', subdir)
+        txt += self.module_generator.prepend_paths('PATH', self.subdir)
+        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', self.subdir)
+        txt += self.module_generator.prepend_paths('LIBRARY_PATH', self.subdir)
         return txt
 
     def sanity_check_step(self):
         """Custom sanity check for Ansys Electronics Desktop."""
-        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
-        if len(idirs) == 1:
-            subdir = os.path.relpath(idirs[0], self.installdir)
-        else:
-            raise EasyBuildError("Failed to locate single install subdirectory v*/Linux*/")
+        if not self.subdir:
+            self._set_subdir()
 
         custom_paths = {
-            'files': [os.path.join(subdir, 'ansysedt')],
-            'dirs': [subdir],
+            'files': [os.path.join(self.subdir, 'ansysedt')],
+            'dirs': [self.subdir],
         }
 
-        executable = os.path.join(subdir, 'ansysedt')
-        inpfile = os.path.join(subdir, 'Examples', 'RMxprt', 'lssm', 'sm-1.aedt')
+        executable = os.path.join(self.subdir, 'ansysedt')
+        inpfile = os.path.join(self.subdir, 'Examples', 'RMxprt', 'lssm', 'sm-1.aedt')
         custom_commands = ['./%s -ng -BatchSolve -Distributed %s' % (executable, inpfile)]
 
         super(EB_AEDT, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From 8a6033105f66e1a26e3f1abee1f274d8949155e5 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Thu, 11 Apr 2024 11:06:03 +0000
Subject: [PATCH 069/134] Skip adding path if empty dir, add more sanity check

---
 easybuild/easyblocks/o/optislang.py | 47 ++++++++++++++---------------
 1 file changed, 23 insertions(+), 24 deletions(-)

diff --git a/easybuild/easyblocks/o/optislang.py b/easybuild/easyblocks/o/optislang.py
index 0e345c1310..acdf16ea81 100644
--- a/easybuild/easyblocks/o/optislang.py
+++ b/easybuild/easyblocks/o/optislang.py
@@ -27,6 +27,7 @@
 
 @author: Chia-Jung Hsu (Chalmers University for Technology)
 """
+import glob
 import os
 import re
 import stat
@@ -44,7 +45,6 @@ class EB_optiSLang(PackedBinary):
     def __init__(self, *args, **kwargs):
         """Initialize optiSLang-specific variables."""
         super(EB_optiSLang, self).__init__(*args, **kwargs)
-        self.ansysver = None
 
     def install_step(self):
         """Custom install procedure for ANSYS optiSLang."""
@@ -67,41 +67,40 @@ def install_step(self):
 
         adjust_permissions(self.installdir, stat.S_IWOTH, add=False)
 
-    def set_ansysver(self):
-        """Determine name of version subdirectory in installation directory."""
-        entries = os.listdir(self.installdir)
-        version_dir_regex = re.compile('^v[0-9]+')
-        version_dirs = [e for e in entries if version_dir_regex.match(e)]
-        if len(version_dirs) == 1:
-            self.ansysver = version_dirs[0]
-        else:
-            raise EasyBuildError("Failed to isolate version subdirectory in %s: %s", self.installdir, entries)
-
     def make_module_req_guess(self):
         """Custom extra module file entries for ANSYS optiSLang."""
 
-        if self.ansysver is None:
-            self.set_ansysver()
-
         guesses = super(EB_optiSLang, self).make_module_req_guess()
-        dirs = [
-            'aisol/bin/linx64',
-            'dpf/bin/linux64',
-            'optiSLang',
-        ]
 
-        guesses['PATH'] = [os.path.join(self.ansysver, d) for d in dirs]
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+            bindirs = [
+                'aisol/bin/linx64',
+                'dpf/bin/linux64',
+                'optiSLang',
+            ]
+            guesses['PATH'] = [os.path.join(subdir, d) for d in bindirs]
 
         return guesses
 
     def sanity_check_step(self):
         """Custom sanity check for ANSYS optiSLang."""
 
-        if self.ansysver is None:
-            self.set_ansysver()
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+        else:
+            raise EasyBuildError("Failed to locate single install subdirectory v*/")
+
+        errorlogfile = os.path.join(self.installdir, "install.err")
+        if os.path.isfile(errorlogfile):
+            raise EasyBuildError("Found error log from optiSLang installer %s" % errorlogfile)
 
         custom_paths = {
-            'files': [os.path.join(self.ansysver, 'optiSLang', x) for x in ['optislang', 'optislang-python']],
-            'dirs': [os.path.join(self.ansysver, x) for x in ['aisol', 'dpf']]
+            'files': [os.path.join(subdir, 'optiSLang', x) for x in ['optislang', 'optislang-python']],
+            'dirs': [os.path.join(subdir, x) for x in ['aisol', 'dpf']]
         }
+        custom_commands = ['./optislang --help'] 
+
         super(EB_optiSLang, self).sanity_check_step(custom_paths=custom_paths)

From 7d4c1051db841e95fcc58b677ce0b72b74d08801 Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Thu, 11 Apr 2024 12:56:34 +0000
Subject: [PATCH 070/134] Fix sanity check command

---
 easybuild/easyblocks/o/optislang.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/o/optislang.py b/easybuild/easyblocks/o/optislang.py
index acdf16ea81..b92190b1f8 100644
--- a/easybuild/easyblocks/o/optislang.py
+++ b/easybuild/easyblocks/o/optislang.py
@@ -29,7 +29,6 @@
 """
 import glob
 import os
-import re
 import stat
 import tempfile
 
@@ -101,6 +100,6 @@ def sanity_check_step(self):
             'files': [os.path.join(subdir, 'optiSLang', x) for x in ['optislang', 'optislang-python']],
             'dirs': [os.path.join(subdir, x) for x in ['aisol', 'dpf']]
         }
-        custom_commands = ['./optislang --help'] 
+        custom_commands = ['optislang --help'] 
 
-        super(EB_optiSLang, self).sanity_check_step(custom_paths=custom_paths)
+        super(EB_optiSLang, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From 230e0da2ea032db3e4f0108e578173e756eb3080 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@users.noreply.github.com>
Date: Thu, 11 Apr 2024 14:58:12 +0200
Subject: [PATCH 071/134] Fix style

---
 easybuild/easyblocks/o/optislang.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/o/optislang.py b/easybuild/easyblocks/o/optislang.py
index b92190b1f8..84b335e5fd 100644
--- a/easybuild/easyblocks/o/optislang.py
+++ b/easybuild/easyblocks/o/optislang.py
@@ -100,6 +100,6 @@ def sanity_check_step(self):
             'files': [os.path.join(subdir, 'optiSLang', x) for x in ['optislang', 'optislang-python']],
             'dirs': [os.path.join(subdir, x) for x in ['aisol', 'dpf']]
         }
-        custom_commands = ['optislang --help'] 
+        custom_commands = ['optislang --help']
 
         super(EB_optiSLang, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From b7508dffa434069b92657a3f309501903481f4fe Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Fri, 12 Apr 2024 17:07:40 +0200
Subject: [PATCH 072/134] Allow 'nosource: True' in PythonPackage extensions'

---
 easybuild/easyblocks/generic/pythonpackage.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/generic/pythonpackage.py b/easybuild/easyblocks/generic/pythonpackage.py
index da6ca8c2a8..de4bd0b7bc 100644
--- a/easybuild/easyblocks/generic/pythonpackage.py
+++ b/easybuild/easyblocks/generic/pythonpackage.py
@@ -623,7 +623,7 @@ def compose_install_command(self, prefix, extrapath=None, installopts=None):
 
         loc = self.cfg.get('install_src')
         if not loc:
-            if self._should_unpack_source():
+            if self._should_unpack_source() or not self.src:
                 # specify current directory
                 loc = '.'
             elif isinstance(self.src, string_type):
@@ -904,9 +904,6 @@ def install_step(self):
     def run(self, *args, **kwargs):
         """Perform the actual Python package build/installation procedure"""
 
-        if not self.src:
-            raise EasyBuildError("No source found for Python package %s, required for installation. (src: %s)",
-                                 self.name, self.src)
         # we unpack unless explicitly told otherwise
         kwargs.setdefault('unpack_src', self._should_unpack_source())
         super(PythonPackage, self).run(*args, **kwargs)

From 7855ee7045e45788dc285b9ffc60af2da4303dfe Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Fri, 12 Apr 2024 17:38:43 +0000
Subject: [PATCH 073/134] Skip adding path if dir is empty

---
 easybuild/easyblocks/a/aedt.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index 4aa435a8e6..24314b7e44 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -94,13 +94,21 @@ def post_install_step(self):
 
     def make_module_extra(self):
         """Extra module entries for Ansys Electronics Desktop."""
-        if not self.subdir:
-            self._set_subdir()
 
         txt = super(EB_AEDT, self).make_module_extra()
-        txt += self.module_generator.prepend_paths('PATH', self.subdir)
-        txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', self.subdir)
-        txt += self.module_generator.prepend_paths('LIBRARY_PATH', self.subdir)
+        version = self.version[2:].replace('R', '')
+
+        idirs = glob.glob(os.path.join(self.installdir, 'v*/Linux*/'))
+        if len(idirs) == 1:
+            subdir = os.path.relpath(idirs[0], self.installdir)
+            # PyAEDT and other tools use the variable to find available AEDT versions
+            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version, 
+                                                         os.path.join(self.installdir, self.subdir))
+
+            txt += self.module_generator.prepend_paths('PATH', subdir)
+            txt += self.module_generator.prepend_paths('LD_LIBRARY_PATH', subdir)
+            txt += self.module_generator.prepend_paths('LIBRARY_PATH', subdir)
+
         return txt
 
     def sanity_check_step(self):
@@ -113,8 +121,7 @@ def sanity_check_step(self):
             'dirs': [self.subdir],
         }
 
-        executable = os.path.join(self.subdir, 'ansysedt')
         inpfile = os.path.join(self.subdir, 'Examples', 'RMxprt', 'lssm', 'sm-1.aedt')
-        custom_commands = ['./%s -ng -BatchSolve -Distributed %s' % (executable, inpfile)]
+        custom_commands = ['ansysedt -ng -BatchSolve -Distributed %s' % inpfile]
 
         super(EB_AEDT, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)

From 31eefba17334f1248c104bec043fbc1ccaaf00b3 Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@users.noreply.github.com>
Date: Fri, 12 Apr 2024 21:18:16 +0200
Subject: [PATCH 074/134] Fix style

---
 easybuild/easyblocks/a/aedt.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index 24314b7e44..a08fcca2bf 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -102,7 +102,7 @@ def make_module_extra(self):
         if len(idirs) == 1:
             subdir = os.path.relpath(idirs[0], self.installdir)
             # PyAEDT and other tools use the variable to find available AEDT versions
-            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version, 
+            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version,
                                                          os.path.join(self.installdir, self.subdir))
 
             txt += self.module_generator.prepend_paths('PATH', subdir)

From d6755a237aa89aff32fb43bb7a6080d52107bdf8 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 15 Apr 2024 08:52:55 +0100
Subject: [PATCH 075/134] Binary easyblock already adds top level directory, so
 no need to do it in the Stata easyblock

---
 easybuild/easyblocks/s/stata.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/easybuild/easyblocks/s/stata.py b/easybuild/easyblocks/s/stata.py
index cfa31fc951..25e9e6c0da 100644
--- a/easybuild/easyblocks/s/stata.py
+++ b/easybuild/easyblocks/s/stata.py
@@ -75,9 +75,3 @@ def sanity_check_step(self):
         regex = re.compile('libpng.*not found', re.M)
         if regex.search(out):
             raise EasyBuildError("Required libpng library for 'stata' is not available")
-
-    def make_module_req_guess(self):
-        """Add top install directory to $PATH for Stata"""
-        guesses = super(EB_Stata, self).make_module_req_guess()
-        guesses['PATH'] = ['']
-        return guesses

From 9ae80a01f9ba6b79d617a9b9422b9c360935533b Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Thu, 18 Apr 2024 09:39:15 +0000
Subject: [PATCH 076/134] Remove authors left from old file

---
 easybuild/easyblocks/a/aedt.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index a08fcca2bf..8fec82412c 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -25,8 +25,6 @@
 """
 EasyBuild support for installing Ansys Electronics Desktop
 
-@author: Alexi Rivera (Chalmers University of Technology)
-@author: Mikael OEhman (Chalmers University of Technology)
 @author: Chia-Jung Hsu (Chalmers University of Technology)
 """
 import os
@@ -102,7 +100,7 @@ def make_module_extra(self):
         if len(idirs) == 1:
             subdir = os.path.relpath(idirs[0], self.installdir)
             # PyAEDT and other tools use the variable to find available AEDT versions
-            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version,
+            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version, 
                                                          os.path.join(self.installdir, self.subdir))
 
             txt += self.module_generator.prepend_paths('PATH', subdir)

From c5d4ce9dc01ea0d0e8d6ff3934a21050ebead9ad Mon Sep 17 00:00:00 2001
From: c3-builder <c3-builder@vera-skylake-build>
Date: Thu, 18 Apr 2024 09:41:30 +0000
Subject: [PATCH 077/134] Clean whitespace

---
 easybuild/easyblocks/a/aedt.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index 8fec82412c..ff14a7379f 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -100,7 +100,7 @@ def make_module_extra(self):
         if len(idirs) == 1:
             subdir = os.path.relpath(idirs[0], self.installdir)
             # PyAEDT and other tools use the variable to find available AEDT versions
-            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version, 
+            txt += self.module_generator.set_environment('ANSYSEM_ROOT%s' % version,
                                                          os.path.join(self.installdir, self.subdir))
 
             txt += self.module_generator.prepend_paths('PATH', subdir)

From 08cfe0373c6eff1e1874f983d71f1802cfc1f9c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 18 Apr 2024 11:44:06 +0200
Subject: [PATCH 078/134] Update easybuild/easyblocks/a/aedt.py

---
 easybuild/easyblocks/a/aedt.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index ff14a7379f..6b88946414 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2020 Ghent University
+# Copyright 2009-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

From 8e52a4bda611d13365701db1a6011e18967e1b4e Mon Sep 17 00:00:00 2001
From: Chia-Jung Hsu <appolloford@gmail.com>
Date: Thu, 18 Apr 2024 13:48:54 +0000
Subject: [PATCH 079/134] Improve comments

---
 easybuild/easyblocks/a/aedt.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/a/aedt.py b/easybuild/easyblocks/a/aedt.py
index 6b88946414..53d04d506e 100644
--- a/easybuild/easyblocks/a/aedt.py
+++ b/easybuild/easyblocks/a/aedt.py
@@ -81,7 +81,9 @@ def post_install_step(self):
         with open(os.path.join(self.installdir, self.subdir, "VerifyOS.bash"), "w") as f:
             f.write("")
 
-        # Set LC_ALL and LANG for runtime
+        # Follow the settings in .setup_runtime and .setup_runtime_mpi to set LC_ALL and LANG
+        # If LC_ALL is not set properly, AEDT throws the following runtime error:
+        # what():  locale::facet::_S_create_c_locale name not valid
         for fname in [".setup_runtime", ".setup_runtime_mpi"]:
             with open(os.path.join(self.installdir, self.subdir, fname), "r") as f:
                 orig = f.read()

From 4a9bbf88fffe4d816eb478f51943500a1fe55625 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 19 Apr 2024 16:50:42 +0200
Subject: [PATCH 080/134] Added easyblock for MetalWalls

