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RELEASE_NOTES
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RELEASE_NOTES
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This file contains a description of the major changes to the easybuild-easyblocks EasyBuild package.
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 249 software-specific easyblocks and 42 generic easyblocks.
v4.8.0 (7 July 2023)
--------------------
feature release
- add `PerlBundle` generic easyblock for installing a bundle of Perl modules (#2945)
- add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if --rpath is used (#2952)
- minor enhancements and updates, including:
- add support for NVIDIA Hopper CC 9.0 in LAMMPS (#2941)
- add support for `install_cmds` in `Binary` easyblock (#2953)
- various bug fixes, including:
- patch CMake's UnixPaths.cmake script if --sysroot is set (#2248)
- fix incorrect sanity_check_step for torchvision (#2938)
- update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes (#2944)
- improve handling of `optarch` in `Cargo` easyblock (#2947)
- reset modules loaded by PythonPackage to let ExtensionEasyBlock handle `multi_deps` correctly (#2951)
- other changes:
- stop running tests with Python 2.7 since it is no longer supported in GitHub Actions (#2943)
v4.7.2 (27 May 2023)
--------------------
- new generic easyblock for installing Rust crates with cargo: Cargo and CargoPythonPackage (#2902, #2934)
- minor enhancements and updates, including:
- let MATLAB easyblock raise an error if the MATLAB installation key is not provided (#2905)
- print message to inform that GPU package (instead of Kokkos) is used for LAMMPS (#2906)
- enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0 (#2915)
- various bug fixes, including:
- use custom RPATH sanity check for Go packages that doesn't actually check for an RPATH section in the binary (#2913)
- use string '0' to avoid problems when openssl version is not determined (#2914)
- update GCC easyblock to ensure that --sysroot is passed to linker (but only when it needs to be) (#2921)
- add output log to MATLAB installs, actually parse for common errors (#2924)
- enhance Gurobi easyblock to allow using $EB_GUROBI_LICENSE_FILE environment variable (#2926)
- force building torchvision with CUDA support if CUDA is included as dependency by setting `$FORCE_CUDA` (#2931)
- fix exec permission on files in arch bindir for COMSOL (#2932)
v4.7.1 (March 20th 2023)
------------------------
update/bugfix release
- minor enhancements and updates, including:
- fix TensorFlow easyblock for new versions of Bazel & TensorFlow (#2854)
- make NAMD easyblock aware of (pre)testopts (#2856)
- update MesonNinja easyblock for Meson >=0.64.0 (#2861)
- update scipy easyblock for scipy >= 1.9.0 to use meson/ninja (#2862, #2903)
- modify logic in QScintilla easyblock to find the PyQt5 sipdir in more places (#2868)
- add `testinstall` custom easyconfig parameter to PythonPackage easyblock (#2872)
- use -x option for "go install" in GoPackage generic easyblock, to print commands as they are executed (#2878)
- allow disabling pybind11 tests with `runtest = False` (#2892)
- call parent post_install_step in EasyBuildMeta easyblock (so postinstallcmds are taken into account) (#2893)
- update and enhance Maple easyblock for recent versions (#2895)
- relax glob pattern to find Mathematica install script (#2896)
- implement CUDA support in the ELPA EasyBlock & fix CPP configure issue on newer ELPA versions (#2898)
- update Trilinos easyblock to allow disabling of building tests and forward deps + support Trilinos v13.x (#2900)
- enhance Python easyblock to create non-versioned symlink for python-config + check for bin/python and bin/python-config in sanity check (#2904)
- various bug fixes, including:
- do not use -g77 option when installing NVHPC 22.9+ (#2819)
- check that sanity_check_module_loaded attribute exists before querying it in PythonPackage easyblock (#2865)
- fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions (#2869)
- fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets (#2873)
- show template values of exts_default_options in PythonBundle (#2874)
- fix missing initialization of CMakeMake in CMakePythonPackage (#2876)
- fix error when failing pip version check during PythonPackage sanity check (#2877)
- handle templating correctly in CMakeMake when playing with configopts (#2882)
- avoid crash in test step of PyTorch easyblock if runtest is not a command (#2883)
- fix check configure option in FlexiBLAS easyblock (#2886)
- use older `ncgen -H` for older netCDF (#2889)
- fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x (#2897)
- other changes:
- only give read permissions in GitHub Actions workflows (#2863)
- use start dir of extension to install R packages (#2867)
- fix website/docs links in README (#2870)
- add deprecation notice to RPackage extensions with relative paths in start_dir (#2879)
v4.7.0 (January 9th 2023)
-------------------------
feature release
- add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage (#2816) and JuliaBundle (#2830)
- minor enhancements and updates, including:
- enhance TensorFlow easyblock to take into account provided OpenSSL dependency (#2575)
- add fix_shebang to install_step of PythonPackage easyblock so that we can fix shebangs when installing extensions (#2680)
- update PETSc easyblock for newer versions (>= 3.17) (#2796)
- update Clang easyblock to add support for new directory structure in Clang versions >= 14 + support Flang (#2800)
- update Xmipp easyblock since versions >= 3.20.07 use `noAsk` option to configure (#2809)
- add include/opencv4 to $CPATH for OpenCV versions >= 4.0 (#2818)
- add extra option for disabling LAPACK in ESMF (#2821)
- enable building of static libraries for libxml2 >= 2.10 (#2825)
- update Xmipp easyblock to handle effects of CUDA at SYSTEM level and newer CUDA version requirements for stdc++ (#2831)
- update LLVM easyblock to put 'cmake' symlink in place so separate CMake modules required for LLVM 15+ can be found (#2832)
- set $TEMPDIRPATH for testsuite in the BerkeleyGW easyblock, to avoid polluting /tmp (#2836)
- add `configure_no_prefix` option to skip addition of prefix to configure command in ConfigureMake easyblock (#2842)
- update qscintilla.py to be compatible with EB install of PyQt5 >= 5.15 (#2845)
- add UCC to known_dependencies in OpenMPI EasyBlock (#2847)
- update Clang-AOMP easyblock to handle version 5.2 and newer (#2851)
- various bug fixes, including:
- fix installing of Clang with RPATH linking (#2799)
- fix --module-only for Clang + fix sanity check for Clang 11.x (#2800)
- create $XDG_CACHE_HOME for PyTorch tests (#2806)
- make PythonPackage easyblock compatible with --sanity-check-only by loading module early during sanity check step (#2828)
- fix docstring of PythonBundle generic easyblock (#2833)
- fix counting of failures in PyTorch tests (#2834, #2840)
- make sure that ANSYS INSTALL script has execute permissions (#2852, #2853)
- other changes:
- remove useless -openmp build option for MRtrix v3.x (#2822)
- update HDF5 easyblock to use --enable-threadsafe configure option to make C API thread safe (#2824)
- use new EasyBuild logo in README (#2827)
- automatically cancel Github Action workflow runs for outdated commits (#2835)
- use fixed names for bazel/wrapper subdirectories used when building TensorFlow, to make debugging easier (#2841)
- also run unit tests with Python 3.11 (#2844)
- tweak docstring in some generic easyblocks so it renders nicely in auto-generated documentation (#2849)
- update copyright lines for 2023 (#2850)
v4.6.2 (October 21st 2022)
--------------------------
update/bugfix release
- 2 new software-specific easyblock:
- CUDA compatibility libraries (#2764) and mamba (#2808)
- minor enhancements and updates, including:
- update OpenFOAM easyblock to support OpenFOAM 10 + clean up variant/version checks (#2766)
