Merge pull request #3279 from easybuilders/4.9.x

release EasyBuild v4.9.1
easybuilders · Apr 5, 2024 · 66346b5 · 66346b5
2 parents 5106dfa + fe665cd
commit 66346b5
Show file tree

Hide file tree

Showing 308 changed files with 1,674 additions and 748 deletions.
diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -3,7 +3,57 @@ 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 254 software-specific easyblocks and 43 generic easyblocks.
+The latest version of easybuild-easyblocks provides 255 software-specific easyblocks and 43 generic easyblocks.
+
+
+v4.9.1 (5 April 2024)
+---------------------
+
+update/bugfix release
+
+- 1 new software-specific easyblock: DualSPHysics (#3050)
+- minor enhancements and updates, including:
+  - use proxy in sanity check of custom easyblock to install OpenSSL wrapper (#2922)
+  - update Clang-AOMP easyblock for ROCm 5.6 (#2958)
+  - consider both `$EBROOTGCC` and `$EBROOTGCCCORE` in Clang-AOMP easyblock to specify `-DGCC_INSTALL_PREFIX` (#2958)
+  - update WIEN2k easyblock for v23.2 (#3035)
+  - enhance LAMMPS easyblock dynamically add `ARMV81` and `A64FX` to Kokkos CPU mapping based on LAMMPS version (#3036)
+  - add `pip_verbose` option to PythonPackage and set it to True in PyTorch easyblock, to show build output when using pip (#3065)
+  - also support OpenSSL 3 in OpenSSL wrapper easyblock (#3081)
+  - improve error checking in PyTorch easyblock (#3085)
+  - update MCR easyblock for compatibility with versions >= R2022b (#3119)
+  - add `species` easyconfig parameter to VEP easyblock (#3121)
+  - only install Gurobi Python bindings via `setup.py` for Gurobi v10.x and older (#3225)
+  - consistently honor `pretestopts` & `testopts` in `PerlModule` (#3231)
+  - fix OCaml easyblock for recent versions (#3235)
+  - improve QuantumESPRESSO easyblock by cleaning up and extending configure step + running test suite (#3241, #3258)
+  - allow overriding `testinstall` in PyTorch easyconfigs (#3250)
+  - enhance GCC easyblock to set `$LIBRARY_PATH` and disable building of NVPTX offload support on RISC-V systems (#3256)
+  - add support for conda provided by Miniforge (#3260)
+  - set `$GOPATH` in configure step of `GoPackage` easyblock to avoid polluting `$HOME/go` (#3262)
+- various bug fixes, including:
+  - set `$BGW_TEST_MPI_NPROCS` in BerkeleyGW test step (#2950)
+  - fix installation of Python bindings for LAMMPS >= 2Aug2023 + fix sanity check by doing MPI_Finalize (#3036)
+  - fix ELPA preprocessor flag for QuantumESPRESSO >= 7 (#3063)
+  - fix link order in PETSc easyblock for SCOTCH >= 7.x (#3069)
+  - update PyTorch easyblock to avoid configure warnings by disabling some options (#3070)
+  - pick Tcl/Tk lib directory correctly in R easyblock, may be either `lib` or `lib64` (#3072)
+  - use `(=|:=)` in regex because OpenFOAM rule files use `:=` instead of `=` since v2212 (#3073)
+  - add Clang `opt` binary to RPATH wrapper dir (#3076)
+  - improve `generate_crate_list` + parsing of crates in `Cargo` easyblock (#3084)
+  - remove trailing slash in `PETSC_DIR` set by custom easyblock for PETSc (#3086)
+  - use correct TCL configure options for Python 3.11+ (#3087)
+  - tweak `CMakeMake` easyblock to apply CMake policy to select `python` based on `$PATH` order, instead of highest version (#3088)
+  - update `Cargo` easyblock to extract crates into a vendor subdir and overwrite git repo URLs with local paths (#3118)
+  - only add `--with-ucc` for OpenMPI 4.1.4+ (#3223)
+  - remove trailing slash in `SLEPC_DIR` in configure step of custom easyblock for SLEPc (#3229)
+  - fix OpenFOAM easyblock to fix `motorBike` example in sanity check for versions >=11 (#3232)
+  - only run CUDA sanity check command for torchvision if GPU is present (#3236)
+  - ensure localrc is created in the correct subdir for NVHPC v22.9+ (#3240)
+  - remove wrong configure option for LibInt 2.6.x (#3249)
+  - do not rename GCC's include-fixed directory by default + add script to regenerate it (#3254)
+- other changes:
+  - update copyright lines to 2024 (#3268)
 