---
 easybuild/easyblocks/m/metalwalls.py | 148 +++++++++++++++++++++++++++
 1 file changed, 148 insertions(+)
 create mode 100644 easybuild/easyblocks/m/metalwalls.py

diff --git a/easybuild/easyblocks/m/metalwalls.py b/easybuild/easyblocks/m/metalwalls.py
new file mode 100644
index 0000000000..a6bbf41216
--- /dev/null
+++ b/easybuild/easyblocks/m/metalwalls.py
@@ -0,0 +1,148 @@
+##
+# Copyright 2009-2023 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for `metalwalls`, implemented as an easyblock
+
+@author: Davide Grassano (CECAM, EPFL)
+"""
+import os
+
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
+
+from easybuild.easyblocks.generic.makecp import MakeCp
+
+
+class EB_MetalWalls(MakeCp):
+    """Support for building and installing `metalwalls`."""
+
+    def __init__(self, *args, **kwargs):
+        """Add extra config options specific to `metalwalls`."""
+        super(EB_MetalWalls, self).__init__(*args, **kwargs)
+
+        self._build_python_interface = False
+
+
+    def configure_step(self):
+        """Custom configuration procedure for `metalwalls`."""
+        comp_fam = self.toolchain.comp_family()
+
+        f90flags = os.getenv('F90FLAGS', '').split(' ')
+        fppflags = os.getenv('FPPFLAGS', '').split(' ')
+        ldflags = os.getenv('LDFLAGS', '').split(' ')
+        f90wrap = ''
+        f2py = ''
+        fcompiler = ''
+
+        if comp_fam == toolchain.INTELCOMP:
+            jflag = '-module'
+            fppflags = ['-fpp']
+        elif comp_fam == toolchain.GCC:
+            jflag = '-J'
+            fppflags = ['-cpp']
+        else:
+            raise EasyBuildError('Unsupported compiler family: %s' % comp_fam)
+
+        # https://gitlab.com/ampere2/metalwalls/-/wikis/install#plumed
+        plumed = get_software_root('PLUMED')
+        f90wrap = get_software_root('f90wrap')
+
+        tpl_rgx = 'alltests\.append(suite_%s)'
+        if plumed:
+            f90flags += ['-fallow-argument-mismatch'] # Code inside ifdef causes mismatch errors
+            fppflags += ['-DMW_USE_PLUMED']
+            cmd = ['plumed', 'patch', '--new', 'mw2']
+            run_cmd(' '.join(cmd), log_all=False, log_ok=False, simple=False, regexp=False)
+            cmd = ['plumed', 'patch', '--patch', '--shared', '--engine', 'mw2']
+            run_cmd(' '.join(cmd), log_all=True, simple=False)
+        else:
+            self.log.info('PLUMED not found, excluding from test-suite')
+            rgx = tpl_rgx % 'plumed'
+            cmd = ['sed', '-i', "'s/^\( \+\)%s$/\\1pass # %s/'" % (rgx, rgx), 'tests/regression_tests.py']
+            cmd = ['sed', '-i', "'s/%s/pass/'" % rgx, 'tests/regression_tests.py']
+            run_cmd(' '.join(cmd), log_all=True, simple=False)
+
+        if f90wrap:
+            if not get_software_root('mpi4py'):
+                raise EasyBuildError('Building the Python interface requires mpi4py')
+            self._build_python_interface = True
+            f90wrap = 'f90wrap'
+            f2py = 'f2py'
+            fcompiler = os.getenv('F90_SEQ')
+            f90flags += ['-fPIC']
+            self.cfg.update('build_cmd_targets', 'python')
+        else:
+            self.log.info('f90wrap not found, excluding python interface from test-suite')
+            rgx = tpl_rgx % 'python_interface'
+            cmd = ['sed', '-i', "'s/%s/pass/'" % rgx, 'tests/regression_tests.py']
+            run_cmd(' '.join(cmd), log_all=True, simple=False)
+
+        # Add libraries with LAPACK support
+        lapack_shared_libs = os.getenv('LAPACK_SHARED_LIBS', None)
+        if not lapack_shared_libs:
+            raise EasyBuildError('Must use a toolchain with LAPACK support')
+        extra_libs = lapack_shared_libs.replace('.so', '').split(',')
+        extra_libs = [_[3:] for _ in extra_libs if _.startswith('lib')]
+        ldflags += ['-l%s' % lib for lib in extra_libs]
+
+        # Write the `config.mk` file
+        configmk = os.path.join(self.cfg['start_dir'], 'config.mk')
+        with open(configmk, 'w') as f:
+            f.write('F90FLAGS := %s\n' % ' '.join(f90flags))
+            f.write('FPPFLAGS := %s\n' % ' '.join(fppflags))
+            f.write('LDFLAGS := %s\n' % ' '.join(ldflags))
+            f.write('F90WRAP := %s\n' % f90wrap)
+            f.write('F2PY := %s\n' % f2py)
+            f.write('FCOMPILER := %s\n' % fcompiler)
+            f.write('J := %s\n' % jflag)
+
+        with open(configmk, 'r') as f:
+            self.log.info('Contents of generated `config.mk`:\n%s' % f.read())
+
+    def test_step(self):
+        """
+        Test the compilation using `metalwalls`'s test suite.
+        """
+
+        if self._build_python_interface:
+            ppath = os.getenv('PYTHONPATH', '')
+            ppath = os.path.join(self.cfg['start_dir'], 'build', 'python') + ':' + ppath
+            self.log.info('Setting PYTHONPATH for testing to %s' % ppath)
+            env.setvar('PYTHONPATH', ppath)
+
+        super(EB_MetalWalls, self).test_step()
+
+    def make_module_extra(self, extra=None):
+        """Add custom entries to module."""
+
+        txt = super(EB_MetalWalls, self).make_module_extra()
+
+        if self._build_python_interface:
+            txt += self.module_generator.prepend_paths('PYTHONPATH', 'python')
+
+        return txt

From 720b7851729d9d1eceab3bcd21f958748b7713fa Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 19 Apr 2024 17:21:38 +0200
Subject: [PATCH 081/134] Linting and sanity checks

---
 easybuild/easyblocks/m/metalwalls.py | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/m/metalwalls.py b/easybuild/easyblocks/m/metalwalls.py
index a6bbf41216..31157007f9 100644
--- a/easybuild/easyblocks/m/metalwalls.py
+++ b/easybuild/easyblocks/m/metalwalls.py
@@ -46,7 +46,7 @@ def __init__(self, *args, **kwargs):
         super(EB_MetalWalls, self).__init__(*args, **kwargs)
 
         self._build_python_interface = False
-
+        self._extra_schecks = []
 
     def configure_step(self):
         """Custom configuration procedure for `metalwalls`."""
@@ -72,7 +72,7 @@ def configure_step(self):
         plumed = get_software_root('PLUMED')
         f90wrap = get_software_root('f90wrap')
 
-        tpl_rgx = 'alltests\.append(suite_%s)'
+        tpl_rgx = 'alltests\\.append(suite_%s)'
         if plumed:
             f90flags += ['-fallow-argument-mismatch'] # Code inside ifdef causes mismatch errors
             fppflags += ['-DMW_USE_PLUMED']
@@ -83,7 +83,7 @@ def configure_step(self):
         else:
             self.log.info('PLUMED not found, excluding from test-suite')
             rgx = tpl_rgx % 'plumed'
-            cmd = ['sed', '-i', "'s/^\( \+\)%s$/\\1pass # %s/'" % (rgx, rgx), 'tests/regression_tests.py']
+            cmd = ['sed', '-i', "'s/^\\( \\+\\)%s$/\\1pass # %s/'" % (rgx, rgx), 'tests/regression_tests.py']
             cmd = ['sed', '-i', "'s/%s/pass/'" % rgx, 'tests/regression_tests.py']
             run_cmd(' '.join(cmd), log_all=True, simple=False)
 
@@ -96,6 +96,9 @@ def configure_step(self):
             fcompiler = os.getenv('F90_SEQ')
             f90flags += ['-fPIC']
             self.cfg.update('build_cmd_targets', 'python')
+            self.cfg.update('files_to_copy', 'build/python')
+            self._extra_schecks += ['python/mw.py', 'python/metalwalls.py']
+
         else:
             self.log.info('f90wrap not found, excluding python interface from test-suite')
             rgx = tpl_rgx % 'python_interface'
@@ -146,3 +149,15 @@ def make_module_extra(self, extra=None):
             txt += self.module_generator.prepend_paths('PYTHONPATH', 'python')
 
         return txt
+
+    def sanity_check_step(self):
+        """Custom sanity check for Quantum ESPRESSO."""
+
+        bins = ['mw']
+
+        custom_paths = {
+            'files': [os.path.join('bin', x) for x in bins] + self._extra_schecks,
+            'dirs': []
+        }
+
+        super(EB_MetalWalls, self).sanity_check_step(custom_paths=custom_paths)

From 3c3765df606e7e98aa8c6dbcce44adcf75a7413a Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Fri, 19 Apr 2024 17:35:51 +0200
Subject: [PATCH 082/134] linting

---
 easybuild/easyblocks/m/metalwalls.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/m/metalwalls.py b/easybuild/easyblocks/m/metalwalls.py
index 31157007f9..2288092b00 100644
--- a/easybuild/easyblocks/m/metalwalls.py
+++ b/easybuild/easyblocks/m/metalwalls.py
@@ -74,7 +74,7 @@ def configure_step(self):
 
         tpl_rgx = 'alltests\\.append(suite_%s)'
         if plumed:
-            f90flags += ['-fallow-argument-mismatch'] # Code inside ifdef causes mismatch errors
+            f90flags += ['-fallow-argument-mismatch']  # Code inside ifdef causes mismatch errors
             fppflags += ['-DMW_USE_PLUMED']
             cmd = ['plumed', 'patch', '--new', 'mw2']
             run_cmd(' '.join(cmd), log_all=False, log_ok=False, simple=False, regexp=False)

From a2be222ed064fafb8ca01bcc6786d50c11fca5b8 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Mon, 22 Apr 2024 18:23:18 +0000
Subject: [PATCH 083/134] Don't manipulate setup.py for Python 3.12+

It's gone in Python 3.12, see
https://docs.python.org/3/whatsnew/3.12.html#build-changes
---
 easybuild/easyblocks/p/python.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/p/python.py b/easybuild/easyblocks/p/python.py
index 0f42c6e41f..f2fe976cb7 100644
--- a/easybuild/easyblocks/p/python.py
+++ b/easybuild/easyblocks/p/python.py
@@ -195,8 +195,9 @@ def patch_step(self, *args, **kwargs):
         # if we're installing Python with an alternate sysroot,
         # we need to patch setup.py which includes hardcoded paths like /usr/include and /lib64;
         # this fixes problems like not being able to build the _ssl module ("Could not build the ssl module")
+        # Python 3.12 doesn't have setup.py any more
         sysroot = build_option('sysroot')
-        if sysroot:
+        if sysroot and LooseVersion(self.version) < LooseVersion('3.12'):
             sysroot_inc_dirs, sysroot_lib_dirs = [], []
 
             for pattern in ['include*', os.path.join('usr', 'include*')]:

From 7c4996a89e9c11b02df7938df5024937e4ee0af6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 24 Apr 2024 10:04:20 +0200
Subject: [PATCH 084/134] also auto-disable quad-precision on RISC-V

---
 easybuild/easyblocks/f/fftw.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/f/fftw.py b/easybuild/easyblocks/f/fftw.py
index ff3788a4e2..baa287e2d5 100644
--- a/easybuild/easyblocks/f/fftw.py
+++ b/easybuild/easyblocks/f/fftw.py
@@ -37,7 +37,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.modules import get_software_version
-from easybuild.tools.systemtools import AARCH32, AARCH64, POWER, X86_64
+from easybuild.tools.systemtools import AARCH32, AARCH64, POWER, RISCV32, RISCV64, X86_64
 from easybuild.tools.systemtools import get_cpu_architecture, get_cpu_features, get_shared_lib_ext
 from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC
 from easybuild.tools.utilities import nub
@@ -141,7 +141,7 @@ def __init__(self, *args, **kwargs):
                     setattr(self, flag, True)
 
         # Auto-disable quad-precision on ARM and POWER, as it is unsupported
-        if self.cfg['with_quad_prec'] and cpu_arch in [AARCH32, AARCH64, POWER]:
+        if self.cfg['with_quad_prec'] and cpu_arch in [AARCH32, AARCH64, POWER, RISCV32, RISCV64]:
             self.cfg['with_quad_prec'] = False
             self.log.debug("Quad-precision automatically disabled; not supported on %s.", cpu_arch)
 

From 7be0c26032aeeb88a7137e48030fde1532e06886 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 27 Apr 2024 15:29:50 +0000
Subject: [PATCH 085/134] remove alternative flex license manager environment
 variable

---
 easybuild/easyblocks/a/abaqus.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyblocks/a/abaqus.py b/easybuild/easyblocks/a/abaqus.py
index 7f6eb0820a..8bb0ec7280 100644
--- a/easybuild/easyblocks/a/abaqus.py
+++ b/easybuild/easyblocks/a/abaqus.py
@@ -372,8 +372,6 @@ def make_module_extra(self):
         txt = super(EB_ABAQUS, self).make_module_extra()
         license_file = os.getenv('EB_ABAQUS_LICENSE_FILE', None)
         if license_file is not None:
-            txt += self.module_generator.prepend_paths('LM_LICENSE_FILE', [license_file], allow_abs=True)
-            # also needed for some versions:
             txt += self.module_generator.prepend_paths('ABAQUSLM_LICENSE_FILE', [license_file], allow_abs=True)
 
         return txt

From 5e1010b980214807b6e75f1f4eb53f3801f5b996 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sun, 28 Apr 2024 14:21:46 +0200
Subject: [PATCH 086/134] don't set configure_cmd, stick to regular configure
 script

---
 easybuild/easyblocks/u/ucx_plugins.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/u/ucx_plugins.py b/easybuild/easyblocks/u/ucx_plugins.py
index d6a8227202..77e799d581 100644
--- a/easybuild/easyblocks/u/ucx_plugins.py
+++ b/easybuild/easyblocks/u/ucx_plugins.py
@@ -77,7 +77,6 @@ def configure_step(self):
         if not get_software_root('UCX'):
             raise EasyBuildError("UCX is a required dependency")
 
-        self.cfg['configure_cmd'] = 'contrib/configure-release'
         self.cfg.update('preconfigopts', 'autoreconf -i &&')
 
         configopts = '--enable-optimizations --without-java --disable-doxygen-doc '

From b0035e8d7fc8d646101529bd601876d802f701ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sun, 28 Apr 2024 14:23:06 +0200
Subject: [PATCH 087/134] add the configure flags from
 contrib/configure-release to configopts

---
 easybuild/easyblocks/u/ucx_plugins.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyblocks/u/ucx_plugins.py b/easybuild/easyblocks/u/ucx_plugins.py
index 77e799d581..3cba0e277c 100644
--- a/easybuild/easyblocks/u/ucx_plugins.py
+++ b/easybuild/easyblocks/u/ucx_plugins.py
@@ -82,6 +82,8 @@ def configure_step(self):
         configopts = '--enable-optimizations --without-java --disable-doxygen-doc '
         # omit the lib subdirectory since we are just installing plugins
         configopts += '--libdir=%(installdir)s '
+        # include the configure options from contrib/configure-release
+        configopts += '--disable-logging --disable-debug --disable-assertions --disable-params-check '
 
         cudaroot = get_software_root('CUDAcore') or get_software_root('CUDA')
         if cudaroot:

From 1bfd25373dca72660f725b65e87833420d8dd936 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 7 May 2024 15:34:47 +0200
Subject: [PATCH 088/134] swicth OpenMP in GAMESS-US through GMS_OPENMP and
 disable toolchain option

---
 easybuild/easyblocks/g/gamess_us.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index 60b2b32397..a3d0625cae 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -104,6 +104,13 @@ def __init__(self, *args, **kwargs):
                 error_msg = "Temporary dir for tests '%s' will cause problems with rungms csh script"
                 raise EasyBuildError(error_msg, self.testdir)
 
+        # OpenMP cannot be enabled across the board, activate it only through
+        # GMS_OPENMP so that it gets enabled by the build where needed
+        self.omp_enabled = False
+        if self.toolchain.options.get('openmp', None):
+            self.omp_enabled = True
+            self.toolchain.options['openmp'] = False
+
     def extract_step(self):
         """Extract sources."""
         # strip off 'gamess' part to avoid having everything in a 'gamess' subdirectory
@@ -153,12 +160,7 @@ def configure_step(self):
         installinfo_opts.update(fortran_version)
 
         # OpenMP config
-        if self.toolchain.options.get('openmp', None):
-            omp_enabled = "true"
-        else:
-            omp_enabled = "false"
-
-        installinfo_opts["GMS_OPENMP"] = omp_enabled
+        installinfo_opts["GMS_OPENMP"] = self.omp_enabled
 
         # Math library config
         known_mathlibs = ['imkl', 'OpenBLAS', 'ATLAS', 'ACML']
@@ -186,7 +188,7 @@ def configure_step(self):
             installinfo_opts["GMS_MKL_VERNO"] = mkl_version
 
             if LooseVersion(self.version) >= LooseVersion('20230601'):
-                installinfo_opts["GMS_THREADED_BLAS"] = omp_enabled
+                installinfo_opts["GMS_THREADED_BLAS"] = self.omp_enabled
 
         elif mathlib == 'openblas':
             mathlib_flags = "-lopenblas -lgfortran"

From 49e0c87a146f9b9acc02244c9a3b35e7ce196cea Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 7 May 2024 15:36:06 +0200
Subject: [PATCH 089/134] use real booleans for true/false install.info options
 in GAMESS-US easyblock

---
 easybuild/easyblocks/g/gamess_us.py | 45 +++++++++++++++--------------
 1 file changed, 24 insertions(+), 21 deletions(-)

diff --git a/easybuild/easyblocks/g/gamess_us.py b/easybuild/easyblocks/g/gamess_us.py
index a3d0625cae..ca03c51714 100644
--- a/easybuild/easyblocks/g/gamess_us.py
+++ b/easybuild/easyblocks/g/gamess_us.py
@@ -260,26 +260,26 @@ def configure_step(self):
         # TODO: add support for GPUs
         if LooseVersion(self.version) >= LooseVersion('20230601'):
             # offloading onto Intel GPUs
-            installinfo_opts["GMS_OPENMP_OFFLOAD"] = "false"
+            installinfo_opts["GMS_OPENMP_OFFLOAD"] = False
 
         # These are extra programs which for now we simply set all to FALSE
-        installinfo_opts["GMS_MSUCC"] = "false"
+        installinfo_opts["GMS_MSUCC"] = False
         installinfo_opts["GMS_PHI"] = "none"
         installinfo_opts["GMS_SHMTYPE"] = "sysv"
-        installinfo_opts["GMS_LIBCCHEM"] = "false"  # libcchem
+        installinfo_opts["GMS_LIBCCHEM"] = False  # libcchem
         if LooseVersion(self.version) >= LooseVersion('20230601'):
             # install options for libcchem2
-            installinfo_opts["GMS_HPCCHEM"] = "false"
-            installinfo_opts["GMS_HPCCHEM_USE_DATA_SERVERS"] = "false"
+            installinfo_opts["GMS_HPCCHEM"] = False
+            installinfo_opts["GMS_HPCCHEM_USE_DATA_SERVERS"] = False
             # build Michigan State University code
-            installinfo_opts["GMS_MSUAUTO"] = "false"
+            installinfo_opts["GMS_MSUAUTO"] = False
 
         # Optional plug-ins and interfaces
         # libXC
         if LooseVersion(self.version) >= LooseVersion('20200101'):
-            installinfo_opts['GMS_LIBXC'] = "false"
+            installinfo_opts['GMS_LIBXC'] = False
             if get_software_root('libxc'):
-                installinfo_opts['GMS_LIBXC'] = "true"
+                installinfo_opts['GMS_LIBXC'] = True
                 # the linker needs to be patched to use external libXC
                 lixc_libs = [os.path.join(os.environ['EBROOTLIBXC'], 'lib', lib) for lib in ['libxcf03.a', 'libxc.a']]
                 libxc_linker_flags = ' '.join(lixc_libs)
@@ -292,26 +292,26 @@ def configure_step(self):
                     raise EasyBuildError("Failed to patch %s: %s", lked, err)
         # MDI
         # needs https://github.com/MolSSI-MDI/MDI_Library
-        installinfo_opts['GMS_MDI'] = "false"
+        installinfo_opts['GMS_MDI'] = False
         # NBO
-        installinfo_opts['NBO'] = "false"
+        installinfo_opts['NBO'] = False
         if get_software_root('NBO'):
-            installinfo_opts['NBO'] = "true"
+            installinfo_opts['NBO'] = True
         # NEO
-        installinfo_opts['NEO'] = "false"
+        installinfo_opts['NEO'] = False
         # RISM
         if LooseVersion(self.version) >= LooseVersion('20230601'):
-            installinfo_opts['RISM'] = "false"
+            installinfo_opts['RISM'] = False
         # TINKER
-        installinfo_opts['TINKER'] = "false"
+        installinfo_opts['TINKER'] = False
         if get_software_root('TINKER'):
-            installinfo_opts['TINKER'] = "true"
+            installinfo_opts['TINKER'] = True
         # VB2000
-        installinfo_opts['VB2000'] = "false"
+        installinfo_opts['VB2000'] = False
         # VM2
-        installinfo_opts['GMS_VM2'] = "false"
+        installinfo_opts['GMS_VM2'] = False
         # XMVB
-        installinfo_opts['XMVB'] = "false"
+        installinfo_opts['XMVB'] = False
 
         # add include paths from dependencies
         installinfo_opts["GMS_FPE_FLAGS"] = '"%s"' % os.environ['CPPFLAGS']
@@ -319,10 +319,13 @@ def configure_step(self):
         # installinfo_opts["GMS_FPE_FLAGS"] = '"%s"' % os.environ['CPPFLAGS'] + "-ffpe-trap=invalid,zero,overflow"
 
         # write install.info file with configuration settings
-        # format: setenv KEY VALUE
         installinfo_file = os.path.join(self.builddir, GAMESS_INSTALL_INFO)
-        txt = '\n'.join(["setenv %s %s" % (k, installinfo_opts[k]) for k in installinfo_opts])
-        write_file(installinfo_file, txt)
+        # replace boolean options with their string representation
+        boolean_opts = {opt: str(val).lower() for opt, val in installinfo_opts.items() if val in [True, False]}
+        installinfo_opts.update(boolean_opts)
+        # format: setenv KEY VALUE
+        installinfo_txt = '\n'.join(["setenv %s %s" % (k, installinfo_opts[k]) for k in installinfo_opts])
+        write_file(installinfo_file, installinfo_txt)
         self.log.debug("Contents of %s:\n%s" % (installinfo_file, read_file(installinfo_file)))
 
         # patch hardcoded settings in rungms to use values specified in easyconfig file

From a6bb74410f7033c5da564ef02b5cbb34d144b2e0 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Tue, 7 May 2024 17:16:31 +0200
Subject: [PATCH 090/134] Added GPU compilation

---
 easybuild/easyblocks/m/metalwalls.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyblocks/m/metalwalls.py b/easybuild/easyblocks/m/metalwalls.py
index 2288092b00..2bbdef5f10 100644
--- a/easybuild/easyblocks/m/metalwalls.py
+++ b/easybuild/easyblocks/m/metalwalls.py
@@ -65,6 +65,12 @@ def configure_step(self):
         elif comp_fam == toolchain.GCC:
             jflag = '-J'
             fppflags = ['-cpp']
+        elif comp_fam == toolchain.NVHPC:
+            if self.toolchain.options.get('usempi', False):
+                raise EasyBuildError('NVHPC compilation does not support MPI')
+            jflag = '-module '  # Space is needed
+            fppflags = ['-DMW_SERIAL', '-Mpreprocess']
+            f90flags += ['-Minline', '-acc', '-gpu=managed']
         else:
             raise EasyBuildError('Unsupported compiler family: %s' % comp_fam)
 

From b72bfdc077b8f9e1588fb8ae4aaf144e03ef6ad4 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 7 May 2024 22:20:11 +0200
Subject: [PATCH 091/134] add libjpeg-turbo to include dir for torchvision
 easyblock

---
 easybuild/easyblocks/t/torchvision.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index 928574e50a..64577506c4 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -31,7 +31,7 @@
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_pylibdir
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
-from easybuild.tools.modules import get_software_version
+from easybuild.tools.modules import get_software_version, get_software_root
 import easybuild.tools.environment as env
 
 
@@ -78,6 +78,11 @@ def configure_step(self):
             if cuda_cc:
                 env.setvar('TORCH_CUDA_ARCH_LIST', ';'.join(cuda_cc))
 
+        libjpeg = get_software_root('libjpeg-turbo')
+        if libjpeg and 'TORCHVISION_INCLUDE' not in self.cfg['preinstallopts']:
+            vision_include = 'TORCHVISION_INCLUDE="$EBROOTLIBJPEGMINTURBO/include:$TORCHVISION_INCLUDE"'
+            self.cfg.update('preinstallopts', vision_include)
+
         super(EB_torchvision, self).configure_step()
 
     def sanity_check_step(self):

From 88b5dc4be87bf92da249e12cf3e04f79ab2c7ade Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 7 May 2024 23:14:39 +0200
Subject: [PATCH 092/134] add riscv64 support

---
 easybuild/easyblocks/j/java.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/j/java.py b/easybuild/easyblocks/j/java.py
index bca89cc6b2..5731a193bb 100644
--- a/easybuild/easyblocks/j/java.py
+++ b/easybuild/easyblocks/j/java.py
@@ -38,7 +38,7 @@
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import adjust_permissions, change_dir, copy_dir, copy_file, remove_dir, which
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import AARCH64, POWER, X86_64, get_cpu_architecture, get_shared_lib_ext
+from easybuild.tools.systemtools import AARCH64, POWER, RISCV64, X86_64, get_cpu_architecture, get_shared_lib_ext
 from easybuild.tools.utilities import nub
 
 
@@ -54,6 +54,8 @@ def __init__(self, *args, **kwargs):
             jdkarch = 'aarch64'
         elif myarch == POWER:
             jdkarch = 'ppc64le'
+        elif myarch == RISCV64:
+            jdkarch = 'riscv64'
         elif myarch == X86_64:
             jdkarch = 'x64'
         else:

From 7fdc69564c538d2fe9134895be504c9a94763d3e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 7 May 2024 23:29:41 +0200
Subject: [PATCH 093/134] add RISC-V support

---
 easybuild/easyblocks/m/mesa.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/m/mesa.py b/easybuild/easyblocks/m/mesa.py
index 4a73625185..e482ac9c13 100644
--- a/easybuild/easyblocks/m/mesa.py
+++ b/easybuild/easyblocks/m/mesa.py
@@ -35,7 +35,7 @@
 
 from easybuild.easyblocks.generic.mesonninja import MesonNinja
 from easybuild.tools.filetools import copy_dir
-from easybuild.tools.systemtools import POWER, X86_64, AARCH64
+from easybuild.tools.systemtools import POWER, X86_64, AARCH64, RISCV64
 from easybuild.tools.systemtools import get_cpu_architecture, get_cpu_features, get_shared_lib_ext
 
 
@@ -69,6 +69,7 @@ def __init__(self, *args, **kwargs):
                 X86_64: ['swrast'],
                 POWER: ['swrast'],
                 AARCH64: ['swrast'],
+                RISCV64: ['swrast'],
             }
             if LooseVersion(self.version) < LooseVersion('22'):
                 # swr driver support removed in Mesa 22.0

From 3e29db25ff6c8fb93804fb4eeb6cc1ce81790ab7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 7 May 2024 23:34:43 +0200
Subject: [PATCH 094/134] add RISC-V support

---
 easybuild/easyblocks/c/clang.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/c/clang.py b/easybuild/easyblocks/c/clang.py
index b945553969..af9c105910 100644
--- a/easybuild/easyblocks/c/clang.py
+++ b/easybuild/easyblocks/c/clang.py
@@ -49,13 +49,13 @@
 from easybuild.tools.filetools import apply_regex_substitutions, change_dir, mkdir, symlink, which
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
-from easybuild.tools.systemtools import AARCH32, AARCH64, POWER, X86_64
+from easybuild.tools.systemtools import AARCH32, AARCH64, POWER, RISCV64, X86_64
 from easybuild.tools.systemtools import get_cpu_architecture, get_os_name, get_os_version, get_shared_lib_ext
 from easybuild.tools.environment import setvar
 
 # List of all possible build targets for Clang
 CLANG_TARGETS = ["all", "AArch64", "AMDGPU", "ARM", "CppBackend", "Hexagon", "Mips",
-                 "MBlaze", "MSP430", "NVPTX", "PowerPC", "R600", "Sparc",
+                 "MBlaze", "MSP430", "NVPTX", "PowerPC", "R600", "RISCV", "Sparc",
                  "SystemZ", "X86", "XCore"]
 
 # Mapping of EasyBuild CPU architecture names to list of default LLVM target names
@@ -63,6 +63,7 @@
     AARCH32: ['ARM'],
     AARCH64: ['AArch64'],
     POWER: ['PowerPC'],
+    RISCV64: ['RISCV'],
     X86_64: ['X86'],
 }
 

From 671331c1c787f041c6284d8bd9dcb33f6f54d03b Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 8 May 2024 11:45:31 +0200
Subject: [PATCH 095/134] use envvar and add sanity check

---
 easybuild/easyblocks/t/torchvision.py | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index 64577506c4..3106d3b8d9 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -28,6 +28,8 @@
 @author: Alexander Grund (TU Dresden)
 @author: Kenneth Hoste (HPC-UGent)
 """
+import os
+
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_pylibdir
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
@@ -80,21 +82,21 @@ def configure_step(self):
 
         libjpeg = get_software_root('libjpeg-turbo')
         if libjpeg and 'TORCHVISION_INCLUDE' not in self.cfg['preinstallopts']:
-            vision_include = 'TORCHVISION_INCLUDE="$EBROOTLIBJPEGMINTURBO/include:$TORCHVISION_INCLUDE"'
-            self.cfg.update('preinstallopts', vision_include)
+            # vision_include = 'TORCHVISION_INCLUDE="$EBROOTLIBJPEGMINTURBO/include:$TORCHVISION_INCLUDE"'
+            # self.cfg.update('preinstallopts', vision_include)
+            env.setvar('TORCHVISION_INCLUDE', os.path.join(os.getenv('EBROOTLIBJPEGMINTURBO'), 'include'))
 
         super(EB_torchvision, self).configure_step()
 
     def sanity_check_step(self):
         """Custom sanity check for torchvision."""
-        custom_commands = None
+        custom_commands = []
         custom_paths = None
 