- added support for ESMPy in ESMF (#2789)
- enhance OpenBLAS easyblock to support running LAPACK test suite + checking how many tests fail (#2801)
- make numexpr easyblock aware of toolchain with GCC + imkl (#2810)
- add sanity check commands for netCDF (#2811)
- various bug fixes, including:
- handle problems copying symlink that points to CUDA folder that is not created for non CUDA builds of SuiteSparse (#2790)
- don't install docs (to avoid trouble with Java) + add Rocky support for ABAQUS (#2792)
- correctly count the number of failing tests (not failing test suites) in PyTorch builds (#2794, #2803)
- fix docstring for PyTorch easyblock (#2795)
- handle iterative builds with MakeCp easyblock (#2798)
- accept both None and empty value for optarch to let OpenCV detect host CPU (#2804)
- enhance EasyBuildMeta easyblock: auto-enable installing with pip + fix setup.py of easyconfigs package so installation with setuptools >= 61.0 works (#2805)
- use `python -m pip` instead of `pip` in PythonPackage easyblock (#2807)
- other changes:
- make the test output from PythonPackage less verbose by disabling default search for error patterns done by run_cmd (2797)
v4.6.1 (September 12th 2022)
----------------------------
update/bugfix release
- minor enhancements and updates, including:
- update LAMMPS easyblock for LAMMPS/23Jun22 (#2213)
- reduce the number of command line options for 'cmake' command in CMakeMake generic easyblock (#2514)
- update libQGLViewer easyblock to take into account changes in the shared library names depending on Qt versions they are compiled with (#2730)
- improve PLUMED detection in GROMACS easyblock (#2749)
- make `$LD_LIBRARY_PATH` detection more robust for LAMMPS (#2765)
- enhance NVHPC easyblock to avoid superfluous warning (#2767)
- enhance PyTorch easyblock to also capture tests failing with signal (#2768)
- enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when return_output_ec=True (#2770)
- set $NVHPC_CUDA_HOME for NVHPC 22.7+ (#2776)
- various bug fixes, including:
- make Amber easyblock aware of FlexiBLAS (#2720)
- update PyTorch easyblock to configure without breakpad support on POWER (#2763)
- use lib* in post_install step of FFTW.MPI easyblock to fix paths not being found on Linux distros favouring lib64 (like Suse/SLES) (#2771)
- use det_cmake_version function to determine CMake version in CMakeMake generic easyblock (#2772)
- don't enable building of ld.gold when installing binutils on a RISC-V system + don't configure GCC to use gold as default linker on a RISC-V system (#2780)
- tweak Amber(Tools) easyblock to run tests from top-level directory (#2781)
- fix version check for NVPTX library in sanity check of Clang easyblock (#2783)
- other changes:
- update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#2779)
v4.6.0 (July 8th 2022)
----------------------
feature release
- new software-specific easyblock for STAR-CCM+ (#1613)
- minor enhancements and updates, including:
- update Siesta EasyBlock to support GCC 10+ by adding -fallow-argument-mismatch Fortran compiler option (#2690)
- enable building of shared library for Libint 2.7+ (#2738)
- allow some PyTorch tests to fail + print warning if one or more tests fail (#2742)
- also support OpenSSL 3.0 in OpenSSL wrapper easyblock (#2746)
- add more logging to install_pc_files method of OpenSSL wrapper easyblock (#2752)
- make WPS easyblock aware of (pre)buildopts (#2754)
- add Abseil system dependency for TensorFlow 2.9+ (#2757)
- disable altivec when building FFTW versions < 3.4 with single-precision with GCC on POWER (#2758)
- various bug fixes, including:
- make VEP easyblock compatible with --sanity-check-only (#2743)
- update Rosetta easyblock to take into account that $LD_LIBRARY_PATH, $CPATH, $PATH may not be defined (#2744)
- only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension (#2747)
- make sure that CMakeMakeCp uses correct build dir (#2748)
- enhance Bazel easyblock to avoid writing to $HOME in sanity check (#2756)
v4.5.5 (June 8th 2022)
----------------------
update/bugfix release
- new software-specific easyblock for FFTW.MPI (#2724)
- minor enhancements and updates, including:
- update NEURON easyblock to use CMakeMake for recent versions (#2304)
- enhance Clang easyblock to add support for building with AMDGPU offload (#2684, #2729)
- update sanity check in OpenMPI easyblock to support OpenMPI v5.0.0 (#2709)
- don't use gold linker by default for GCC >= 11.3 (#2711)
- update sanity check in R easyblock for versions >= 4.2.0, since S.h is not included anymore (#2713)
- update ABAQUS easyblock for ABAQUS 2022 (#2716)
- update LLVM easyblock for LLVM v14.0.x (#2718)
- update Mesa easyblock to remove swr driver configopts for versions 22+ (#2719)
- enhance Clang easyblock to support also installing Python bindings (#2721, #2725)
- enhance SuperLU easyblock to support building on top of FlexiBLAS and be compatible with SuperLU v5.3 (#2722)
- update TensorFlow easyblock for version 2.8.0 (#2723)
- modify FFTW's sanity check step to allow checking only for MPI parts of FFTW installation (#2724)
- add support to ConfigureMake for tweaking (first part of) test command via 'test_cmd' (#2726, #2737)
- enhance MrBayes easyblock with custom sanity check command (#2727)
- update cudnnarch string templates used to compose source tarball names from cuDNN 8.3.3 onwards (#2728)
- add sanity check command to OpenSSL wrapper easyblock to verify that system certificates are available to OpenSSL (#2735)
- ignore exit code of pkg-config command in OpenSSL wrapper easyblock, since with pkgconf they exit with a non-zero exit code if the OS package is not installed (#2736)
- various bug fixes, including:
- remove system-compiled binutils dirs from $LDFLAGS in binutils easyblock (#2712)
- fix for FreeSurfer easyblock: define $FREESURFER needed by recon_all (#2717)
- also symlink cert.pem in from-source OpenSSL installation (if it exists) (#2735)
v4.5.4 (March 31st 2022)
------------------------
update/bugfix release
- minor enhancements and updates, including:
- update Clang-AOMP easyblock to add support for ROCm v5.0 (#2681)
- enable system SSL certificates in OpenSSL installations (#2683)
- enhance MRtrix easyblock: build in parallel + enable OpenMP support for MRtrix >= 3.0 (#2685)
- avoid dependency on 'which' command in sanity check for Python, use 'command -v' instead (#2687)
- enhance Tarball easyblock to support using it for installing extensions (#2688)
- update wxPython easyblock to support wxPython v4.1 (#2689)
- enhance Gurobi easyblock to also update $MATLABPATH (#2691)
- build single-file shared libraries for imkl so it can be used as FlexiBLAS backend via $FLEXIBLAS_LIBRARY_PATH (#2694)
- various bug fixes, including:
- added regex to replace /lib/cpp with cpp in OpenFOAM's wmake rules file (#2331)
- set $NINJAFLAGS to make sure Ninja doesn't use all visible cores when building Qt5 (#2338)
- update Siesta EasyBlock to use serial FFTW (#2662)
- fix support for imkl for numexpr 2.8.0+ in numexpr easyblock (#2678)
- make sure TensorFlow doesn't see the nvptx-none dir when searching for gcc include dir (#2682)
- force use of bash for Anaconda install script (#2692)
- add guess for path to add to $MANPATH for intel-compilers (#2696)
- change permissions of the Java build directory to avoid permission denied error (#2698)
- also consider $MKLROOT/lib/pkgconfig for $PKG_CONFIG_PATH for imkl (#2701)
- close log after installing Bundle component (#2702)
- replace hardcoded /tmp to make sure that Bazel build respects $TMPDIR (#2703)
- other changes:
- minor code cleanup in numexpr easyblock (#2679)
- update copyright lines for 2022 (#2705)
v4.5.3 (February 11th 2022)
---------------------------
update/bugfix release
- new software-specific easyblock for reticulate R package (#2668)
- minor enhancements and updates, including:
- set CUDA target architecture(s) for GROMACS based on cuda_cc_semicolon_sep template value (#2655)