 
 v4.9.0 (30 December 2023)

diff --git a/easybuild/__init__.py b/easybuild/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/__init__.py b/easybuild/easyblocks/__init__.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),
@@ -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('4.9.0')
+VERSION = LooseVersion('4.9.1')
 UNKNOWN = 'UNKNOWN'
 
 

diff --git a/easybuild/easyblocks/a/abaqus.py b/easybuild/easyblocks/a/abaqus.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/acml.py b/easybuild/easyblocks/a/acml.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/adf.py b/easybuild/easyblocks/a/adf.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2016-2023 Ghent University
+# Copyright 2016-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/a/advisor.py b/easybuild/easyblocks/a/advisor.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/aladin.py b/easybuild/easyblocks/a/aladin.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/allinea.py b/easybuild/easyblocks/a/allinea.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2023 Ghent University
+# Copyright 2013-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/a/amber.py b/easybuild/easyblocks/a/amber.py
@@ -1,6 +1,6 @@
 ##
-# Copyright 2009-2023 Ghent University
-# Copyright 2015-2023 Stanford University
+# Copyright 2009-2024 Ghent University
+# Copyright 2015-2024 Stanford University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/a/anaconda.py b/easybuild/easyblocks/a/anaconda.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/ansys.py b/easybuild/easyblocks/a/ansys.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/ant.py b/easybuild/easyblocks/a/ant.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/aocc.py b/easybuild/easyblocks/a/aocc.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2020-2023 Forschungszentrum Juelich GmbH
+# Copyright 2020-2024 Forschungszentrum Juelich GmbH
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.

diff --git a/easybuild/easyblocks/a/aomp.py b/easybuild/easyblocks/a/aomp.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2021-2023 Ghent University
+# Copyright 2021-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/a/arb.py b/easybuild/easyblocks/a/arb.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/armadillo.py b/easybuild/easyblocks/a/armadillo.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/a/atlas.py b/easybuild/easyblocks/a/atlas.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/bamtools.py b/easybuild/easyblocks/b/bamtools.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 The Cyprus Institute
+# Copyright 2009-2024 The Cyprus Institute
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/b/bazel.py b/easybuild/easyblocks/b/bazel.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/berkeleygw.py b/easybuild/easyblocks/b/berkeleygw.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),
@@ -177,7 +177,8 @@ def test_step(self):
         """Custom test step for BerkeleyGW."""
         if self.cfg['runtest'] is not False:
             self.cfg['runtest'] = 'check'
-            setvar('OMP_NUM_THREADS', '4')
+            setvar('BGW_TEST_MPI_NPROCS', '2')
+            setvar('OMP_NUM_THREADS', '2')
             setvar('TEMPDIRPATH', os.path.join(self.builddir, 'tmp'))
         super(EB_BerkeleyGW, self).test_step()
 