         # check whether torchvision was indeed built with CUDA support,
         # cfr. https://discuss.pytorch.org/t/notimplementederror-could-not-run-torchvision-nms-with-arguments-from-\
         #      the-cuda-backend-this-could-be-because-the-operator-doesnt-exist-for-this-backend/132352/4
         if self.with_cuda:
-            custom_commands = []
             python_code = '\n'.join([
                 "import torch, torchvision",
                 "if torch.cuda.device_count():",
@@ -108,4 +110,14 @@ def sanity_check_step(self):
                 'dirs': [det_pylibdir()],
             }
 
+        if get_software_root('libjpeg-turbo'):
+            # check wither torchvision was built with libjpeg support
+            # if not, will show error "RuntimeError: encode_jpeg: torchvision not compiled with libjpeg support"
+            python_code = '\n'.join([
+                "import torch, torchvision",
+                "image_tensor = torch.zeros(1, 1, 1, dtype=torch.uint8)",
+                "print(torchvision.io.image.encode_jpeg(image_tensor))",
+            ])
+            custom_commands.append('python -c "%s"' % python_code)
+
         return super(EB_torchvision, self).sanity_check_step(custom_commands=custom_commands, custom_paths=custom_paths)

From 89331871d68656c5dfc52fb8a1493a1890640200 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 8 May 2024 11:47:24 +0200
Subject: [PATCH 096/134] remove comments

---
 easybuild/easyblocks/t/torchvision.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index 3106d3b8d9..4c5b2f961d 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -82,8 +82,6 @@ def configure_step(self):
 
         libjpeg = get_software_root('libjpeg-turbo')
         if libjpeg and 'TORCHVISION_INCLUDE' not in self.cfg['preinstallopts']:
-            # vision_include = 'TORCHVISION_INCLUDE="$EBROOTLIBJPEGMINTURBO/include:$TORCHVISION_INCLUDE"'
-            # self.cfg.update('preinstallopts', vision_include)
             env.setvar('TORCHVISION_INCLUDE', os.path.join(os.getenv('EBROOTLIBJPEGMINTURBO'), 'include'))
 
         super(EB_torchvision, self).configure_step()

From 903e59c128d7b5071783f6f520d0d0be32c57931 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 8 May 2024 17:36:11 +0200
Subject: [PATCH 097/134] use libjpeg_root

---
 easybuild/easyblocks/t/torchvision.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index 4c5b2f961d..18b08d25dc 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -80,9 +80,9 @@ def configure_step(self):
             if cuda_cc:
                 env.setvar('TORCH_CUDA_ARCH_LIST', ';'.join(cuda_cc))
 
-        libjpeg = get_software_root('libjpeg-turbo')
-        if libjpeg and 'TORCHVISION_INCLUDE' not in self.cfg['preinstallopts']:
-            env.setvar('TORCHVISION_INCLUDE', os.path.join(os.getenv('EBROOTLIBJPEGMINTURBO'), 'include'))
+        libjpeg_root = get_software_root('libjpeg-turbo')
+        if libjpeg_root and 'TORCHVISION_INCLUDE' not in self.cfg['preinstallopts']:
+            env.setvar('TORCHVISION_INCLUDE', os.path.join(libjpeg_root, 'include'))
 
         super(EB_torchvision, self).configure_step()
 
@@ -109,7 +109,7 @@ def sanity_check_step(self):
             }
 
         if get_software_root('libjpeg-turbo'):
-            # check wither torchvision was built with libjpeg support
+            # check if torchvision was built with libjpeg support
             # if not, will show error "RuntimeError: encode_jpeg: torchvision not compiled with libjpeg support"
             python_code = '\n'.join([
                 "import torch, torchvision",

From 0445cde9c6b72238e204045acd3eb81d8adcbb50 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 10 May 2024 18:26:24 +0100
Subject: [PATCH 098/134] do not run unit tests on Python 3.5

---
 .github/workflows/unit_tests.yml | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index b1cf6dc64a..69165889aa 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -13,12 +13,12 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python: [3.5, 3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
+        python: [3.6, 3.7, 3.8, 3.9, '3.10', '3.11']
         modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14, modules-tcl-1.147, modules-3.2.10, modules-4.1.4]
         module_syntax: [Lua, Tcl]
         # exclude some configuration for non-Lmod modules tool:
         # - don't test with Lua module syntax (only supported in Lmod)
-        # - don't test with Python 3.5 and 3.7+ (only with 3.6), to limit test configurations
+        # - don't test with Python 3.7+ (only with 3.6), to limit test configurations
         exclude:
           - modules_tool: modules-tcl-1.147
             module_syntax: Lua
@@ -26,8 +26,6 @@ jobs:
             module_syntax: Lua
           - modules_tool: modules-4.1.4
             module_syntax: Lua
-          - modules_tool: modules-tcl-1.147
-            python: 3.5
           - modules_tool: modules-tcl-1.147
             python: 3.7
           - modules_tool: modules-tcl-1.147
@@ -37,9 +35,6 @@ jobs:
           - modules_tool: modules-tcl-1.147
             python: '3.10'
           - modules_tool: modules-tcl-1.147
-            python: '3.11'
-          - modules_tool: modules-3.2.10
-            python: 3.5
           - modules_tool: modules-3.2.10
             python: 3.7
           - modules_tool: modules-3.2.10
@@ -50,8 +45,6 @@ jobs:
             python: '3.10'
           - modules_tool: modules-3.2.10
             python: '3.11'
-          - modules_tool: modules-4.1.4
-            python: 3.5
           - modules_tool: modules-4.1.4
             python: 3.7
           - modules_tool: modules-4.1.4

From 7f3bc6f933dad3896ac348fdc2fdc54211f37b3c Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 10 May 2024 18:44:22 +0100
Subject: [PATCH 099/134] restore accidentally deleted line

---
 .github/workflows/unit_tests.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index 69165889aa..3cd95ff88d 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -35,6 +35,7 @@ jobs:
           - modules_tool: modules-tcl-1.147
             python: '3.10'
           - modules_tool: modules-tcl-1.147
+            python: '3.11'
           - modules_tool: modules-3.2.10
             python: 3.7
           - modules_tool: modules-3.2.10

From eae3bdd861de7491490d3d3c01145111c65c9a0d Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 13 May 2024 15:24:15 +0200
Subject: [PATCH 100/134] Add a sanity check for OpenFOAM's  to make sure it
 finds the compiler commands

---
 easybuild/easyblocks/o/openfoam.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyblocks/o/openfoam.py b/easybuild/easyblocks/o/openfoam.py
index db69ddc569..2cd60f364c 100644
--- a/easybuild/easyblocks/o/openfoam.py
+++ b/easybuild/easyblocks/o/openfoam.py
@@ -486,6 +486,11 @@ def sanity_check_step(self):
             test_foammonitor = "! foamMonitor -h 2>&1 | grep 'not installed'"
             custom_commands.append(' && '.join([load_openfoam_env, test_foammonitor]))
 
+        if self.is_dot_com and self.looseversion >= LooseVersion("2012"):
+            # Make sure that wmake can see the compilers
+            test_wmake_compilers = ["command -V $(wmake -show-cxx)", "command -V $(wmake -show-c)"]
+            custom_commands.append(' && '.join([load_openfoam_env] + test_wmake_compilers))
+
         custom_paths = {
             'files': [os.path.join(self.openfoamdir, 'etc', x) for x in ["bashrc", "cshrc"]] + bins + libs,
             'dirs': dirs,

From 3cbe88540cff4ecd8b21995ee9952d56a771eb5a Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 14 May 2024 14:59:28 +0200
Subject: [PATCH 101/134] Always override the compiler version check for CUDA
 installations

---
 easybuild/easyblocks/c/cuda.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/easybuild/easyblocks/c/cuda.py b/easybuild/easyblocks/c/cuda.py
index 46b3c58854..e024bf2c32 100644
--- a/easybuild/easyblocks/c/cuda.py
+++ b/easybuild/easyblocks/c/cuda.py
@@ -156,6 +156,15 @@ def install_step(self):
         # Use C locale to avoid localized questions and crash on CUDA 10.1
         self.cfg.update('preinstallopts', "export LANG=C && ")
 
+        # As a CUDA recipe gets older and the OS gets updated, it is
+        # likely that the system GCC becomes too new for the CUDA version.
+        # Since in EasyBuild we know/expect that CUDA will only ever get used
+        # as a dependency within the context of a toolchain, we can override
+        # the compiler version check that would cause the installation to
+        # fail.
+        self.cfg.update('installopts', "--override")
+
+
         cmd = "%(preinstallopts)s %(interpreter)s %(script)s %(installopts)s" % {
             'preinstallopts': self.cfg['preinstallopts'],
             'interpreter': install_interpreter,

From cd416f0453b063897f7f17359997073903d6c8a6 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 14 May 2024 15:03:44 +0200
Subject: [PATCH 102/134] Lint

---
 easybuild/easyblocks/c/cuda.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/c/cuda.py b/easybuild/easyblocks/c/cuda.py
index e024bf2c32..10d6bc3083 100644
--- a/easybuild/easyblocks/c/cuda.py
+++ b/easybuild/easyblocks/c/cuda.py
@@ -164,7 +164,6 @@ def install_step(self):
         # fail.
         self.cfg.update('installopts', "--override")
 
-
         cmd = "%(preinstallopts)s %(interpreter)s %(script)s %(installopts)s" % {
             'preinstallopts': self.cfg['preinstallopts'],
             'interpreter': install_interpreter,

From b131ada63c3affd7b7dc4015d8eac255dba01602 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Wed, 15 May 2024 15:33:38 +0200
Subject: [PATCH 103/134] Fix for plumed genereting patch file inside module
 location

---
 easybuild/easyblocks/m/metalwalls.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/m/metalwalls.py b/easybuild/easyblocks/m/metalwalls.py
index 2bbdef5f10..ce22c36187 100644
--- a/easybuild/easyblocks/m/metalwalls.py
+++ b/easybuild/easyblocks/m/metalwalls.py
@@ -82,9 +82,9 @@ def configure_step(self):
         if plumed:
             f90flags += ['-fallow-argument-mismatch']  # Code inside ifdef causes mismatch errors
             fppflags += ['-DMW_USE_PLUMED']
-            cmd = ['plumed', 'patch', '--new', 'mw2']
+            cmd = ['touch', 'mw2.diff']
             run_cmd(' '.join(cmd), log_all=False, log_ok=False, simple=False, regexp=False)
-            cmd = ['plumed', 'patch', '--patch', '--shared', '--engine', 'mw2']
+            cmd = ['plumed', 'patch', '-d mw2.diff', '--patch', '--shared', '--engine', 'mw2']
             run_cmd(' '.join(cmd), log_all=True, simple=False)
         else:
             self.log.info('PLUMED not found, excluding from test-suite')

From 39195f93c94731cf07959945c5d97c895062fffb Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Wed, 15 May 2024 15:44:22 +0200
Subject: [PATCH 104/134] Added compatibility check with f90wraps

---
 easybuild/easyblocks/m/metalwalls.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/m/metalwalls.py b/easybuild/easyblocks/m/metalwalls.py
index ce22c36187..1241249a7a 100644
--- a/easybuild/easyblocks/m/metalwalls.py
+++ b/easybuild/easyblocks/m/metalwalls.py
@@ -31,8 +31,9 @@
 
 import easybuild.tools.environment as env
 import easybuild.tools.toolchain as toolchain
+from easybuild.tools import LooseVersion
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.modules import get_software_root
+from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 
 from easybuild.easyblocks.generic.makecp import MakeCp
@@ -77,6 +78,11 @@ def configure_step(self):
         # https://gitlab.com/ampere2/metalwalls/-/wikis/install#plumed
         plumed = get_software_root('PLUMED')
         f90wrap = get_software_root('f90wrap')
+        f90wrap_version = get_software_version('f90wrap')
+
+        if LooseVersion(self.version) <= LooseVersion('21.06.1'):
+            if LooseVersion(f90wrap_version) > LooseVersion('0.2.13'):
+                raise EasyBuildError('MetalWalls version %s requires f90wrap <= 0.2.13' % self.version)
 
         tpl_rgx = 'alltests\\.append(suite_%s)'
         if plumed:

From e07ac51615c39cf70aead1053fd9de9680ff390f Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 24 May 2024 17:12:36 +0200
Subject: [PATCH 105/134] adjust OpenSSL version regex and OpenSSL header
 version check in OpenSSL wrapper easyblock

---
 easybuild/easyblocks/o/openssl_wrapper.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 247a018d62..53cb27aa2c 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -101,7 +101,7 @@ def __init__(self, *args, **kwargs):
 
         # Regex pattern to find version strings in OpenSSL libraries and headers
         full_version_regex = re.compile(r'[0-9]+\.[0-9]+\.[0-9]+[a-z]?')
-        openssl_version_regex = re.compile(r'OpenSSL\s+([0-9]+\.[0-9]+(\.[0-9]+[a-z]?)*)', re.M)
+        openssl_version_regex = re.compile(r'(?i)OpenSSL[\s_]+([0-9]+\.[0-9]+(\.[0-9]+[a-z]?)*)', re.M)
 
         # Libraries packaged in OpenSSL
         openssl_libs = ['libssl', 'libcrypto']
@@ -259,13 +259,23 @@ def __init__(self, *args, **kwargs):
                     err_msg = "System OpenSSL header '%s' does not contain any recognizable version string"
                     raise EasyBuildError(err_msg, opensslv_path)
 
-                if header_version == self.system_ssl['version']:
+                header_version_major = header_version.split('.')[0]
+                system_ssl_version_major = self.system_ssl['version'].split('.')[0]
+
+                # Compare only major version of header for OpenSSL 3+
+                # This is needed on Debian-based distros
+                if LooseVersion(self.version) >= LooseVersion('3'):
+                    header_found = (header_version_major == system_ssl_version_major)
+                else:
+                    header_found = (header_version == self.system_ssl['version'])
+
+                if header_found:
                     self.system_ssl['include'] = include_dir
                     info_msg = "Found OpenSSL headers v%s in host system: %s"
                     self.log.info(info_msg, header_version, self.system_ssl['include'])
                     break
                 else:
-                    dbg_msg = "System OpenSSL header version '%s' doesn not match library version '%s'"
+                    dbg_msg = "System OpenSSL header version '%s' does not match library version '%s'"
                     self.log.debug(dbg_msg, header_version, self.system_ssl['version'])
             else:
                 self.log.info("System OpenSSL header file %s not found", opensslv_path)

From 67bb99069cb26f128c939076df7a3125a9deed71 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 24 May 2024 20:05:17 +0200
Subject: [PATCH 106/134] avoid sanity check on the software itself for
 CargoPythonBundle easyblock

---
 easybuild/easyblocks/generic/cargopythonbundle.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easybuild/easyblocks/generic/cargopythonbundle.py b/easybuild/easyblocks/generic/cargopythonbundle.py
index 090a38dff4..117004dc2b 100644
--- a/easybuild/easyblocks/generic/cargopythonbundle.py
+++ b/easybuild/easyblocks/generic/cargopythonbundle.py
@@ -53,6 +53,14 @@ def __init__(self, *args, **kwargs):
         self.check_for_sources = False  # make Bundle allow sources (as crates are treated as sources)
         super(CargoPythonBundle, self).__init__(*args, **kwargs)
 