- add support to NAMD easyblock to opt out of building with CUDA support even if CUDA is included as dependency (#2666)
- update sanity check in CUDA easyblock: CUDA 11.6 no longer includes samples (#2669)
- various bug fixes, including:
- also run easyblocks test suite with Python 3.8-3.10 + consistently use actions/setup-python@v2 in CI workflows (#2664)
- specify easybuild.io as EasyBuild homepage in setup.py (#2667)
- other changes:
- remove vulnerable binaries from sanity check of HDF5, no longer installed by default with HDF5 1.10.8 (#2670)
v4.5.2 (January 24th 2022)
--------------------------
update/bugfix release
- minor enhancements and updates, including:
- remove necessity for license for oneAPI versions (>= 2021.x) in itac easyblock (#2492)
- add CUDA support in SuiteSparse easyblock (#2627)
- use all available cores for running Perl test suite (#2637)
- add option to not copy the license file for Gurobi (#2639, #2641)
- update AOCC easyblock to support version 3.2.0 (#2643)
- don't grep for specific version in --version output of Intel compiler commands for versions 2022.x (#2644)
- add support for enabling sanity checks for specific components in the Bundle easyblock (#2649)
- update Libint easyblock for LibInt v2.7.0 which requires configuring via CMake (#2650)
- update Mathematica easyblock for version 13 (#2652)
- add sanity check command for Bazel (#2653)
- update NAMD easyblock to allow non-system csh (#2654)
- enhance CUDA easyblock to create version independent pkgconfig files (#2656)
- add util subdirectory to $PATH for WPS (#2658)
- various bug fixes, including:
- convert version numbers to stricly numerical in Siesta easyblock (#2553)
- fix shebang of scripts in Perl installation if installation prefix is too long (#2640)
- enhance IntelBase easyblock to avoid crash when $USER is not set (#2642)
- fix quotes in definition of default platform macro and enhance sanity check in GATE easyblock (#2645)
- avoid excessively long shebang line in compile script for WRF (#2648)
- fix checking of Intel Fortran compiler version in CP2K easyblock for recent toolchains (#2651)
v4.5.1 (December 13th 2021)
---------------------------
update/bugfix release
- new software-specific easyblock for Clang-AOMP (#2617)
- minor enhancements and updates, including:
- enhance Rpm generic easyblock to support installing tarball of RPMs (by unpacking it first) + take into account (pre)installopts (#2580)
- add option to control use of MKL-DNN in jaxlib easyblock (#2619)
- update SAMtools easyblock to support installation of SAMtools 1.14 (#2620)
- add option to ignore PLUMED version check for GROMACS (#2621)
- update Inspector easyblock for recent versions (>= 2021, oneAPI versions) (#2624)
- enhance tbb easyblock by adding option to build Python bindings (#2626)
- fix patching of CMakeLists.txt in for Eigen v3.4 (#2633)
- various bug fixes, including:
- update CP2K easyblock to use -D__MKL for CP2K versions newer than 2.3 (#2586)
- set OpenMPI configuration for ORCA sanity check (#2596)
- allow oversubscription in OpenMPI sanity check (#2611)
- set wm_* class variables in OpenFOAM easyblock constructor (to fix --sanity-check-only) (#2616)
- remove newline from easybuild-easyblocks package description (required to avoid installation error with setuptools>=59.0.0) (#2623)
- avoid patching binary files + other enhancements for MUMmer easyblock (#2630)
- enable build-in-installdir mode in constructor of PETSc and SLEPc easyblocks (#2631)
- skip netcdf4-python tests that require network connectivity (#2634)
v4.5.0 (October 29th 2021)
--------------------------
feature release
- new software-specific easyblock for imkl-FFTW (#2599)
- minor enhancements and updates, including:
- add support for installing R extensions in parallel (#2408)
- update MotionCor2 easyblock to consider to locations for built binary (#2541, #2598)
- let GROMACS runtime logs show EasyBuild was used by setting -DGMX_VERSION_STRING_OF_FORK configuration option (#2571)
- adjust qa list in WIEN2k easyblock to handle new questions + fix sanity check for v21.1 (#2572)
- enhance GCC easyblock to add support for AMD GPU offloading (#2578)
- add support for specifying subdirectory for target installation directory in CMakMake (#2579)
- enhance COMSOL easyblock to change permission on build directory during extract step (to allow using patches) (#2584)
- enhance FlexiBLAS easyblock to support building with Intel MKL (imkl) as backend (#2588)
- update MATLAB easyblock for 2021b (jre is no longer included) (#2589)
- update OpenCV easyblock to detect GTK3 and GTK2 dependencies (next to GTK+) (#2591)
- avoid that path to CUDA install directory is added to $PATH (#2593)
- enhance imkl easyblock to add support for installing with NVHPC (#2595)
- enhance PETSc easyblock to run tests in parallel (#2601)
- update ELSI easyblock to support two new external dependencies (#2602)
- add custom custom easyconfig parameter 'backends' in FlexiBLAS easyblock to specify backends (#2605)
- detect problem with compiling CPU detection code in configure output in GROMACS easyblock (#2609)
- use correct include directory for FlexiBLAS (#2610)
- various bug fixes, including:
- unset $EASYBUILD_* environment variables when running sanity check in EasyBuildMeta easyblock + also unset $MODULES_LMCONFLICT to avoid conflict when loading EasyBuild module (#2568)
- ensure that all ABAQUS components get installed for ABAQUS 2021.x (+ add support for enabling/disabling fe-safe) (#2569)
- fix subdir path in VTune easyblock for 2021.x versions + add sanity check command (#2576)
- make sure custom easyblock for installing EasyBuild respects requested version of Python (like $EB_PYTHON) (#2581)
- restore RPATH wrappers for OpenMPI sanity check (#2582)
- fix installation of libcp2k for recent CP2K versions (#2585)
- make version regex in OpenSSL wrapper easyblock less strict (version string does not always end with a letter) (#2597)
- redefine collect_exts_file_info instead of now deprecated fetch_extension_sources in OCaml easyblock (#2603)
- other changes:
- don't use --config=mkl for TensorFlow 2.4+ (#2583)
- this fixes some performance related issues for TensorFlow, see https://github.com/easybuilders/easybuild-easyblocks/issues/2577 and https://github.com/easybuilders/easybuild-easyconfigs/issues/14120
- fix support for recent imkl version in numexpr easyblock (#2606)
- derive custom easyblock from MotionCor2 from PackedBinary instead of EasyBlock (#2607)
v4.4.2 (September 7th 2021)
---------------------------
update/bugfix release
- 4 new software-specific easyblocks:
- CRISPR-DAV (#2487), jaxlib (#2545), ORCA (#2504), RepeatModeler (#2470)
- minor enhancements, including:
- update ABAQUS easyblock to support installation of v2020 (#2034)
- enable make check and sanity check exec for OpenMPI (#2444)
- fixed sanity check for later versions of Molpro (#2499)
- add Ampere to known GPU architectures for Kokkos in LAMMPS easyblock (#2510)
- update sanity check in ESMF easyblock to take into account new binary names from version 8.1.0 onwards (#2512)
- use report_test_failure in TensorFlow easyblock (#2519)
- add suport for imkl 2021.x in easyblocks for
- Amber (#2527), BerkeleyGW (#2528), CP2K (#2529), FreeFEM (#2530), GROMACS (#2531), numexpr (#2532)
- add install_src option and enhance buildcmd option in PythonPackage easyblock (#2534)
- make sure AOCC commands like clang/flang pick up GCCcore as GCC toolchain (#2538)
- create CMakeConfig files for tbb >= 2020 (#2539)
- find source dir for libunwind when building ldd for Clang versions >= 12.0.1 (#2540)
- fix motorBike test in sanity check for OpenFOAM 9 (#2544)
- generate and install pkg-config files for OpenSSL wrapper (#2549)
- don't run 'setup.py config' for numpy >= 1.21, since it's no longer supported (#2554)
- update WIEN2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (#2558)
- remove PCRE from list of system libraries for TensorFlow 2.6.0 (#2559)