diff --git a/easybuild/easyblocks/b/binutils.py b/easybuild/easyblocks/b/binutils.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/bioconductor.py b/easybuild/easyblocks/b/bioconductor.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/bisearch.py b/easybuild/easyblocks/b/bisearch.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/blacs.py b/easybuild/easyblocks/b/blacs.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/blat.py b/easybuild/easyblocks/b/blat.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 the Cyprus Institute
+# Copyright 2009-2024 the Cyprus Institute
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/b/blender.py b/easybuild/easyblocks/b/blender.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/boost.py b/easybuild/easyblocks/b/boost.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/b/bowtie.py b/easybuild/easyblocks/b/bowtie.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2023 Ghent University
+# Copyright 2013-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/b/bowtie2.py b/easybuild/easyblocks/b/bowtie2.py
@@ -1,7 +1,7 @@
 ##
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 #
-# Copyright:: Copyright 2012-2023 Uni.Lu/LCSB, NTUA
+# Copyright:: Copyright 2012-2024 Uni.Lu/LCSB, NTUA
 # Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste
 # License::   MIT/GPL
 # $Id$

diff --git a/easybuild/easyblocks/b/bwa.py b/easybuild/easyblocks/b/bwa.py
@@ -1,7 +1,7 @@
 ##
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 #
-# Copyright:: Copyright 2012-2023 Uni.Lu/LCSB, NTUA
+# Copyright:: Copyright 2012-2024 Uni.Lu/LCSB, NTUA
 # Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Kenneth Hoste
 # Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
 # License::   MIT/GPL

diff --git a/easybuild/easyblocks/b/bwise.py b/easybuild/easyblocks/b/bwise.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2018-2023 Free University of Brussels
+# Copyright 2018-2024 Free University of Brussels
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/b/bzip2.py b/easybuild/easyblocks/b/bzip2.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/c/cblas.py b/easybuild/easyblocks/c/cblas.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2023 Ghent University
+# Copyright 2013-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/c/cfdemcoupling.py b/easybuild/easyblocks/c/cfdemcoupling.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2018-2023 Ghent University
+# Copyright 2018-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/c/cgal.py b/easybuild/easyblocks/c/cgal.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2009-2023 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),

diff --git a/easybuild/easyblocks/c/chapel.py b/easybuild/easyblocks/c/chapel.py
@@ -1,7 +1,7 @@
 ##
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 #
-# Copyright:: Copyright 2012-2023 Uni.Lu/LCSB, NTUA
+# Copyright:: Copyright 2012-2024 Uni.Lu/LCSB, NTUA
 # Authors::   Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste
 # License::   MIT/GPL
 # $Id$

diff --git a/easybuild/easyblocks/c/charmm.py b/easybuild/easyblocks/c/charmm.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2013-2023 Ghent University
+# Copyright 2013-2024 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),

diff --git a/easybuild/easyblocks/c/clang.py b/easybuild/easyblocks/c/clang.py
@@ -1,6 +1,6 @@
 ##
-# Copyright 2013-2023 Dmitri Gribenko
-# Copyright 2013-2023 Ghent University
+# Copyright 2013-2024 Dmitri Gribenko
+# Copyright 2013-2024 Ghent University
 #
 # This file is triple-licensed under GPLv2 (see below), MIT, and
 # BSD three-clause licenses.
@@ -46,7 +46,7 @@
 from easybuild.tools import run
 from easybuild.tools.build_log import EasyBuildError, print_warning
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import apply_regex_substitutions, change_dir, mkdir, which
+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
@@ -505,6 +505,11 @@ def build_with_prev_stage(self, prev_obj, next_obj):
             my_clang_toolchain.prepare_rpath_wrappers()
             self.log.info("Prepared clang rpath wrappers")
 
+            # add symlink for 'opt' to wrapper dir, since Clang expects it in the same directory
+            # see https://github.com/easybuilders/easybuild-easyblocks/issues/3075
+            clang_wrapper_dir = os.path.dirname(which('clang'))
+            symlink(os.path.join(prev_obj_path, 'opt'), os.path.join(clang_wrapper_dir, 'opt'))
+
             # RPATH wrappers add -Wl,rpath arguments to all command lines, including when it is just compiling
             # Clang by default warns about that, and then some configure tests use -Werror which turns those warnings
             # into errors. As a result, those configure tests fail, even though the compiler supports the requested