+        # Cargo inherits from ExtensionEasyBlock, thus EB treats the software itself as an extension
+        # Setting modulename to False to ensure that sanity checks are performed on the extensions only
+        self.options = {'modulename': False}
+
     def extract_step(self):
         """Specifically use the overloaded variant from Cargo as is populates vendored sources with checksums."""
         return Cargo.extract_step(self)
+
+    # def sanity_check_step(self, *args, **kwargs):
+    #     self.cfg['sources'] = None
+    #     super(CargoPythonBundle, self).sanity_check_step(*args, **kwargs)

From fa440b18992685e1e9fa9e9f333273c05f4d7065 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 24 May 2024 20:15:35 +0200
Subject: [PATCH 107/134] remove old comments

---
 easybuild/easyblocks/generic/cargopythonbundle.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargopythonbundle.py b/easybuild/easyblocks/generic/cargopythonbundle.py
index 117004dc2b..d76ccde612 100644
--- a/easybuild/easyblocks/generic/cargopythonbundle.py
+++ b/easybuild/easyblocks/generic/cargopythonbundle.py
@@ -60,7 +60,3 @@ def __init__(self, *args, **kwargs):
     def extract_step(self):
         """Specifically use the overloaded variant from Cargo as is populates vendored sources with checksums."""
         return Cargo.extract_step(self)
-
-    # def sanity_check_step(self, *args, **kwargs):
-    #     self.cfg['sources'] = None
-    #     super(CargoPythonBundle, self).sanity_check_step(*args, **kwargs)

From e67ce87b8b13dd74fcaa423832bbf98450753976 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 May 2024 00:08:37 +0200
Subject: [PATCH 108/134] add non-standard include path used by RHEL-based
 systems to install OpenSSL v3 headers alongside OpenSSL v1.1

---
 easybuild/easyblocks/o/openssl_wrapper.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 53cb27aa2c..85f3a343b3 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -242,6 +242,10 @@ def __init__(self, *args, **kwargs):
             # but version 1.1 can be installed in 'include/openssl11/openssl' as well, for example in CentOS 7
             # prefer 'include/openssl' as long as the version of headers matches
             ssl_include_subdirs.append(os.path.join('openssl11', self.name.lower()))
+        elif LooseVersion(self.version) >= LooseVersion('3'):
+            # but version 3.x can be installed in 'include/openssl3/openssl' as well, for example in RHEL 8 derivatives
+            # prefer 'include/openssl' as long as the version of headers matches
+            ssl_include_subdirs.append(os.path.join('openssl3', self.name.lower()))
 
         ssl_include_dirs = [os.path.join(incd, subd) for incd in sys_include_dirs for subd in ssl_include_subdirs]
         ssl_include_dirs = [include for include in ssl_include_dirs if os.path.isdir(include)]

From a8fffcb6bf02220252248ee36f2e5e04d8ead544 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 May 2024 02:23:01 +0200
Subject: [PATCH 109/134] add non-standard binary name used by RHEL-based
 systems that install OpenSSL v3 alongside OpenSSL v1.1

---
 easybuild/easyblocks/o/openssl_wrapper.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 85f3a343b3..eed4ec76cf 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -294,6 +294,9 @@ def __init__(self, *args, **kwargs):
         if self.majmin_version == '1.1':
             # prefer 'openssl11' over 'openssl' with v1.1
             self.system_ssl['bin'] = which('openssl11')
+        elif LooseVersion(self.version) >= LooseVersion('3'):
+            # prefer 'openssl3' over 'openssl' with v3.x
+            self.system_ssl['bin'] = which('openssl3')
 
         if not self.system_ssl['bin']:
             self.system_ssl['bin'] = which('openssl')

From bf408fad7736fc349739501496011f5bff193005 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 May 2024 01:38:39 +0200
Subject: [PATCH 110/134] consider all versions found from strings in OpenSSL
 libraries and pick the highest one

---
 easybuild/easyblocks/o/openssl_wrapper.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index eed4ec76cf..8416f16ca4 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -180,8 +180,14 @@ def __init__(self, *args, **kwargs):
                         # filename lacks the full version, fallback to version strings within the library
                         solib_strings = read_file(system_solib, mode="rb").decode('utf-8', 'replace')
                         try:
-                            openssl_version = openssl_version_regex.search(solib_strings).group(1)
-                        except AttributeError:
+                            openssl_support_versions = openssl_version_regex.findall(solib_strings)
+                            openssl_support_versions.sort()
+                            dbg_msg = "System OpenSSL library '%s' supports versions: %s"
+                            dbg_msg_support_versions = ', '.join([''.join(v) for v in openssl_support_versions])
+                            self.log.debug(dbg_msg, system_solib, dbg_msg_support_versions)
+                            # pick highest supported version
+                            openssl_version = openssl_support_versions[-1][0]
+                        except IndexError:
                             dbg_msg = "Could not detect the full version of system OpenSSL library: %s"
                             self.log.debug(dbg_msg, system_solib)
                     # check that system version fulfills requirements

From a0d42f342d89e7d697e60927b4fb990816b463db Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 May 2024 02:00:10 +0200
Subject: [PATCH 111/134] simplify code checking OpenSSL system libraries

---
 easybuild/easyblocks/o/openssl_wrapper.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 8416f16ca4..2438a79e04 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -168,11 +168,13 @@ def __init__(self, *args, **kwargs):
 
         # Check the system libraries of OpenSSL
         # Find library file and compare its version string
+        target_system_ssl = {}
         for idx, solibs in enumerate(system_versioned_libs):
+            target_system_ssl['version'] = '0'
+            target_system_ssl['libs'] = []
             for solib in solibs:
                 system_solib = find_library_path(solib)
                 if system_solib:
-                    openssl_version = '0'
                     # get version of system library filename
                     try:
                         openssl_version = full_version_regex.search(os.path.realpath(system_solib)).group(0)
@@ -194,22 +196,21 @@ def __init__(self, *args, **kwargs):
                     if LooseVersion(openssl_version) >= LooseVersion(min_openssl_version):
                         dbg_msg = "System OpenSSL library '%s' with version %s fulfills requested version %s"
                         self.log.debug(dbg_msg, system_solib, openssl_version, min_openssl_version)
-                        self.system_ssl['libs'].append(system_solib)
+                        target_system_ssl['version'] = openssl_version
+                        target_system_ssl['libs'].append(system_solib)
                     else:
                         dbg_msg = "System OpenSSL library '%s' with version %s is older than requested version %s"
                         self.log.debug(dbg_msg, system_solib, openssl_version, min_openssl_version)
                 else:
                     # one of the OpenSSL libraries is missing, switch to next group of versioned libs
-                    self.system_ssl['libs'] = []
                     break
 
-            if len(self.system_ssl['libs']) == len(openssl_libs):
-                # keep these libraries as possible targets for this installation
-                target_system_ssl_libs = system_versioned_libs[idx]
+            if len(target_system_ssl['libs']) == len(openssl_libs):
+                # target libraries found, ignore further options
                 break
 
-        if len(self.system_ssl['libs']) == len(openssl_libs):
-            self.system_ssl['version'] = openssl_version
+        if len(target_system_ssl['libs']) == len(openssl_libs):
+            self.system_ssl.update(target_system_ssl)
             info_msg = "Found OpenSSL library version %s in host system: %s"
             self.log.info(info_msg, self.system_ssl['version'], os.path.dirname(self.system_ssl['libs'][0]))
         else:
@@ -314,7 +315,7 @@ def __init__(self, *args, **kwargs):
             return
 
         # system OpenSSL is fine, change target libraries to the ones found in it
-        self.target_ssl_libs = target_system_ssl_libs
+        self.target_ssl_libs = [os.path.basename(solib) for solib in target_system_ssl["libs"]]
         self.log.info("Target system OpenSSL libraries: %s", self.target_ssl_libs)
 
     def fetch_step(self, *args, **kwargs):

From c24b4f704ccaf3a16cce0788f89c1dc40383da8d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 May 2024 02:21:14 +0200
Subject: [PATCH 112/134] replace case insensitive pattern with corresponding
 flag in re.compile

---
 easybuild/easyblocks/o/openssl_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 2438a79e04..80d6bb6cd6 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -101,7 +101,7 @@ def __init__(self, *args, **kwargs):
 
         # Regex pattern to find version strings in OpenSSL libraries and headers
         full_version_regex = re.compile(r'[0-9]+\.[0-9]+\.[0-9]+[a-z]?')
-        openssl_version_regex = re.compile(r'(?i)OpenSSL[\s_]+([0-9]+\.[0-9]+(\.[0-9]+[a-z]?)*)', re.M)
+        openssl_version_regex = re.compile(r'OpenSSL[\s_]+([0-9]+\.[0-9]+(\.[0-9]+[a-z]?)*)', re.M | re.I)
 
         # Libraries packaged in OpenSSL
         openssl_libs = ['libssl', 'libcrypto']

From 40120e6c230bec7ed609cd9485b5486126b528ae Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 May 2024 02:28:06 +0200
Subject: [PATCH 113/134] system OpenSSL header version only needs to be higher
 than required minimum version in wrapper easyconfig

---
 easybuild/easyblocks/o/openssl_wrapper.py | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 80d6bb6cd6..ceddbfe430 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -270,17 +270,7 @@ def __init__(self, *args, **kwargs):
                     err_msg = "System OpenSSL header '%s' does not contain any recognizable version string"
                     raise EasyBuildError(err_msg, opensslv_path)
 
-                header_version_major = header_version.split('.')[0]
-                system_ssl_version_major = self.system_ssl['version'].split('.')[0]
-
-                # Compare only major version of header for OpenSSL 3+
-                # This is needed on Debian-based distros
-                if LooseVersion(self.version) >= LooseVersion('3'):
-                    header_found = (header_version_major == system_ssl_version_major)
-                else:
-                    header_found = (header_version == self.system_ssl['version'])
-
-                if header_found:
+                if LooseVersion(header_version) >= LooseVersion(min_openssl_version):
                     self.system_ssl['include'] = include_dir
                     info_msg = "Found OpenSSL headers v%s in host system: %s"
                     self.log.info(info_msg, header_version, self.system_ssl['include'])

From c5b86271aff049e5336be2d0046d234ef781dfd3 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 10:16:01 +0200
Subject: [PATCH 114/134] remove unused idx variable from OpenSSL wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index ceddbfe430..c213bea616 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -169,7 +169,7 @@ def __init__(self, *args, **kwargs):
         # Check the system libraries of OpenSSL
         # Find library file and compare its version string
         target_system_ssl = {}
-        for idx, solibs in enumerate(system_versioned_libs):
+        for solibs in system_versioned_libs:
             target_system_ssl['version'] = '0'
             target_system_ssl['libs'] = []
             for solib in solibs:

From b8c29bd13161d37bf7c032785a59c2dcfe75e8fa Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 10:17:54 +0200
Subject: [PATCH 115/134] hide pkg-config commands from trace output in OpenSSL
 wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index c213bea616..67ad2dede6 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -464,7 +464,7 @@ def install_pc_files(self):
                 # check suffixed names with v1.1
                 pc_name_suffix = pc_name + '11'
                 pc_exists_cmd = "pkg-config --exists %s" % pc_name_suffix
-                if run_cmd(pc_exists_cmd, simple=True, log_ok=False, log_all=False):
+                if run_cmd(pc_exists_cmd, simple=True, log_ok=False, log_all=False, trace=False):
                     self.log.info("%s exists", pc_name_suffix)
                     pc_name = pc_name_suffix
 
@@ -473,7 +473,7 @@ def install_pc_files(self):
             for require_type in ['Requires', 'Requires.private']:
                 require_print = require_type.lower().replace('.', '-')
                 pc_print_cmd = "pkg-config --print-%s %s" % (require_print, pc_name)
-                out, _ = run_cmd(pc_print_cmd, simple=False, log_ok=False)
+                out, _ = run_cmd(pc_print_cmd, simple=False, log_ok=False, trace=False)
                 self.log.info("Output of '%s': %s", pc_print_cmd, out)
 
                 if out:
@@ -494,12 +494,12 @@ def install_pc_files(self):
                 pc_file['cflags'] = "Cflags: -I${includedir}"
                 # infer private libs through pkg-config
                 pc_libs_cmd = "pkg-config --libs %s" % pc_name
-                out, _ = run_cmd(pc_libs_cmd, simple=False, log_ok=False)
+                out, _ = run_cmd(pc_libs_cmd, simple=False, log_ok=False, trace=False)
                 self.log.info("Output of '%s': %s", pc_libs_cmd, out)
                 linker_libs = out
 
                 pc_libs_static_cmd = "pkg-config --libs --static %s" % pc_name
-                out, _ = run_cmd(pc_libs_static_cmd, simple=False, log_ok=False)
+                out, _ = run_cmd(pc_libs_static_cmd, simple=False, log_ok=False, trace=False)
                 self.log.info("Output of '%s': %s", pc_libs_static_cmd, out)
 
                 libs_priv = "%s " % out.rstrip()

From 4073a3145b66fcf91c5f65f880798ef8f33343d2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 10:55:23 +0200
Subject: [PATCH 116/134] replace majmin_version with generation attribute in
 OpenSSL wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 34 ++++++++++-------------
 1 file changed, 14 insertions(+), 20 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 67ad2dede6..8a15528f2a 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -73,16 +73,15 @@ def __init__(self, *args, **kwargs):
         """Locate the installation files of OpenSSL in the host system"""
         super(EB_OpenSSL_wrapper, self).__init__(*args, **kwargs)
 
-        # Wrapper should have at least a major minor version numbers for OpenSSL before version 3+
-        if LooseVersion(self.version) >= LooseVersion('3') and self.version.count('.') == 0:
-            self.majmin_version = self.version
-        else:
+        if LooseVersion(self.version) < LooseVersion('2'):
             try:
                 subversions = self.version.split('.')
-                self.majmin_version = '%s.%s' % (subversions[0], subversions[1])
+                self.generation = '%s.%s' % (subversions[0], subversions[1])
             except (AttributeError, IndexError):
-                err_msg = "Wrapper OpenSSL version does not have any subversion: %s"
+                err_msg = "Wrapper for OpenSSL v1 version is missing a minor version: %s"
                 raise EasyBuildError(err_msg, self.version)
+        elif LooseVersion(self.version) < LooseVersion('4'):
+                self.generation = "3"
 
         # Set minimum OpenSSL version
         min_openssl_version = self.cfg.get('minimum_openssl_version')
@@ -117,10 +116,6 @@ def __init__(self, *args, **kwargs):
                 LINUX: ('so.1.1', ),
                 DARWIN: ('1.1.dylib', ),
             },
-            '3.0': {
-                LINUX: ('so.3', ),
-                DARWIN: ('3.dylib', ),
-            },
             '3': {
                 LINUX: ('so.3', ),
                 DARWIN: ('3.dylib', ),
@@ -128,16 +123,16 @@ def __init__(self, *args, **kwargs):
         }
 
         os_type = get_os_type()
-        if self.majmin_version in openssl_libext and os_type in openssl_libext[self.majmin_version]:
+        if self.generation in openssl_libext and os_type in openssl_libext[self.generation]:
             # generate matrix of versioned .so filenames
             system_versioned_libs = [
                 ['%s.%s' % (lib, ext) for lib in openssl_libs]
-                for ext in openssl_libext[self.majmin_version][os_type]
+                for ext in openssl_libext[self.generation][os_type]
             ]
             self.log.info("Matrix of version library names: %s", system_versioned_libs)
         else:
-            err_msg = "Don't know name of OpenSSL system library for version %s and OS type %s"
-            raise EasyBuildError(err_msg, self.majmin_version, os_type)
+            err_msg = "OpenSSL system library for version %s and OS type %s is unsupported"
+            raise EasyBuildError(err_msg, self.generation, os_type)
 