- add support for also installing Tosca component in ABAQUS (#2560)
- update ABAQUS easyblock to support installing of version 2021 with hot fixes (#2562)
- update sanity check in VTune easyblock for 2021.x versions (#2563)
- various bug fixes, including:
- handle failure of running nvidia-smi in TensorFlow tests (#2506)
- remove Python 2.6 from list of supported Python versions in setup.py (#2507)
- clean up installation of Tkinter (#2509)
- remove redundant $CPATH entry of tbb modules + fix --module-only (#2511)
- honor --ignore-test-failure in PythonPackage (#2516)
- use correct GTK+ version for OpenCV based on dependencies (#2520)
- ensure Python prep is done in sanity check + support debug builds in TensorFlow easyblock (#2522)
- correct cleanup of single-letter local variable in __init__ of easybuild.easyblocks (#2524)
- reset runtest to None in CMakePythonPackage (#2536)
- set $I_MPI_ROOT correctly for 2021.x in impi easyblock (#2537)
- let Bundle easyblock pick up custom easyblock for components based on name if no easyblock is specified explicitly (#2543, #2547)
- explicitely use only OpenBLAS for PyTorch if MKL is not used (#2448)
- keep symlinks in cuDNN installations (#2550)
- use ${BLAS,LAPACK}_SHARED_LIBS in GROMACS easyblock for FlexiBLAS-based toolchains (#2552)
- copy the list to avoid changing the original lists in DEFAULT_TARGETS_MAP for Clang and LLVM (#2556)
- fix pathsep join bug that breaks installation of CUDA versions < 10.1 if $PERL5LIB is defined (#2561)
- other changes:
- simplify Boost easyblock (#2513)
- remove deprecated options from PythonPackage (#2535)
v4.4.1 (July 6th 2021)
----------------------
update/bugfix release
- 5 new software-specific easyblocks:
- AOMP (#2435, #2462, #2464), FreeFEM (#1969), NCCL (built from source) (#2337, #2460), torchvision (#2467), UCX plugins (#2491)
- minor enhancements, including:
- enhance Amber easyblock to support installing Amber via CMake (#2445)
- enhance ConfigureMake generic easyblock to add support for building multiple build targets (#2449, #2479, #2480)
- enhance sanity check for Clang to verify if CUDA offload library was produced (#2454)
- update custom easyblock for Boost to always build single and multi threaded versions (#2456)
- enhance sitecustomize.py in Python easyblock to support overriding core Python packages, and allowing overriding in virtualenv (#2458, #2483)
- update CMakeMake to handle old and new Boost/Boost.Python builds using custom easyblock for Boost (#2461)
- add file prefix option to XALT easyblock (#2463)
- enhance Java easyblock to define %(jdkarch)s template (#2472)
- adjust Perl easyblock to only check for a 'man' subdirectory if groff is a dependency (#2474)
- support arbitrary version strings in OpenSSL wrapper and add minimum_openssl_version option (#2475)
- enhance Python easyblock to explicitly disable installing core-pip when install_pip is not True (#2476)
- enhance intel-compiler easyblock to inlude multipath include dir in $CPATH (#2477)
- enhance Hypre easyblock to enable CUDA support (#2482)
- update Xmipp easyblock for new version (v3.20.07) (#2486)
- enhance FFTW easyblock to skip tests if --mpi-tests EasyBuild configuration option is disabled (#2490)
- use PYPI_SOURCE as the default for source_urls of extensions of Python easyconfigs (#2493)
- various bug fixes, including:
- only use siterc fix for NVHPC < 21.3 (#2453)
- fix CPU-only runtime for dpcpp-generated executables in custom easyblock for intel-compilers (#2457)
- always add distinct_host_configuration=false to build command for TensorFlow (#2459)
- disable installation of bundled BioPerl and HTSLib if they are dependencies of VEP (#2468)
- don't use list value for command to detect installed Python packages in TensorFlow easyblock (#2469)
- change Bundle easyblock to also collect altroot and altversion in the module step so they are set when running --module-only (#2485)
- always strip output from "gcc -print-multiarch" in intel-compilers easyblock (#2489)
- don't overwrite all of exts_default_options in TensorFlow easyblock (#2494)
- enhance GCC easyblock to make sure that system GCC provides LTO support, and disable LTO when building MPFR if not (#2498)
- rework the dependency handling of OpenMPI to use explicit configure options to disable features if required
dependency is not provided (#2500, #2501)
v4.4.0 (June 2nd 2021)
----------------------
feature release
- 3 new software-specific easyblocks:
- FlexiBLAS (#2369, #2422, #2424, #2426)
- dm-reverb (#2413)
- custom easyblock to install OpenSSL wrapper for OpenSSL installed in OS, with fallback to build and install OpenSSL from source if not available in OS (#2429)
- minor enhancements, including:
- also add -pthread to prebuildopts of cryptography (#2270)
- don't unpack Python wheel (*.whl) files by default in generic PythonPackage easyblock (#2366, #2442)
- enable installation of samples for CUDA > 10.1 (#2374)
- add option to disable pip connecting to PyPi (enable use of --no-index) (#2390)
- update MotionCor2 easyblock to handle new version and be aware of CUDAcore (#2394)
- make it possible to force disabling kernel features in Qt easyblock (#2403)
- update imkl easyblock to support oneAPI versions (>= 2021.x) (#2407)
- add "gurobi_cl --help" as default sanity check command for Gurobi (#2411)
- enhance BWA easyblock to copy includes and libraries (#2417)
- allow 'default' versions to be defined by ModuleRC easyblock (#2418)
- enhance MesonNinja and CMakeMake easyblocks to create unused build dir when separate_build_dir is set (#2419)
- enable sanity_pip_check by default for Python easyconfigs if pip >= 9.0 will be installed (#2423)
- enhance FFTW easyblock to support SVE CPU feature and building with Fujitsu compiler (#2425)
- make ScaLAPACK easyblock aware of FlexiBLAS (#2427)
- update imkl easyblock to unpack example tarballs and set $MKL_EXAMPLES (+ some code cleanup) (#2430)
- update list of system libs for TensorFlow 2.5 (#2432)
- allow disabling MPI tests when installing Intel MPI (impi) via --disable-mpi-tests (#2440)
- exclude bottleneck tests in PyTorch (#2450)
- various bug fixes, including:
- ensure lib subdirectory is found in stage 2 of GCC installation + fall back to lib64 (#2339)
- fix permission on MATLAB installer config file so it can be written to (#2385)
- fix problem with installing older CUDA versions that uses the Perl based installer (#2387)
- enhance Python easyblock: add option to install pip with core Python, tweak defaults, create unversioned pip symlink (#2388)
- fix installopts before installing the extension in GROMACS easyblock (#2391)
- updated numpy easyblock to use read_file for patch (#2395)
- use explicit build toolset and compiler path in Boost easyblock (#2402)
- replace hardcoded '2021.1.1' with 'self.version' in impi easyblock (#2405)
- set $SANDCASTLE when running PyTorch tests to disable some tests as-if we are on Facebook's CI (#2412)
- make GROMACS easyblock work with --module-only (#2414)
- make sure OpenFOAM sanity checks don't require builddir write permissions (#2415)
- make Tkinter easyblock work with --module-only (#2416)
- also disable altivec with FFTW 3.3.9 on POWER (#2437)
- make sure that self.python_cmd is set before using it in PythonPackage.sanity_check_step (#2447)
- other changes, including:
- update setup.py to indicate compatibility with Python 3.8 and 3.9 (#2384)
- use on_error rather than deprecated log_error named argument for which function (#2406)
- remove cuda_compute_capabilities from custom easyconfig parameters for Clang, LAMMPS and TensorFlow (now supported as general easyconfig parameter) (#2433)
v4.3.4 (April 9th 2021)
-----------------------
update/bugfix release
- minor enhancements, including:
- make OpenCV easyblock aware of protobuf, libwebp and OpenEXR dependencies provided via EasyBuild (#2346)
- update CP2K easyblock w.r.t. running regtest for CP2K v8.1 (#2350)
- update GROMACS easyblock for GROMACS/2021 with CUDA (#2353)
- adjust call to python-config for Python >= 3.8 in VMD easyblock (#2355)
- enhance cuDNN and CUDA easyblocks to support aarch64 (#2356)
- pass down compiler flags provided by EasyBuild in g2clib easyblock (#2357)
- update VTune easyblock for version 2020 (#2359)
- make WRF and WPS easyblocks aware of (pre)configopts (#2361)
- add Clang version 12.0.0 for AOCC 3.0.0 to mapping in custom easyblock for AOCC (#2362)
- use PYPI_SOURCE as the default for source_urls of PythonPackage (#2364, #2370)
- enhance PythonPackage easyblock to catch faulty version (0.0.0) for installed Python packages (#2367, #2377)
- enhance BWA easyblock: pass compiler flags + use filetools functions (#2368)
- various bug fixes, including:
- set $R_LIBS_SITE rather than $R_LIBS when installing R packages (#2326)
- update PETSc easyblock to take into account that ScaLAPACK installation may not have header files + fix building in parallel (#2348)
- disable CMake user package repository in CMakeMake generic easyblock (#2351)
- update LAPACK easyblock to keep control of compiler options for versions >= 3.9.0 (#2358)
- also set $TORCH_CUDA_ARCH_LIST for PyTorch tests (#2363)
- enhance Hadoop easyblock to avoid copying same native library twice (#2371)
- fix pip extension download pattern for PythonPackage easyblock (#2372)
- make the CUDA stub libs take preference over system libs when linking (#2373)
- improve Python package version check and add unversioned_packages easyconfig parameter (#2377)
v4.3.3 (February 23rd 2021)
---------------------------
update/bugfix release
- 2 new software-specific easyblocks:
- AOCC (#2295), Intel compilers (v2021.x, oneAPI) (#2305)
- minor enhancements, including:
- run motorBike tutorial case as sanity check for recent (community) OpenFOAM versions (#2201)
- add foamMonitor to sanity checks of OpenFOAM (#2256)
- create versioned symlinks for CMake commands + create symlink for 'cmake3' in PyTorch easyblock if cmake3 command is not found (#2259)
- improve Bazel easyblock: add support for running tests, enable static linking, use build dir rather than tmpdir, verbose output (#2285)
- add support for skipping steps in Python packages installed as extension + print progress on individual steps for installing Python packages as extensions (#2290)
- update BerkeleyGW easyblock to support GCC 10 and fftlib (#2297)
- update QuantumESPRESSO easyblock to support GCC 10 (#2298)
- update Clang easyblock to add support for building extra tools + leveraging hwloc and Z3 as optional dependencies (#2310)
- add support for running TensorFlow CPU and GPU tests (#2263, #2292, #2312)
- update impi easyblock for impi 2021.x (oneAPI) (#2313)
- update QuantumESPRESSO easyblock to handle v6.7 (#2319)
- update OpenFOAM easyblock for changes in v2012 (#2321)
- add sanity check commands to GCC (including LTO support) (#2322)
- update FLUENT sanity check for v2021R1 (#2334)
- various bug fixes, including:
- filter out user packages in LAMMPS easyblock if corresponding dependency isn't included + only set -DUSER-INTEL on x86_64 systems (#2254)
- unify handling of pylibdirs and don't add duplicated $PYTHONPATH in PythonBundle (#2281)
- enhance Amber easyblock to fix running of update_amber script when 'python' command is not available in OS (#2282)
- guard 'module unload' statements in modules for Cray* toolchains (#2286)
- set $PYTHONNOUSERSITE in PythonBundle.extensions_step to avoid picking up on Python packages installed in $HOME (#2289)
- create less temporary directories for TensorFlow by (only) using --output_user_root (#2293)
- fix logic w.r.t. enabling Python support in PETSc (#2299)
- make builddeps a list of names in SLEPc easyblock (#2300)
- make builddeps a list of names in Trilinos easyblock (#2301)
- make sure the installation of libiberty.a in the binutils easyblock goes into a populated directory (#2308)
- fix for building GCC with --sysroot on ppc64le (#2315)
- fix OpenFOAM sanity check on POWER (#2320)
- use library search paths of compiler for RPATH when building binutils with system compiler + enhance sanity check by running --version for binutils commands (#2323, #2327)
- pass $CXXFLAGS to PDT's configure script via '-useropt' (#2324)
- pass down compilation flags from build environment for ESMF (#2325)
- update URLs for test data for WRF to https (#2335)
- read MATLAB configuration file in binary mode to avoid UTF-8 encoding errors when using Python 3.6 (#2340)
- fix Boost sanity check on POWER (#2291) and aarch64 (#2341)
- other changes, including:
- rework module-only tests to use unique software name (rather than 'foo') (#2287)
- prefer default value for extra options in easyblock tests (#2280, #2302)
- add check for accepted EULA in custom easyblock for NVHPC (#2311)
- update optional feature support of TensorFlow (#2314)
- make symlinking of posix_c.so to posix.so in test suite configuration conditional (#2330)
v4.3.2 (December 10th 2020)
---------------------------
update/bugfix release
- 2 new software-specific easyblocks:
- code-server (#2255), Metagenome-Atlas (#2219)
- minor enhancements, including:
- add -fallow-argument-mismatch option when building CP2K 7.1 or older with GCC 10.x (#2223)
- update TensorFlow easyblock for upcoming TensorFlow 2.4 (#2225)
- add support for building Clang with OpenMP offload support (#2229)
- enhance OpenMPI easyblock to catch any --with-ucx* configure options (#2230)
- take into account preinstallopts and installopts in custom easyblock for NCL (#2234)
- add support for withnvptx easyconfig parameter, to enable GPU offloading, in GCC easyblock (#2235)
- take into account versions like '4.x' in OpenFOAM easyblock (#2239)
- also add 'bin' subdir to $PATH when installing a Python package (#2244)
- various bug fixes, including:
- fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK (#2212)
- fix version check in Qt5 easyblock w.r.t. disabling features on old Linux kernel versions (#2220)
- always define $FCCPP in QuantumESPRESSO easyblock (not just when using Intel compilers) (#2221)
- allow wxPython to be installed as an extension (#2227, #2275)
- only configure Python with --enable-optimizations when compiling Python with (recent) GCC compiler (#2228)
- fix sanity check for Boost MT libraries (#2231)
- fix hardcoded path in NVHPC easyblock to support multiple architectures (#2233)
- fix CPASSERT test faults on RHEL8 in CP2K easyblock (#2236)
- stop silently ignoring failing numpy tests, but include support for ignoring (failing) numpy tests (#2238, #2271)
- append to module guesses in easyblocks for Chapel, icc, imkl and impi (rather than overwriting guesses from parent easyblock) (#2242)
- weed out duplicates when determining paths to include-fixed subdirectory in GCC easyblock (#2245)
- prepend all hardcoded /usr/* paths with sysroot in Python's setup.py installation script (#2246)
- don't try to patch newer versions of Bazel where the patches won't apply (#2249)
- fix setting of $RUNPARALLEL in HDF5 easyblock (#2250)
- move --build and --host logic to run_configure_cmd in GCC easyblock (#2252)
- set $UCX_TLS in module for impi installation on top of UCX, and allow it to be overwritten in impi easyconfig file (#2253, #2258)
- enhance PyTorch easyblock to ensure it finds MKL (via $MKLROOT) (#2257)
- use integer division to determine number MPI ranks to use in WRF test step (#2266)
- also specify locincpth and glibpth configure options for Perl based on --sysroot (#2268)
- other changes, including:
- add link to GCC mailing list thread confirming that binutils should not be configured with --with-sysroot=$EASYBUILD_SYSROOT when GCC is being configured like that (#2215)
- pass paths to patch one by one to apply_regex_substitutions in GCC easyblock when --sysroot is set (#2217)
- workaround for regression in apply_regex_substitutions introduced in EasyBuild v4.3.1 (which was fixed for v4.3.2)
v4.3.1 (October 29th 2020)