         # by default target the first option of each OpenSSL library,
         # which corresponds to installation from source
@@ -148,10 +143,9 @@ def __init__(self, *args, **kwargs):
         openssl_engines = {
             '1.0': 'engines',
             '1.1': 'engines-1.1',
-            '3.0': 'engines-3',
             '3': 'engines-3',
         }
-        self.target_ssl_engine = openssl_engines[self.majmin_version]
+        self.target_ssl_engine = openssl_engines[self.generation]
 
         # Paths to system libraries and headers of OpenSSL
         self.system_ssl = {
@@ -245,11 +239,11 @@ def __init__(self, *args, **kwargs):
 
         # headers are located in 'include/openssl' by default
         ssl_include_subdirs = ['openssl']
-        if self.majmin_version == '1.1':
+        if self.generation == '1.1':
             # but version 1.1 can be installed in 'include/openssl11/openssl' as well, for example in CentOS 7
             # prefer 'include/openssl' as long as the version of headers matches
             ssl_include_subdirs.append(os.path.join('openssl11', self.name.lower()))
-        elif LooseVersion(self.version) >= LooseVersion('3'):
+        elif self.generation == '3':
             # but version 3.x can be installed in 'include/openssl3/openssl' as well, for example in RHEL 8 derivatives
             # prefer 'include/openssl' as long as the version of headers matches
             ssl_include_subdirs.append(os.path.join('openssl3', self.name.lower()))
@@ -408,7 +402,7 @@ def sanity_check_step(self):
 
         custom_commands = [
             # make sure that version mentioned in output of 'openssl version' matches version we are using
-            "ssl_ver=$(openssl version); [ ${ssl_ver:8:%s} == '%s' ]" % (ssl_ver_comp_chars, self.majmin_version),
+            "ssl_ver=$(openssl version); [ ${ssl_ver:8:%s} == '%s' ]" % (ssl_ver_comp_chars, self.generation),
             ("echo | openssl s_client%s -connect github.com:443 -verify 9 "
              "| grep 'Verify return code: 0 (ok)'" % proxy_arg),
         ]
@@ -460,7 +454,7 @@ def install_pc_files(self):
 
             # component name in system pkg-config
             pc_name = pc_comp
-            if self.majmin_version == '1.1':
+            if self.generation == '1.1':
                 # check suffixed names with v1.1
                 pc_name_suffix = pc_name + '11'
                 pc_exists_cmd = "pkg-config --exists %s" % pc_name_suffix

From 2d73932cc0117afb7613541d6ba88959b248736c Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 10:59:14 +0200
Subject: [PATCH 117/134] fix error message on failed header version check in
 OpenSSL wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 8a15528f2a..ee97a3040b 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -270,8 +270,8 @@ def __init__(self, *args, **kwargs):
                     self.log.info(info_msg, header_version, self.system_ssl['include'])
                     break
                 else:
-                    dbg_msg = "System OpenSSL header version '%s' does not match library version '%s'"
-                    self.log.debug(dbg_msg, header_version, self.system_ssl['version'])
+                    dbg_msg = "System OpenSSL header version '%s' does not fulfill minimum version requirement '%s'"
+                    self.log.debug(dbg_msg, header_version, min_openssl_version)
             else:
                 self.log.info("System OpenSSL header file %s not found", opensslv_path)
 

From 476a7da99e5ef44433e4ce738fa46a288027722b Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 11:40:48 +0200
Subject: [PATCH 118/134] check openssl executable version at detection time in
 OpenSSL wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 41 +++++++++++++++++------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index ee97a3040b..26a1fdaa74 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -282,20 +282,22 @@ def __init__(self, *args, **kwargs):
             raise EasyBuildError(err_msg, self.version, self.system_ssl['version'])
 
         # Check system OpenSSL binary
-        if self.majmin_version == '1.1':
-            # prefer 'openssl11' over 'openssl' with v1.1
-            self.system_ssl['bin'] = which('openssl11')
-        elif LooseVersion(self.version) >= LooseVersion('3'):
-            # prefer 'openssl3' over 'openssl' with v3.x
-            self.system_ssl['bin'] = which('openssl3')
+        target_ssl_bins = ['openssl']
+        if self.generation == '1.1':
+            target_ssl_bins.insert(0, 'openssl11')  # prefer 'openssl11' over 'openssl' with v1.1
+        elif self.generation == '3':
+            target_ssl_bins.insert(0, 'openssl3')  # prefer 'openssl3' over 'openssl' with v3
 
-        if not self.system_ssl['bin']:
-            self.system_ssl['bin'] = which('openssl')
+        for target_bin in target_ssl_bins:
+            target_bin_path, target_bin_version = self.get_openssl_bin_version(target_bin)
+            if target_bin_version == self.system_ssl['version']:
+                self.system_ssl['bin'] = target_bin_path
+                break
 
         if self.system_ssl['bin']:
-            self.log.info("System OpenSSL binary found: %s", self.system_ssl['bin'])
+            self.log.info("System OpenSSL binary for version %s found: %s", self.system_ssl['version'], self.system_ssl['bin'])
         else:
-            self.log.info("System OpenSSL binary not found!")
+            self.log.info("System OpenSSL binary for version %s not found!", self.system_ssl['version'])
             return
 
         # system OpenSSL is fine, change target libraries to the ones found in it
@@ -409,6 +411,25 @@ def sanity_check_step(self):
 
         super(Bundle, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
 
+    def get_openssl_bin_version(self, bin_name):
+        """Check OpenSSL executable version"""
+        bin_path = which(bin_name)
+        if not bin_path:
+            self.log.debug("OpenSSL executable '%s' not found", bin_name)
+            return None, None
+
+        cmd = "%s version" % bin_path
+        out, _ = run_cmd(cmd, simple=False, log_ok=False, trace=False)
+
+        try:
+            bin_version = out.split(' ')[1]
+        except (AttributeError, IndexError):
+            raise EasyBuildError("Failed to check version of OpenSSL executable: %s", bin_path)
+        else:
+            self.log.debug("Version of OpenSSL executable '%s': %s", bin_path, bin_version)
+
+        return bin_path, bin_version
+
     def install_pc_files(self):
         """Install pkg-config files for the wrapper"""
 

From f54a5fb8dab0b20c16c89aea88ca6fa92fe529fa Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 11:48:14 +0200
Subject: [PATCH 119/134] use pattern matching to sanity check version of
 openssl executbale in OpenSSL wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 26a1fdaa74..1359e33857 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -397,14 +397,9 @@ def sanity_check_step(self):
             if proxy_parsed.netloc:
                 proxy_arg = ' -proxy %s' % proxy_parsed.netloc
 
-        if LooseVersion(self.version) >= LooseVersion('3') and self.version.count('.') == 0:
-            ssl_ver_comp_chars = 1
-        else:
-            ssl_ver_comp_chars = 3
-
         custom_commands = [
             # make sure that version mentioned in output of 'openssl version' matches version we are using
-            "ssl_ver=$(openssl version); [ ${ssl_ver:8:%s} == '%s' ]" % (ssl_ver_comp_chars, self.generation),
+            '[[ "$(openssl version)" =~ ^OpenSSL.%s ]]' % self.generation,
             ("echo | openssl s_client%s -connect github.com:443 -verify 9 "
              "| grep 'Verify return code: 0 (ok)'" % proxy_arg),
         ]

From bc1acde23b059f308a73685d94d8325577518d50 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 11:54:34 +0200
Subject: [PATCH 120/134] fix codestyle issues in OpenSSL wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 1359e33857..ad33adba2e 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -81,7 +81,7 @@ def __init__(self, *args, **kwargs):
                 err_msg = "Wrapper for OpenSSL v1 version is missing a minor version: %s"
                 raise EasyBuildError(err_msg, self.version)
         elif LooseVersion(self.version) < LooseVersion('4'):
-                self.generation = "3"
+            self.generation = "3"
 
         # Set minimum OpenSSL version
         min_openssl_version = self.cfg.get('minimum_openssl_version')
@@ -295,7 +295,8 @@ def __init__(self, *args, **kwargs):
                 break
 
         if self.system_ssl['bin']:
-            self.log.info("System OpenSSL binary for version %s found: %s", self.system_ssl['version'], self.system_ssl['bin'])
+            log_msg = "System OpenSSL binary for version %s found: %s"
+            self.log.info(log_msg, self.system_ssl['version'], self.system_ssl['bin'])
         else:
             self.log.info("System OpenSSL binary for version %s not found!", self.system_ssl['version'])
             return

From b0cbd354f0cc574eb6080037b26c100dd7562593 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 17:01:28 +0200
Subject: [PATCH 121/134] define version of OpenSSL wrapper from executable and
 allow mismatch between components

---
 easybuild/easyblocks/o/openssl_wrapper.py | 68 +++++++++++------------
 1 file changed, 33 insertions(+), 35 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index ad33adba2e..082fdaa09b 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -162,51 +162,48 @@ def __init__(self, *args, **kwargs):
 
         # Check the system libraries of OpenSSL
         # Find library file and compare its version string
-        target_system_ssl = {}
         for solibs in system_versioned_libs:
-            target_system_ssl['version'] = '0'
-            target_system_ssl['libs'] = []
+            target_ssl_libs = []
             for solib in solibs:
                 system_solib = find_library_path(solib)
-                if system_solib:
+                if not system_solib:
+                    # this OpenSSL library is missing, move on to next group of versioned libs
+                    break
+
+                try:
                     # get version of system library filename
+                    ssl_lib_version = full_version_regex.search(os.path.realpath(system_solib)).group(0)
+                except AttributeError:
+                    # filename lacks the full version, fallback to version strings within the library
+                    solib_strings = read_file(system_solib, mode="rb").decode('utf-8', 'replace')
                     try:
-                        openssl_version = full_version_regex.search(os.path.realpath(system_solib)).group(0)
-                    except AttributeError:
-                        # filename lacks the full version, fallback to version strings within the library
-                        solib_strings = read_file(system_solib, mode="rb").decode('utf-8', 'replace')
-                        try:
-                            openssl_support_versions = openssl_version_regex.findall(solib_strings)
-                            openssl_support_versions.sort()
-                            dbg_msg = "System OpenSSL library '%s' supports versions: %s"
-                            dbg_msg_support_versions = ', '.join([''.join(v) for v in openssl_support_versions])
-                            self.log.debug(dbg_msg, system_solib, dbg_msg_support_versions)
-                            # pick highest supported version
-                            openssl_version = openssl_support_versions[-1][0]
-                        except IndexError:
-                            dbg_msg = "Could not detect the full version of system OpenSSL library: %s"
-                            self.log.debug(dbg_msg, system_solib)
-                    # check that system version fulfills requirements
-                    if LooseVersion(openssl_version) >= LooseVersion(min_openssl_version):
-                        dbg_msg = "System OpenSSL library '%s' with version %s fulfills requested version %s"
-                        self.log.debug(dbg_msg, system_solib, openssl_version, min_openssl_version)
-                        target_system_ssl['version'] = openssl_version
-                        target_system_ssl['libs'].append(system_solib)
-                    else:
-                        dbg_msg = "System OpenSSL library '%s' with version %s is older than requested version %s"
-                        self.log.debug(dbg_msg, system_solib, openssl_version, min_openssl_version)
+                        ssl_lib_support_versions = openssl_version_regex.findall(solib_strings)
+                        ssl_lib_support_versions.sort()
+                        dbg_msg = "System OpenSSL library '%s' supports versions: %s"
+                        dbg_msg_support_versions = ', '.join([''.join(v) for v in ssl_lib_support_versions])
+                        self.log.debug(dbg_msg, system_solib, dbg_msg_support_versions)
+                        # pick highest supported version
+                        ssl_lib_version = ssl_lib_support_versions[-1][0]
+                    except IndexError:
+                        dbg_msg = "Could not detect the full version of system OpenSSL library: %s"
+                        self.log.debug(dbg_msg, system_solib)
+                # check that system library version fulfills requirements
+                if LooseVersion(ssl_lib_version) >= LooseVersion(min_openssl_version):
+                    dbg_msg = "System OpenSSL library '%s' with version %s fulfills requested version %s"
+                    self.log.debug(dbg_msg, system_solib, ssl_lib_version, min_openssl_version)
+                    target_ssl_libs.append(system_solib)
                 else:
-                    # one of the OpenSSL libraries is missing, switch to next group of versioned libs
-                    break
+                    dbg_msg = "System OpenSSL library '%s' with version %s is older than requested version %s"
+                    self.log.debug(dbg_msg, system_solib, ssl_lib_version, min_openssl_version)
 
-            if len(target_system_ssl['libs']) == len(openssl_libs):
+            if len(target_ssl_libs) == len(openssl_libs):
                 # target libraries found, ignore further options
                 break
 
-        if len(target_system_ssl['libs']) == len(openssl_libs):
-            self.system_ssl.update(target_system_ssl)
+        if len(target_ssl_libs) == len(openssl_libs):
+            self.system_ssl['libs'] = target_ssl_libs
             info_msg = "Found OpenSSL library version %s in host system: %s"
-            self.log.info(info_msg, self.system_ssl['version'], os.path.dirname(self.system_ssl['libs'][0]))
+            self.log.info(info_msg, ssl_lib_version, os.path.dirname(self.system_ssl['libs'][0]))
         else:
             self.log.info("OpenSSL library not found in host system, falling back to OpenSSL in EasyBuild")
             return
@@ -290,7 +287,8 @@ def __init__(self, *args, **kwargs):
 
         for target_bin in target_ssl_bins:
             target_bin_path, target_bin_version = self.get_openssl_bin_version(target_bin)
-            if target_bin_version == self.system_ssl['version']:
+            if LooseVersion(target_bin_version) >= LooseVersion(min_openssl_version):
+                self.system_ssl['version'] = target_bin_version
                 self.system_ssl['bin'] = target_bin_path
                 break
 

From e40f78e7ee03dc1e5eaf477bf00ca016a5f650c7 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 18:06:59 +0200
Subject: [PATCH 122/134] define maximum version for OpenSSL wrapper and start
 with executable detection

---
 easybuild/easyblocks/o/openssl_wrapper.py | 115 +++++++++++-----------
 1 file changed, 58 insertions(+), 57 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index 082fdaa09b..ebc1cf2e7e 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -84,19 +84,23 @@ def __init__(self, *args, **kwargs):
             self.generation = "3"
 
         # Set minimum OpenSSL version
-        min_openssl_version = self.cfg.get('minimum_openssl_version')
-
-        if not min_openssl_version:
-            min_openssl_version = self.version
-        elif not isinstance(min_openssl_version, string_type):
-            min_openssl_version = str(min_openssl_version)
-
+        self.min_version = self.cfg.get('minimum_openssl_version')
+        if not self.min_version:
+            self.min_version = self.version
+        elif not isinstance(self.min_version, string_type):
+            self.min_version = str(self.min_version)
         # Minimum OpenSSL version can only increase depth of wrapper version
-        if min_openssl_version.startswith(self.version):
-            self.log.debug("Requiring minimum OpenSSL version: %s", min_openssl_version)
+        if self.min_version.startswith(self.version):
+            self.log.debug("Requiring minimum OpenSSL version: %s", self.min_version)
         else:
             err_msg = "Requested minimum OpenSSL version '%s' does not fit in wrapper easyconfig version '%s'"
-            raise EasyBuildError(err_msg, min_openssl_version, self.version)
+            raise EasyBuildError(err_msg, self.min_version, self.version)
+
+        # Set maximum OpenSSL version (increase smallest revision by 1)
+        max_version_parts = [int(subv) for subv in self.version.split('.')]
+        max_version_parts[-1] += 1
+        self.max_version = '.'.join([str(subv) for subv in max_version_parts])
+        self.log.debug("Restricting maximum OpenSSL version: %s", self.max_version)
 
         # Regex pattern to find version strings in OpenSSL libraries and headers
         full_version_regex = re.compile(r'[0-9]+\.[0-9]+\.[0-9]+[a-z]?')
@@ -134,20 +138,14 @@ def __init__(self, *args, **kwargs):
             err_msg = "OpenSSL system library for version %s and OS type %s is unsupported"
             raise EasyBuildError(err_msg, self.generation, os_type)
 
-        # by default target the first option of each OpenSSL library,
-        # which corresponds to installation from source
-        self.target_ssl_libs = system_versioned_libs[0]
-        self.log.info("Target OpenSSL libraries: %s", self.target_ssl_libs)
-
         # folders containing engines libraries
         openssl_engines = {
             '1.0': 'engines',
             '1.1': 'engines-1.1',
             '3': 'engines-3',
         }
-        self.target_ssl_engine = openssl_engines[self.generation]
 
-        # Paths to system libraries and headers of OpenSSL
+        # Paths to system components of OpenSSL
         self.system_ssl = {
             'bin': None,
             'engines': None,
@@ -160,6 +158,30 @@ def __init__(self, *args, **kwargs):
             self.log.info("Not wrapping system OpenSSL installation by user request")
             return
 
+        # Check system OpenSSL binary
+        target_ssl_bins = ['openssl']
+        if self.generation == '1.1':
+            target_ssl_bins.insert(0, 'openssl11')  # prefer 'openssl11' over 'openssl' with v1.1
+        elif self.generation == '3':
+            target_ssl_bins.insert(0, 'openssl3')  # prefer 'openssl3' over 'openssl' with v3
+
+        for ssl_bin in target_ssl_bins:
+            ssl_bin_path, ssl_bin_version = self.get_openssl_bin_version(ssl_bin)
+            if ssl_bin_path:
+                if LooseVersion(self.min_version) <= LooseVersion(ssl_bin_version) < LooseVersion(self.max_version):
+                    self.system_ssl['version'] = ssl_bin_version
+                    self.system_ssl['bin'] = ssl_bin_path
+                    break
+
+        if self.system_ssl['bin'] and self.system_ssl['version']:
+            log_msg = "System OpenSSL binary for version %s found: %s"
+            self.log.info(log_msg, self.system_ssl['version'], self.system_ssl['bin'])
+        else:
+            log_msg = "OpenSSL binary for version %s not found in host system! "
+            log_msg += "Falling back to building OpenSSL from source"
+            self.log.info(log_msg, self.version)
+            return
+
         # Check the system libraries of OpenSSL
         # Find library file and compare its version string
         for solibs in system_versioned_libs:
@@ -188,13 +210,13 @@ def __init__(self, *args, **kwargs):
                         dbg_msg = "Could not detect the full version of system OpenSSL library: %s"
                         self.log.debug(dbg_msg, system_solib)
                 # check that system library version fulfills requirements
-                if LooseVersion(ssl_lib_version) >= LooseVersion(min_openssl_version):
+                if LooseVersion(self.min_version) <= LooseVersion(ssl_lib_version) < LooseVersion(self.max_version):
                     dbg_msg = "System OpenSSL library '%s' with version %s fulfills requested version %s"
-                    self.log.debug(dbg_msg, system_solib, ssl_lib_version, min_openssl_version)
+                    self.log.debug(dbg_msg, system_solib, ssl_lib_version, self.min_version)
                     target_ssl_libs.append(system_solib)
                 else:
                     dbg_msg = "System OpenSSL library '%s' with version %s is older than requested version %s"
-                    self.log.debug(dbg_msg, system_solib, ssl_lib_version, min_openssl_version)
+                    self.log.debug(dbg_msg, system_solib, ssl_lib_version, self.min_version)
 
             if len(target_ssl_libs) == len(openssl_libs):
                 # target libraries found, ignore further options
@@ -205,14 +227,16 @@ def __init__(self, *args, **kwargs):
             info_msg = "Found OpenSSL library version %s in host system: %s"
             self.log.info(info_msg, ssl_lib_version, os.path.dirname(self.system_ssl['libs'][0]))
         else:
-            self.log.info("OpenSSL library not found in host system, falling back to OpenSSL in EasyBuild")
+            log_msg = "OpenSSL library for version %s not found in host system! "
+            log_msg += "Falling back to building OpenSSL from source"
+            self.log.info(log_msg, self.system_ssl['version'])
             return
 
         # Directory with engine libraries
         lib_dir = os.path.dirname(self.system_ssl['libs'][0])
         lib_engines_dir = [
-            os.path.join(lib_dir, 'openssl', self.target_ssl_engine),
-            os.path.join(lib_dir, self.target_ssl_engine),
+            os.path.join(lib_dir, 'openssl', openssl_engines[self.generation]),
+            os.path.join(lib_dir, openssl_engines[self.generation]),
         ]
 
         for engines_path in lib_engines_dir:
@@ -222,7 +246,9 @@ def __init__(self, *args, **kwargs):
                 break
 
         if not self.system_ssl['engines']:
-            self.log.info("OpenSSL engines not found in host system, falling back to OpenSSL in EasyBuild")
+            log_msg = "OpenSSL engines for version %s not found in host system! "
+            log_msg += "Falling back to building OpenSSL from source"
+            self.log.info(log_msg, self.system_ssl['version'])
             return
 
         # Check system include paths for OpenSSL headers
@@ -256,19 +282,19 @@ def __init__(self, *args, **kwargs):
                 # check version reported by opensslv.h
                 opensslv = read_file(opensslv_path)
                 try:
-                    header_version = openssl_version_regex.search(opensslv).group(1)
+                    ssl_head_version = openssl_version_regex.search(opensslv).group(1)
                 except AttributeError:
                     err_msg = "System OpenSSL header '%s' does not contain any recognizable version string"
                     raise EasyBuildError(err_msg, opensslv_path)
 
-                if LooseVersion(header_version) >= LooseVersion(min_openssl_version):
+                if LooseVersion(self.min_version) <= LooseVersion(ssl_head_version) < LooseVersion(self.max_version):
                     self.system_ssl['include'] = include_dir
                     info_msg = "Found OpenSSL headers v%s in host system: %s"
-                    self.log.info(info_msg, header_version, self.system_ssl['include'])
+                    self.log.info(info_msg, ssl_head_version, self.system_ssl['include'])
                     break
                 else:
                     dbg_msg = "System OpenSSL header version '%s' does not fulfill minimum version requirement '%s'"
-                    self.log.debug(dbg_msg, header_version, min_openssl_version)
+                    self.log.debug(dbg_msg, ssl_head_version, self.min_version)
             else:
                 self.log.info("System OpenSSL header file %s not found", opensslv_path)
 
@@ -278,31 +304,6 @@ def __init__(self, *args, **kwargs):
                        "source in EasyBuild by setting 'wrap_system_openssl = False' in the OpenSSL easyconfig.")
             raise EasyBuildError(err_msg, self.version, self.system_ssl['version'])
 
-        # Check system OpenSSL binary
-        target_ssl_bins = ['openssl']
-        if self.generation == '1.1':
-            target_ssl_bins.insert(0, 'openssl11')  # prefer 'openssl11' over 'openssl' with v1.1
-        elif self.generation == '3':
-            target_ssl_bins.insert(0, 'openssl3')  # prefer 'openssl3' over 'openssl' with v3
-
-        for target_bin in target_ssl_bins:
-            target_bin_path, target_bin_version = self.get_openssl_bin_version(target_bin)
-            if LooseVersion(target_bin_version) >= LooseVersion(min_openssl_version):
-                self.system_ssl['version'] = target_bin_version
-                self.system_ssl['bin'] = target_bin_path
-                break
-
-        if self.system_ssl['bin']:
-            log_msg = "System OpenSSL binary for version %s found: %s"
-            self.log.info(log_msg, self.system_ssl['version'], self.system_ssl['bin'])
-        else:
-            self.log.info("System OpenSSL binary for version %s not found!", self.system_ssl['version'])
-            return
-
-        # system OpenSSL is fine, change target libraries to the ones found in it
-        self.target_ssl_libs = [os.path.basename(solib) for solib in target_system_ssl["libs"]]
-        self.log.info("Target system OpenSSL libraries: %s", self.target_ssl_libs)
-
     def fetch_step(self, *args, **kwargs):
         """Fetch sources if OpenSSL component is needed"""
         if not all(self.system_ssl[key] for key in ('bin', 'engines', 'include', 'libs')):
@@ -370,15 +371,15 @@ def sanity_check_step(self):
         """Custom sanity check for OpenSSL wrapper."""
         shlib_ext = get_shared_lib_ext()
 
-        ssl_libs = ['%s.%s' % (libso.split('.')[0], shlib_ext) for libso in self.target_ssl_libs]
-        ssl_libs.extend(self.target_ssl_libs)
+        ssl_libs = [os.path.basename(solib) for solib in self.system_ssl["libs"]]
+        ssl_libs.extend(['%s.%s' % (solib.split('.')[0], shlib_ext) for solib in ssl_libs])
 
         ssl_files = [os.path.join('bin', self.name.lower())]
         ssl_files.extend(os.path.join('lib', libso) for libso in ssl_libs)
 
         ssl_dirs = [
             os.path.join('include', self.name.lower()),
-            os.path.join('lib', self.target_ssl_engine),
+            os.path.join('lib', os.path.basename(self.system_ssl["engines"])),
             os.path.join('lib', 'pkgconfig'),
         ]
 
@@ -444,7 +445,7 @@ def install_pc_files(self):
             'libcrypto': {
                 'name': 'OpenSSL-libcrypto',
                 'description': 'OpenSSL cryptography library',
-                'enginesdir': self.target_ssl_engine,
+                'enginesdir': os.path.basename(self.system_ssl["engines"]),
             },
             'libssl': {
                 'name': 'OpenSSL-libssl',

From 48bc68d276cbf60f730813b09431d23e85397a3a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 18:47:35 +0200
Subject: [PATCH 123/134] define target components per generation in OpenSSL
 wrapper

---
 easybuild/easyblocks/o/openssl_wrapper.py | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index ebc1cf2e7e..d758d684a0 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -145,6 +145,14 @@ def __init__(self, *args, **kwargs):
             '3': 'engines-3',
         }
 
+        # Define targets for this generation
+        # They are used to sanity check both installations from source or wrappers
+        self.generation_targets = {
+            'bin': 'openssl',
+            'engines': openssl_engines[self.generation],
+            'libs': system_versioned_libs[0],  # first set of libs match source installs
+        }
+
         # Paths to system components of OpenSSL
         self.system_ssl = {
             'bin': None,
@@ -224,6 +232,7 @@ def __init__(self, *args, **kwargs):
 
         if len(target_ssl_libs) == len(openssl_libs):
             self.system_ssl['libs'] = target_ssl_libs
+            self.generation_targets['libs'] = [os.path.basename(solib) for solib in target_ssl_libs]
             info_msg = "Found OpenSSL library version %s in host system: %s"
             self.log.info(info_msg, ssl_lib_version, os.path.dirname(self.system_ssl['libs'][0]))
         else:
@@ -371,15 +380,15 @@ def sanity_check_step(self):
         """Custom sanity check for OpenSSL wrapper."""
         shlib_ext = get_shared_lib_ext()
 
-        ssl_libs = [os.path.basename(solib) for solib in self.system_ssl["libs"]]
-        ssl_libs.extend(['%s.%s' % (solib.split('.')[0], shlib_ext) for solib in ssl_libs])
+        ssl_libs = ['%s.%s' % (solib.split('.')[0], shlib_ext) for solib in self.generation_targets['libs']]
+        ssl_libs.extend(self.generation_targets['libs'])
 
         ssl_files = [os.path.join('bin', self.name.lower())]
         ssl_files.extend(os.path.join('lib', libso) for libso in ssl_libs)
 
         ssl_dirs = [
             os.path.join('include', self.name.lower()),
-            os.path.join('lib', os.path.basename(self.system_ssl["engines"])),
+            os.path.join('lib', self.generation_targets["engines"]),
             os.path.join('lib', 'pkgconfig'),
         ]
 
@@ -445,7 +454,7 @@ def install_pc_files(self):
             'libcrypto': {
                 'name': 'OpenSSL-libcrypto',
                 'description': 'OpenSSL cryptography library',
-                'enginesdir': os.path.basename(self.system_ssl["engines"]),
+                'enginesdir': self.generation_targets["engines"],
             },
             'libssl': {
                 'name': 'OpenSSL-libssl',

From 3128f50e721513ddb3cd53d5e9c05617a5fedd89 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 29 May 2024 18:55:29 +0200
Subject: [PATCH 124/134] use generation target to detect and sanity check
 OpenSSL executable

---
 easybuild/easyblocks/o/openssl_wrapper.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index d758d684a0..d776c43a02 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -167,7 +167,7 @@ def __init__(self, *args, **kwargs):
             return
 
         # Check system OpenSSL binary
-        target_ssl_bins = ['openssl']
+        target_ssl_bins = [self.generation_targets['bin']]
         if self.generation == '1.1':
             target_ssl_bins.insert(0, 'openssl11')  # prefer 'openssl11' over 'openssl' with v1.1
         elif self.generation == '3':
@@ -383,7 +383,7 @@ def sanity_check_step(self):
         ssl_libs = ['%s.%s' % (solib.split('.')[0], shlib_ext) for solib in self.generation_targets['libs']]
         ssl_libs.extend(self.generation_targets['libs'])
 
-        ssl_files = [os.path.join('bin', self.name.lower())]
+        ssl_files = [os.path.join('bin', self.generation_targets['bin'])]
         ssl_files.extend(os.path.join('lib', libso) for libso in ssl_libs)
 
         ssl_dirs = [

From de01fd1fbdf5369ec6caa6a3ace0119c072e1ed1 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 31 May 2024 15:30:42 +0200
Subject: [PATCH 125/134] fix issue 3345

---
 easybuild/easyblocks/i/intel_compilers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/i/intel_compilers.py b/easybuild/easyblocks/i/intel_compilers.py
index c3fce10a99..f633fc4657 100644
--- a/easybuild/easyblocks/i/intel_compilers.py
+++ b/easybuild/easyblocks/i/intel_compilers.py
@@ -177,7 +177,7 @@ def make_module_extra(self):
         multiarch_out, ec = run_cmd("gcc -print-multiarch", simple=False)
         multiarch_out = multiarch_out.strip()
         if ec == 0 and multiarch_out:
-            multiarch_inc_dir, ec = run_cmd("gcc -E -Wp,-v -xc /dev/null 2>&1 | grep %s$" % multiarch_out)
+            multiarch_inc_dir, ec = run_cmd("gcc -E -Wp,-v -xc /dev/null 2>&1 | grep %s$ | grep -v GCCcore" % multiarch_out)
             if ec == 0 and multiarch_inc_dir:
                 multiarch_inc_dir = multiarch_inc_dir.strip()
                 self.log.info("Adding multiarch include path %s to $CPATH in generated module file", multiarch_inc_dir)