--------------------------
update/bugfix release
- 2 new software-specific easyblocks:
- CFDEMcoupling (#1439), NVHPC (#2190)
- minor enhancements, including:
- support having PyQt5 installed as part of Qt5 in QScintilla easyblock (#2040)
- update TensorFlow easyblock to put Bazel build files in build directory + avoid unnecessary runtime patching (#2166)
- update CBLAS easyblock for toolchains that include imkl (#2175)
- add workaround for duplicate prefix path in Eigen CMake config (#2176)
- enable CTEST_OUTPUT_ON_FAILURE for CMakeMake test step (#2181)
- add XLA build support to TensorFlow easyblock (#2182)
- also consider libfabric dep (--with-ofi) when setting default OpenMPI configure options (#2184)
- make easyblock for installing CMake aware of --sysroot (#2187)
- make OpenBLAS respect the parallelism set by easybuild (#2191)
- handle option of building Michigan State University CCT3 & CCSD3A methods in GAMESS_US easyblock (#2194)
- add support to RubyGem easyblock for installing zipped gems (#2203)
- update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0) (#2205)
- update Score-P easyblock to add support for NVHPC toolchain (#2206)
- various bug fixes, including:
- add torch/lib subdirectory in Python lib dir to $LD_LIBRARY_PATH for PyTorch installations (#2183)
- update MUMmer easyblock to use apply_regex_substitutions and copy_file functions (#2185)
- configure OpenMPI 4.x with --without-verbs when using UCX (#2188)
- take into account that zlib may be listed in --filter-deps in custom easyblock for XML R package (#2189)
- add sanity check commands to Clang easyblock and print warning for missing ncurses (#2193)
- enhance OpenFOAM easyblock to add symlinks for libraries to ensure 'mpi' versions have preference over 'dummy' versions (#2196)
- leverage installed OpenSSL/BoringSSL when cURL is used as a dependency for TensorFlow (#2197)
- add -ffree-line-length-none to gfortran flags in Siesta easyblock (#2204)
- respect --disable-mpi-tests in Siesta easyblock (#2207)
- other changes, including:
- set $EB_INSTALLPYTHON in module generated for EasyBuild rather than setting $EB_PYTHON, to allow overriding Python command to be used for running EasyBuild with $EB_PYTHON (#2109)
- remove unused custom easyblock for DIRAC (#2192, #2198)
v4.3.0 (September 13th 2020)
----------------------------
feature release
- 2 new software-specific easyblocks:
- pybind11 (#2115), PyTorch (#2104)
- minor enhancements, including:
- update MATLAB easyblock to use new binary installer for versions >= 2020a (#2058)
- add use_pip_requirement custom easyconfig parameter to PythonPackage easyblock to allow providing a requirements file to the pip command, as a source (#2064)
- update CP2K easyblock for recent versions (>= 7.0) (#2069)
- add multi_deps support into custom easyblock for QScintilla (#2077)
- update Mothur easyblock for v1.44.0 and higher (#2084)
- update MotionCor2 easyblock to add support for v1.3.2 (#2100)
- update Tinker easyblock to handle skipping of tests depending on version and link with fftw_omp (#2102)
- launch test & sanity check commands through mpirun for netcdf4-python if MPI support is enabled (#2106)
- check for installation of pip & setuptools in Python 3.4+ (#2108)
- update QuantumESPRESSO easyblock to support version 6.6 (#2112)
- allow NAMD to be built on POWER, and also use the CUDA arch info (#2113, #2123)
- update Libint easyblock for versions >= 2.6.0 + add custom easyconfig parameter to enable Fortran support (#2116)
- update TensorFlow easyblock to use system/EasyBuild installed libraries (#2117, #2165, #2163, #2172)
- add support in NAMD easyblock to pass additional C++ compiler options for building Charm++ component with + wrap them in single quotes (#2118)
- automatically add required '-G Ninja' option when using CMakeNinja easyblock + add 'generator' custom easyconfig parameter for CMakeMake (#2120)
- make several easyblocks aware of --sysroot EasyBuild configuration option: binutils (#2147, #2159), CMakeMake (#2152), GCC (#2143), Perl (#2142), Python (#2148, #2149)
- make Mesa easyblock aware of aarch64 (#2153)
- enhance sanity check in custom Doxygen easyblock to catch broken installation (#2171)
- various bug fixes, including:
- make TensorFlow easyblock ignore the PKG_REVISION identifier if NCCL version if it exists (#2085)
- remove version check against the version.txt file in CUDA easyblock (#2097)
- add 'lib' symlink in tbb installation directory when building from source (#2103)
- handle GNUInstallDirs special cases in CMakeMake easyblock (#2105, #2124)
- patch ELPA's manual_cpp script to fix hardcoded '/usr/bin/python' (#2107)
- make TensorFlow easyblock also set $GCC_HOST_COMPILER_PREFIX to specify binutils location (#2110)
- ensure stand-alone Python package being installed is in view when running 'pip check' by loading fake module first (#2114)
- be more patient when running interactive configure script for WRF (#2119)
- make sure self.start_dir is set to a full path before constructing installation command in RPackage easyblock (#2125)
- correctly check whether 'modinc' easyconfig parameter is set to True in CP2K easyblock (#2138)
- update PSI easyblock to correctly find Python and enable PCMSolver/CheMPS2 (#2141)
- fix running GROMACS tests when using 'eb --rpath' (#2144, #2154)
- remove existing Python installation directory if both 'eb --rpath' and --enable-optimizations configuration option are used (#2146)
- ensure libQt5Core.so is compatible with older Linux kernels by disabling renameat2 and getentropy features (#2151)
- solve issue where pybind11 picks up on the system Python instead of one provided by a module (#2158)
- fix Qt5 easyblock to support installation on Arm/aarch64 (requires platform to be linux-g++) (#2160)
- fix OpenFOAM easyblock to support installation on Arm/aarch64 systems (#2162)
- explicitely enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (#2164)
- fix sanity check in Mathematica easyblock for 11.x versions older than 11.3 (#2168)
- unset $COLUMNS if it is set to '0' before running Perl's configure script (#2169)
- other changes:
- filter out Python in SLEPc configure (#2101)
- switch to status badge based on tests run in GitHub Actions CI in README (#2126)
- fix code style issues to make flake8 checks pass (#2128-#2137, #2140, #2145, #2155)
- limit test configurations in Travis CI to only Python 2.6 (#2139)
v4.2.2 (July 8th 2020)
----------------------
update/bugfix release
- 3 new software-specific easyblocks:
- LLVM (#2065), Scipion (#1847), XALT (#1942)
- minor enhancements, including:
- use 'wclean -platform' instead of 'wcleanPlatform' for OpenFOAM v2006 & newer (#2088)
- various bug fixes, including:
- only build OpenCV with IPP support on x86_64 systems (#2056)
- make sure CFLAGS and MYCFLAGS are used in Lua easyblock (#2062)
- also accept 'exist_lic' as valid value for 'license_file' in IntelBase easyblock (#2067)
- fix minor bug in shared libs handling and correctly setup SuiteSparse variables in Trilinos easyblock (#2071)
- make sure PythonBundle uses correct 'python' command in extensions filter + also add lib64/python*/site-packages to $PYTHONPATH (if it exists) (#2075, #2081)
- fix build environment for WRF by patching shebang in compile script (#2079)
- fix order of intel64/lib paths in generated module for impi (and drop intel64/lib/release_mt) (#2080)
- set $XDG_CACHE_HOME to avoid abuse of $HOME/.cache/pip when installing DOLFIN (#2082)
- make VMD easyblock Python 3 compatible (#2083)
- rename include-fixed subdirectory in GCC installation to avoid problems after OS upgrade (#2087, #2093, #2094)
- use glob pattern to determine name of Mathematica installation script (#2089)
- use mpirun for sanity check commands in LAMMPS easyblock (#2096)
v4.2.1 (May 20th 2020)
----------------------
update/bugfix release
- add generic easyblock for installing Go packages: GoPackage (#2042)
- minor enhancements, including:
- update config.guess for all R packages, required installing R + extensions on Linux/POWER systems (#1949)
- add support for preinstallopts and install in subdirectory to Tarball generic easyblock (#1989, #2049)
- rewrite GROMACS easyblock to install all four variations (single/double precision, with/without MPI) in the same directory (#1991)
- add custom 'subdir_version' easyconfig parameter for FLUENT (#2021)
- use updated config.guess in GCC easyblock (#2033, #2059)
- add extra question pattern to support installing CPLEX 12.10 (#2038)
- add support for building NWChem on top of external GlobalArrays + also define $LAPACK_LIB (required for NWChem 7.x) (#2043)
- execute minimal test in sanity check commands in impi easyblock (#2045)
- update for MotionCor2 easyblock for v1.3.1 (#2046)
- fixes + enhancements for PETSc easyblock (#2048)
- various bug fixes, including:
- use correct version in ELPA preprocessor flag used for QuantumESPRESSO v6.x (#2027)
- generically find the arch folder and add top-level bin/lib symlinks in PDT & TAU easyblocks (#2029)
- fix typo in LAMMPS easyblock preventing disabling the USER-INTEL package via configopts (#2031)
- let CMakeMake remove 'easybuild_obj' build directory if it already exists (#2032)
- include own lib dir in RPATH before system lib dirs in binutils easyblock (#2044)
- clean $CPATH before building ROOT to avoid clash between external LLVM loaded as a dependency and internal LLVM used by ROOT (#2047)
- don't let extract_file change directory in various easyblocks (#2051)
- make postinstallcmds available to Mathematica easyconfigs + add bin/Executables to $PATH (#2052)
- fix the extra dirs added to PATH in FreeSurfer easyblock (#2053)
- correct download url for test data in WPS easyblock (#2055)
- fix typo in warning in TensorFlow easyblock (#2057)
- fix failing sanity check under --module-only in GCC easyblock (#2059)
- other changes:
- add configure options for CubeLib/CubeWriter dependencies in Score-P easyblock (#2030)
- remove local find_glob_pattern in Blender & ROOT easyblocks, use function provided by filetools instead (#2037)
v4.2.0 (April 14th 2020)
------------------------
feature release
- 7 new software-specific easyblocks:
- BerkeleyGW (#1951), CMake (#1936), ELSI (#1883), LAMMPS (#1964, #1975, #1978, #1982, #1997), libdrm (#1983), Mesa (#1892, #2006), SEPP (#1998)
- minor enhancements, including:
- make ParMETIS easyblock compatible with custom configopts (#1774)
- update Trinity easyblock for v2.9.0 (#1906)
- disable ROCM and Android workspace explicitely in TensorFlow easyblock (#1944)
- update QuantumESPRESSO easyblock for version 6.5 (#1947)
- update Siesta easyblock to support MaX-1.0 release (#1954)
- update Ferret easyblock for versions >= 7.5.0 (#1956)
- update XCrySDen easyblock to support Togl dependency (#1959)
- pass value for TARGET specified in buildopts to testopts and installopts in OpenBLAS easyblock (#1960)
- fix netCDF(-Fortran) support in Siesta easyblock (#1967, 1971)
- add NCDF_PARALLEL and METIS support to Siesta easyblock (#1973)
- add support for 'use_pip_extras' custom easyconfig parameter in PythonPackage easyblock (#1980)
- update Open Babel easyblock for version 3.0.0 (#1992)
- allow differing names for TensorFlow wheel (#1995)
- make MATLAB runtime available from MATLAB (#2008)
- various bug fixes, including:
- fix linking of Hypre to external BLAS/LAPACK + support building (only) static/shared library (#1885)
- fix MPI-CXX dependency of PETSc (#1917)
- limit amount of parallelism in TensorFlow easyblock (#1934)
- support GCCcore and gcc4.8 (if that dir exists) in function get_tbb_gccprefix in tbb easyblock (#1943)
- restore default flake8 warnings (#1950)
- remove tests from build_step and raise error on failed tests in OpenBLAS easyblock (#1952, #1955, #1962)
- add optional runtest to the catch for FATAL ERRORS to OpenBLAS easyblock (#1958)
- ensure right 'python' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (#1961)
- make sure lib/python*/lib-dynload exists in Python installation (#1966)
- in version 6.0 of TensorRT, libnvinfer.a is renamed libnvinfer_static.a (#1970)
- handle configopts without configure args in CMake easyblock (#1974)
- use checkout@v2 in GitHub Actions to fix broken re-triggered tests (#1976)
- don't insist that pylibdir always exists in OpenCV easyblock (#1977)
- also set $TRINITY_HOME environment variable in Trinity easyblock (#1979)
- fix sanity check for OpenFOAM-Extend >= 4.1 (#1981)
- fix pattern matching in regex subst for I_MPI_ROOT in impi easyblock (#1986)
- use remove_dir instead of deprecated rmtree2 in various easyblocks (#1993)
- fix "AttributeError: module 'git' has no attribute 'Git'" that may occur when using Python 3 (#1994)
- don't sanity check for QtWebEngine in Qt easyblock when building for POWER (#2000)
- fix installation of TensorFlow in some environments, by setting $PYTHONNOUSERSITE (& more) (#2002, #2020)
- make sure libxml2 is built with XZ provided as dependency (#2005)
- look for Python version directories with suffixes in ROOT easyblock (#2010)
- enable TK, FLTK and OPENGL configure options in VMD easyblock (#2013)
- update the contributing docs (#2014)
- fix numexpr easyblock to allow (correctly) installing it as extension (#2022)
- other changes:
- simplify various CMakeMake-based easyblocks by enhancing CMakeMake (w.r.t. CMAKE_BUILD_TYPE, shared vs static libs, fPIC) (#1929)
- enable out of tree build by default in CMakeMake easyblock (#1933)
- force building Clang without CUDA when it is not found as a proper dependency (#1968)
v4.1.1 (January 16th 2020)
--------------------------
update/bugfix release
- new software-specific easyblock for cryptography (to fix missing -pthread for all versions) (#1874)
- minor enhancements, including:
- update WPS easyblock for v3.6 & newer (#1315)
- update FSL easyblock to support FSL v6.0.2 & newer (#1860)
- add setup_cmake_env function in CMakeMake easyblock which can be leveraged in other easyblocks, and use it for OpenFOAM (#1869)
- remove obsolete configure options for Python + build with optimizations/LTO enabled for recent Python versions (#1876)
- update WPS easyblock for recent versions: set $WRF_DIR to point to location of WRF installation (#1886)
- make sure $LIBLAPACK_MT is set before using it in ESMF easyblock (#1887)
- remove useless PATH entries + add PKG_CONFIG_PATH in imkl easyblock (#1900)
- enhance tbb easyblock to support building on POWER (#1912)
- enhance TensorFlow easyblock to pick up on --cuda-compute-capabilities, and issue a warning if no CUDA compute capabilities are specified (#1913)
- add custom easyconfig parameter 'build_type' to generic CMakeMake easyblock (#1915, #1922)
- various bug fixes, including:
- fix for conda packages that rely on particular versions of Python (#1836)
- fix path for intel and netCDF lib directories in NCL easyblock (#1862)
- fix CUDA 10.1 installation on POWER (#1871)
- change Bazel easyblock to prefer using Java dependency rather than included JDK (fix for POWER9) (#1875)
- remove optarch warning in GROMACS for Cray toolchains (#1879)
- also fix $WM_COMPILE_OPTION in OpenFOAM rc scripts to make debug builds work correctly (#1880)
- limit MPI ranks used for running WRF test cases to max. 4 + include contents of rsl.error.0000 output file in case test failed (#1884)
- update $PYTHONPATH + add "python -c 'import mrtrix3'" as sanity check command for recent MRtrix versions (#1889)
- update sanity check in SAMtools easyblock for version 1.10 (#1890)
- make sure $PYTHONNOUSERSITE it set when performing sanity check for (bundles of) Python package(s) (#1891)
- fix install dir subdir for WPS v4.0+ that is considered for $PATH and $LD_LIBRARY_PATH (#1895)
- impi: don't rebuild libfabric if the source code is not present (#1896)
- also copy component patches to self.cfg in Bundle generic easyblock (#1897)
- skip patch step in Bundle generic easyblock (per-component patches are still applied) (#1898)