From 2b207a22eee8028bcb568b8d05b9ca28546229a0 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 31 May 2024 15:34:37 +0200
Subject: [PATCH 126/134] fix too long line

---
 easybuild/easyblocks/i/intel_compilers.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/i/intel_compilers.py b/easybuild/easyblocks/i/intel_compilers.py
index f633fc4657..383018ede2 100644
--- a/easybuild/easyblocks/i/intel_compilers.py
+++ b/easybuild/easyblocks/i/intel_compilers.py
@@ -177,7 +177,8 @@ def make_module_extra(self):
         multiarch_out, ec = run_cmd("gcc -print-multiarch", simple=False)
         multiarch_out = multiarch_out.strip()
         if ec == 0 and multiarch_out:
-            multiarch_inc_dir, ec = run_cmd("gcc -E -Wp,-v -xc /dev/null 2>&1 | grep %s$ | grep -v GCCcore" % multiarch_out)
+            multi_arch_inc_dir_cmd = "gcc -E -Wp,-v -xc /dev/null 2>&1 | grep %s$ | grep -v GCCcore" % multiarch_out
+            multiarch_inc_dir, ec = run_cmd(multi_arch_inc_dir_cmd)
             if ec == 0 and multiarch_inc_dir:
                 multiarch_inc_dir = multiarch_inc_dir.strip()
                 self.log.info("Adding multiarch include path %s to $CPATH in generated module file", multiarch_inc_dir)

From 81b4294a2b8a9f2fedf90488ce246fc9a5f639b2 Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Fri, 31 May 2024 15:44:00 +0000
Subject: [PATCH 127/134] Allow external PRRTE in openmpi easyblock

---
 easybuild/easyblocks/o/openmpi.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/o/openmpi.py b/easybuild/easyblocks/o/openmpi.py
index 8460aad58a..e8261d0ca3 100644
--- a/easybuild/easyblocks/o/openmpi.py
+++ b/easybuild/easyblocks/o/openmpi.py
@@ -72,6 +72,8 @@ def config_opt_used(key, enable_opt=False):
         known_dependencies = ['CUDA', 'hwloc', 'libevent', 'libfabric', 'PMIx', 'UCX']
         if LooseVersion(self.version) >= '4.1.4':
             known_dependencies.append('UCC')
+        if LooseVersion(self.version) >= '5.0.0':
+            known_dependencies.append('PRRTE')
 
         # Value to use for `--with-<dep>=<value>` if the dependency is not specified in the easyconfig
         # No entry is interpreted as no option added at all
@@ -85,6 +87,8 @@ def config_opt_used(key, enable_opt=False):
             # For these the default is to use an internal copy and not using any is not supported
             for dep in ('hwloc', 'libevent', 'PMIx'):
                 unused_dep_value[dep] = 'internal'
+            if LooseVersion(self.version) >= '5.0.0':
+                unused_dep_value['PRRTE'] = 'internal'
 
         # handle dependencies
         for dep in known_dependencies:
@@ -165,7 +169,8 @@ def sanity_check_step(self):
 
         bin_names = ['mpicc', 'mpicxx', 'mpif90', 'mpifort', 'mpirun', 'ompi_info', 'opal_wrapper']
         if LooseVersion(self.version) >= LooseVersion('5.0.0'):
-            bin_names.append('prterun')
+            if not get_software_root('PRRTE'):
+                bin_names.append('prterun')
         else:
             bin_names.append('orterun')
         bin_files = [os.path.join('bin', x) for x in bin_names]
@@ -173,13 +178,14 @@ def sanity_check_step(self):
         shlib_ext = get_shared_lib_ext()
         lib_names = ['mpi_mpifh', 'mpi', 'open-pal']
         if LooseVersion(self.version) >= LooseVersion('5.0.0'):
-            lib_names.append('prrte')
+            if not get_software_root('PRRTE'):
+                lib_names.append('prrte')
         else:
             lib_names.extend(['ompitrace', 'open-rte'])
         lib_files = [os.path.join('lib', 'lib%s.%s' % (x, shlib_ext)) for x in lib_names]
 
         inc_names = ['mpi-ext', 'mpif-config', 'mpif', 'mpi', 'mpi_portable_platform']
-        if LooseVersion(self.version) >= LooseVersion('5.0.0'):
+        if LooseVersion(self.version) >= LooseVersion('5.0.0') and not get_software_root('PRRTE'):
             inc_names.append('prte')
         inc_files = [os.path.join('include', x + '.h') for x in inc_names]
 

From ac25414e706a9ca5ed39af8e516d797340d89824 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 7 Jun 2024 15:03:49 +0200
Subject: [PATCH 128/134] intel_compilers.py: use grep -v /include-fixed/
 instead of GCCcore to filter out unwanted include path.

---
 easybuild/easyblocks/i/intel_compilers.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/i/intel_compilers.py b/easybuild/easyblocks/i/intel_compilers.py
index 383018ede2..a9c49d04e1 100644
--- a/easybuild/easyblocks/i/intel_compilers.py
+++ b/easybuild/easyblocks/i/intel_compilers.py
@@ -177,7 +177,11 @@ def make_module_extra(self):
         multiarch_out, ec = run_cmd("gcc -print-multiarch", simple=False)
         multiarch_out = multiarch_out.strip()
         if ec == 0 and multiarch_out:
-            multi_arch_inc_dir_cmd = "gcc -E -Wp,-v -xc /dev/null 2>&1 | grep %s$ | grep -v GCCcore" % multiarch_out
+            multi_arch_inc_dir_cmd = '|'.join([
+                "gcc -E -Wp,-v -xc /dev/null 2>&1",
+                "grep %s$" % multiarch_out,
+                "grep -v /include-fixed/",
+            ])
             multiarch_inc_dir, ec = run_cmd(multi_arch_inc_dir_cmd)
             if ec == 0 and multiarch_inc_dir:
                 multiarch_inc_dir = multiarch_inc_dir.strip()

From 2bb9d17c4aa1c3e87e598606a05d8feeb4f74be9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Jun 2024 14:14:37 +0200
Subject: [PATCH 129/134] always specify custom value for sanity_check_paths in
 torchvision easyblock, to fix broken sanity check for bundle that includes
 torchvision as extension (like PyTorch-bundle)

---
 easybuild/easyblocks/t/torchvision.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index 18b08d25dc..a780af92b1 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -89,7 +89,10 @@ def configure_step(self):
     def sanity_check_step(self):
         """Custom sanity check for torchvision."""
         custom_commands = []
-        custom_paths = None
+        custom_paths = {
+            'files': [],
+            'dirs': [det_pylibdir()],
+        }
 
         # check whether torchvision was indeed built with CUDA support,
         # cfr. https://discuss.pytorch.org/t/notimplementederror-could-not-run-torchvision-nms-with-arguments-from-\
@@ -103,10 +106,6 @@ def sanity_check_step(self):
                 "    print(torchvision.ops.nms(boxes, scores, 0.5))",
             ])
             custom_commands.append('python -c "%s"' % python_code)
-            custom_paths = {
-                'files': [],
-                'dirs': [det_pylibdir()],
-            }
 
         if get_software_root('libjpeg-turbo'):
             # check if torchvision was built with libjpeg support

From 53e0dd3570a1610806250b6f4a562207738ca8ef Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Jun 2024 14:48:35 +0200
Subject: [PATCH 130/134] load module before calling det_pylibdir() in sanity
 check for torchvision

---
 easybuild/easyblocks/t/torchvision.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index a780af92b1..378b5525a8 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -88,6 +88,12 @@ def configure_step(self):
 
     def sanity_check_step(self):
         """Custom sanity check for torchvision."""
+
+        # load module early ourselves rather than letting parent sanity_check_step method do so,
+        # so the correct 'python' command is used to by det_pylibdir() below;
+        if hasattr(self, 'sanity_check_module_loaded') and not self.sanity_check_module_loaded:
+            self.fake_mod_data = self.sanity_check_load_module(extension=self.is_extension)
+
         custom_commands = []
         custom_paths = {
             'files': [],

From d5e1dc942ce59081569b66e52159738c723e9063 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 10 Jun 2024 23:13:02 +0200
Subject: [PATCH 131/134] prepare release notes for EasyBuild v4.9.2 + bump
 version to 4.9.2

---
 RELEASE_NOTES                    | 33 +++++++++++++++++++++++++++++++-
 easybuild/easyblocks/__init__.py |  2 +-
 2 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 528e94e069..ba3659f632 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,7 +3,38 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyblocks provides 255 software-specific easyblocks and 43 generic easyblocks.
+The latest version of easybuild-easyblocks provides 259 software-specific easyblocks and 43 generic easyblocks.
+
+
+v4.9.2 (11 June 2024)
+---------------------
+
+update/bugfix release
+
+- 4 new software-specific easyblocks: QuantumESPRESSO with CMake (#3257), aedt (#3281), optiSLang (#3300), MetalWalls (#3311)
+- minor enhancements and updates, including:
+  - refactor GAMESS-US easyblock to directly write install.info (v2) (#3047)
+  - Add ABAQUS license server to generated module (#3277)
+  - Allow 'nosource: True' in PythonPackage extensions' (#3305)
+  - auto-disable FFTW quad precision on RISC-V (#3314)
+  - use regular `configure` instead of wrapper script in easyblock for UCX plugins (#3315)
+  - add libjpeg-turbo to include dir for torchvision easyblock (#3322)
+  - add RISC-V support to Java easyblock (#3323)
+  - add RISC-V support to Mesa easyblock (#3324)
+  - add RISC-V support to Clang easyblock (#3325)
+  - Add a sanity check for OpenFOAM's `wmake` to make sure it finds the compiler commands (#3328)
+  - Always override the compiler version check for CUDA installations (#3329)
+  - allow version mismatchs between OpenSSL components in host system as long as they fulfill version requirements (#3340)
+  - Allow external PRRTE in OpenMPI easyblock (#3347)
+- various bug fixes, including:
+  - don't manipulate setup.py for Python 3.12+ when using alternate sysroot (#3313)
+  - do not run unit tests on Python 3.5 (#3326)
+  - Fix for MetalWalls easyblock w.r.t. PLUMED generating patch file inside module location (#3331)
+  - avoid sanity check on the software itself for CargoPythonBundle easyblock (#3341)
+  - fix malformed `$CPATH` for intel-compilers on Debian/Ubuntu (#3346)
+  - always specify custom value for `sanity_check_paths` in custom easyblock for torchvision (#3353)
+- other changes:
+  - Binary easyblock already adds top level directory to PATH, so no need to do it in the Stata easyblock (#3307)
 
 
 v4.9.1 (5 April 2024)
diff --git a/easybuild/easyblocks/__init__.py b/easybuild/easyblocks/__init__.py
index 56d224f3be..5dfdc5c4f1 100644
--- a/easybuild/easyblocks/__init__.py
+++ b/easybuild/easyblocks/__init__.py
@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.9.2.dev0')
+VERSION = LooseVersion('4.9.2')
 UNKNOWN = 'UNKNOWN'
 
 

From 41bd1402d1798087718e0ef8aef4d57e342e5101 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Jun 2024 08:04:01 +0200
Subject: [PATCH 132/134] minor tweaks to 4.9.2 release notes

---
 RELEASE_NOTES | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index ba3659f632..6ccd23b091 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -11,28 +11,24 @@ v4.9.2 (11 June 2024)
 
 update/bugfix release
 
-- 4 new software-specific easyblocks: QuantumESPRESSO with CMake (#3257), aedt (#3281), optiSLang (#3300), MetalWalls (#3311)
+- 4 new software-specific easyblocks: QuantumESPRESSO with CMake (#3257), aedt (#3281), optiSLang (#3300), MetalWalls (#3311, #3331)
 - minor enhancements and updates, including:
-  - refactor GAMESS-US easyblock to directly write install.info (v2) (#3047)
-  - Add ABAQUS license server to generated module (#3277)
-  - Allow 'nosource: True' in PythonPackage extensions' (#3305)
+  - refactor GAMESS-US easyblock to directly write install.info (#3047)
+  - add ABAQUS license server to generated module (#3277)
+  - allow 'nosource: True' in PythonPackage extensions (#3305)
   - auto-disable FFTW quad precision on RISC-V (#3314)
-  - use regular `configure` instead of wrapper script in easyblock for UCX plugins (#3315)
-  - add libjpeg-turbo to include dir for torchvision easyblock (#3322)
-  - add RISC-V support to Java easyblock (#3323)
-  - add RISC-V support to Mesa easyblock (#3324)
-  - add RISC-V support to Clang easyblock (#3325)
-  - Add a sanity check for OpenFOAM's `wmake` to make sure it finds the compiler commands (#3328)
-  - Always override the compiler version check for CUDA installations (#3329)
+  - use regular 'configure' instead of wrapper script in easyblock for UCX plugins (#3315)
+  - add libjpeg-turbo to include dir for torchvision easyblock (#3322, #3353)
+  - add RISC-V support to custom easyblocks for Clang (#3325), Java (#3323), Mesa (#3324)
+  - add a sanity check for OpenFOAM's 'wmake' to make sure it finds the compiler commands (#3328)
+  - always override the compiler version check for CUDA installations (#3329)
   - allow version mismatchs between OpenSSL components in host system as long as they fulfill version requirements (#3340)
-  - Allow external PRRTE in OpenMPI easyblock (#3347)
+  - allow external PRRTE in OpenMPI easyblock (#3347)
 - various bug fixes, including:
   - don't manipulate setup.py for Python 3.12+ when using alternate sysroot (#3313)
   - do not run unit tests on Python 3.5 (#3326)
-  - Fix for MetalWalls easyblock w.r.t. PLUMED generating patch file inside module location (#3331)
   - avoid sanity check on the software itself for CargoPythonBundle easyblock (#3341)
-  - fix malformed `$CPATH` for intel-compilers on Debian/Ubuntu (#3346)
-  - always specify custom value for `sanity_check_paths` in custom easyblock for torchvision (#3353)
+  - fix malformed '$CPATH' for intel-compilers on Debian/Ubuntu (#3346)
 - other changes:
   - Binary easyblock already adds top level directory to PATH, so no need to do it in the Stata easyblock (#3307)
 

From ac869ebafcbed2e6f83c9ce088703c958ced72e2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Jun 2024 20:23:30 +0200
Subject: [PATCH 133/134] bump release date for EasyBuild v4.9.2 to 12 June
 2024

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 6ccd23b091..73f484d0eb 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -6,7 +6,7 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en
 The latest version of easybuild-easyblocks provides 259 software-specific easyblocks and 43 generic easyblocks.
 
 
-v4.9.2 (11 June 2024)
+v4.9.2 (12 June 2024)
 ---------------------
 
 update/bugfix release

From ba870405758dedd6ba1c9ba7df3aa79e59786cf1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Jun 2024 20:49:59 +0200
Subject: [PATCH 134/134] aedt -> AEDT in v4.9.2 release notes

---
 RELEASE_NOTES | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 73f484d0eb..8050832107 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -11,7 +11,7 @@ v4.9.2 (12 June 2024)
 
 update/bugfix release
 
-- 4 new software-specific easyblocks: QuantumESPRESSO with CMake (#3257), aedt (#3281), optiSLang (#3300), MetalWalls (#3311, #3331)
+- 4 new software-specific easyblocks: QuantumESPRESSO with CMake (#3257), AEDT (#3281), optiSLang (#3300), MetalWalls (#3311, #3331)
 - minor enhancements and updates, including:
   - refactor GAMESS-US easyblock to directly write install.info (#3047)
   - add ABAQUS license server to generated module (#3277)