- derive easyblock for iccifort only from icc easyblock (not ifort), to avoid adding include subdir to $CPATH (#1899)
- add 'export LANG=C' to preinstallopts instead of install_script path in CUDA easyblock (#1902)
- stop setting updating $CPATH and $LIBRARY_PATH for GCC and GCCcore, not required (#1903)
- remove $LIBRARY_PATH entries in iccifort easyblock, already known to icc et al (#1904)
- use major/minor version of Python command being used if req_py_majver/req_py_minver are not specified (#1907)
- define $EB_PYTHON in module for EasyBuild installation, to make sure correct Python version is used at runtime (#1908)
- fix Python easyblock to allow configuring build of Python v3.8 (Setup.dist script was renamed to Setup) (#1909)
- fix netCDF easyblock for version 4.4.0 (#1911)
- correct comment about when we set RUNPARALLEL in HDF5 easyblock (#1914)
- do not sanity check on MATLAB compiler, since it requires a separate license (#1916)
- build HDF5 without MPI C++ extension to avoid breaking linkage for C software that requires HDF5 (#1918, #1919)
- override set_pylibdirs method in VersionIndependentPythonPackage to hard set self.pylibdir to 'lib' (#1924)
- other changes:
- increase timeout for interactive installation command in CUDA easyblock to 1000 sec. (#1878)
- disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#1882)
- stop requiring Python dep for SWIG, just configure with --without-python if Python is not a dependency (#1894)
- update copyright statements for 2020 (#1905)
- make Hound CI code style checker ignore "Black would make changes" produced by flake8-black (#1923)
v4.1.0 (December 4th 2019)
--------------------------
update/bugfix release
- new software-specific easyblock for cuDNN, to allow setting cudnnarch (#1855)
- refactored software-specific easyblock for Xmipp, based on Scons (#1837)
- minor enhancements, including:
- add prebuildopts to Bazel build command (#1838)
- add support to Toolchain generic easyblock for defining $EB* environment variables for toolchain components that use an external module (#1849)
- add support for running 'pip check' during sanity check in generic PythonPackage easyblock (#1853)
- various bug fixes, including:
- clean up /tmp/cuda-installer.log in CUDA easyblock, to avoid segfault in cuda-installer (#1835)
- minor fix to name of Gctf binary (#1840)
- move BLAS toolchain existence check earlier in SuperLU easyblock (#1842)
- fixes for TensorFlow easyblocks w.r.t. Bazel build options & __init__ in top-level google-protobuf package dir (#1843)
- fix support for sequential version in MUMPS easyblock (#1845)
- change default value of files_to_copy to None in MakeCp generic easyblock + code cleanup & use change_dir, copy_dir, copy_file and mkdir function from filetools (#1848)
- prepend -L$EBROOTZLIB/lib to LDFLAGS in SCOTCH easyblock (#1850)
- improve configuration in netCDF and netcdf4_python easyblocks (#1852)
- fix CUDA header paths for TensorFlow versions < 1.14 (#1854)
- handle incorrect regex better in generic CmdCp easyblock (#1861)
- add missing docstrings in cmakeninja easyblock (#1867)
- other changes:
- add GitHub Actions workflow to run easybuild-easyblocks test suite (#1844)
v4.0.1 (October 15th 2019)
--------------------------
update/bugfix release
- one new generic easyblock: CMakeNinja (#1829)
- new software-specific easyblock for Gctf (#1827), MotionCor2 (#1819)
- minor enhancements, including:
- update OpenFOAM easyblock for changes in version 1906 w.r.t. wmake rules (#1772)
- add %(cudaarch)s template variable so that it can be used in CUDA sources (#1797)
- update Boost easyblock for versions >=1.71.0 (#1814)
- update RepeatMasker easyblock for version 4.0.9 (#1815)
- add --verbose flag to 'pip install' when running EB in debug mode (#1822)
- update TensorFlow easyblock to support TensorFlow 2.0 (#1823)
- add support in TensorFlow easyblock to run a custom test script as smoke test (#1824)
- add support for installing QScintilla on top of PyQt5 (#1825)
- update VEP easyblock to make installation compatible with Bio::EnsEMBL::XS (#1828)
- various bug fixes, including:
- enhance TensorFlow easyblock to support installing TF 1.14.0 with CUDA and MPI support (#1811, #1816)
- avoid UnicodeDecodeError when reading 'configure' script and checking for 'Generated by GNU Autoconf' in ConfigureMake (#1817, #1821)
- don't require 'python' command to install libxml2 without Python bindings (#1818)
- make sure "generic=True" actually turns on generic build in GCC easyblock (#1826)
- fix compatibility of Trilinos easyblock with Python 3 (#1831)
v4.0.0 (September 20th 2019)
----------------------------
feature release
- fixes due to backwards-incompatible changes in easyBuild-framework v4.0.0
- use is_system_toolchain() rather than checking toolchain name against DUMMY_TOOLCHAIN_NAME constant (#1690, #1728)
- fix compatibility of various easyblocks with Python 3 (#1640, #1644, #1648, #1721, #1794, #1808, #1795, #1796, #1807, #1809)
- new software-specific easyblocks for OpenMPI (#1789, #1801), iccifort (#1799) and numexpr (#1803, #1804)
- various other enhancements, including:
- removed checks for Boussinesq and sonic solvers for OpenFOAM 7, since those have been deprecated (#1733)
- update Paraver easyblock to support recent versions (#1790)
- various bug fixes, including:
- update the PyPI trove classifiers (#1723)
- make the plugins build use the correct Tcl library version in VMD easyblock (#1786)
- use *_MT libs for BLAS/LAPACK only if openmp is enabled in Trilinos easyblock (#1791)
- filter out empty entries in $CPATH or $C_INCLUDE_PATH when building Perl, since that breaks the build (#1800)
- set $XDG_CACHE_HOME in TensorFlow easyblock to avoid that pip (ab)uses $HOME/.cache (#1802)
- don't load modules for dependencies in CrayToolchain.prepare_step (#1805)
- other changes:
- drop requirement for setuptools as runtime dependency (#1689)
- enable 'check_ldshared' in generic PythonPackage easyblock by default for recent Python versions (#1788)
- stop trying to use setuptools.setup in setup.py, always use distutils.core.setup instead (#1793)
v3.9.4 (August 23rd 2019)
-------------------------
update/bugfix release
- new software-specific easyblock for MSM (#1770, #1775, #1776)
- minor enhancements, including:
- allow specifying the license file directly in MATLAB easyblock (#1712)
- enhance CPLEX easyblock to also build Python bindings (#1738)
- workaround for XCrySDen for Tcl 8.6 (#1749)
- update WIEN2k easyblock to support version 19.1 (#1758)
- resolve custom %(cudaarch)s template value for CUDA sources (#1766)
- enhance sanity check for Blender to make sure that Cycles render engine is available (#1779)
- various bug fixes, including:
- only check for qtwebengine in custom easyblock for Qt(5) if glibc is sufficiently recent (#1771)
- correctly define comp.src in Bundle easyblock, to fix compatibility with easyblocks that leverage self.src (#1777)
- fix Bundle.check_checksums to checksums for extensions are also checked (#1778)
v3.9.3 (July 8th 2019)
----------------------
update/bugfix release
- minor enhancements, including:
- also install docs and demos in Rosetta easyblock (#1745)
- update HEALPix easyblock to work with latest version of HEALPix' configure.sh (#1752)
- make HPCG log pattern more generic, it changed in 3.1 (#1753)
- allow bootstrapping GCC with profile-guided optimizations (#1756)
- only require vsc-base for EasyBuild 2.x and 3.x in EasyBuildMeta easyblock (#1757)
- extend question patterns with 'https' URL entry in Modeller easyblock for recent verisons (#1762)
- modextrapaths implemented on easyblock level, sanity_check_step, gcc_target added in HEALPix easyblock (#1763)
- update OpenBLAS easyblock to be aware of POWER9 support in OpenBLAS 0.3.6 (#1765)
- various bug fixes, including:
- stick to Ubuntu Trusty when testing with Python 2.6 in Travis (#1751)
- fix scripts installation path in SNPhylo easyblock (#1759)