Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20240122173303_new_pr_RELION500_beta20231221

.github/workflows/linting.yml

@@ -28,4 +28,4 @@ jobs:
       run: flake8
 
     - name: Run flake8 to verify PEP8-compliance of Easyconfigs
-      run: flake8 --select W605  --filename '*.eb'
+      run: flake8 --select F,W605  --filename '*.eb'

easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb

@@ -15,7 +15,7 @@ toolchain = {'version': '2015a', 'name': 'foss'}
 sources = [SOURCE_TAR_GZ]
 source_urls = [GNU_SAVANNAH_SOURCE]
 
-checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce']
+checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a']
 
 dependencies = [
     ('XZ', '5.2.2'),

easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb

@@ -15,7 +15,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'}
 sources = [SOURCE_TAR_GZ]
 source_urls = [GNU_SAVANNAH_SOURCE]
 
-checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce']
+checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a']
 
 dependencies = [
     ('XZ', '5.2.2'),
@@ -24,7 +24,6 @@ dependencies = [
 preconfigopts = 'export LIBS="$LIBS -llzma" && '
 
 sanity_check_paths = {
-    'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT],
     'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)],
     'dirs': []
 }

easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb

@@ -15,7 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'}
 sources = [SOURCE_TAR_GZ]
 source_urls = [GNU_SAVANNAH_SOURCE]
 
-checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce']
+checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a']
 
 dependencies = [
     ('XZ', '5.2.2'),
@@ -24,7 +24,6 @@ dependencies = [
 preconfigopts = 'export LIBS="$LIBS -llzma" && '
 
 sanity_check_paths = {
-    'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT],
     'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)],
     'dirs': []
 }

easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb

@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABySS'
+version = '2.3.7'
+
+homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss'
+description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'cstd': 'c++17'}
+
+source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f']
+
+dependencies = [
+    ('Autoconf', '2.71'),
+    ('Automake', '1.16.5'),
+    ('Boost', '1.82.0'),
+    ('sparsehash', '2.0.4'),
+    ('btllib', '1.7.0'),
+]
+
+preconfigopts = "./autogen.sh && "
+configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"'
+
+sanity_check_paths = {
+    'files': ["bin/ABYSS", "bin/ABYSS-P"],
+    'dirs': []
+}
+
+sanity_check_commands = ['ABYSS --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AEDT/AEDT-2024R1.eb

@@ -0,0 +1,16 @@
+name = 'AEDT'
+version = '2024R1'
+
+homepage = 'https://www.ansys.com/products/electronics'
+description = """The Ansys Electronics Desktop (AEDT) is a platform that enables
+true electronics system design. AEDT provides access to the Ansys gold-standard
+electromagnetics simulation solutions such as Ansys HFSS, Ansys Maxwell, Ansys Q3D
+Extractor, Ansys SIwave, and Ansys Icepak using electrical CAD (ECAD) and mechanical
+CAD (MCAD) workflows."""
+
+toolchain = SYSTEM
+
+sources = ['ELECTRONICS_%(version)s_LINX64.tgz']
+checksums = ['7b131adf981ebca1e2f4fe8e607e50323167b69e77180a0ab61b2759d57abca5']
+
+moduleclass = 'phys'

easybuild/easyconfigs/a/AFNI/AFNI-24.0.02-foss-2023a.eb

@@ -0,0 +1,67 @@
+# Updated to version 24.0.02 
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeMake'
+
+name = 'AFNI'
+version = '24.0.02'
+
+homepage = 'http://afni.nimh.nih.gov/'
+description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data -
+ a technique for mapping human brain activity."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True, 'pic': True}
+
+source_urls = ['https://github.com/afni/afni/archive/']
+sources = ['AFNI_%(version)s.tar.gz']
+checksums = ['2915ed5bf98712abe3373bfc285f946fdee6cf1367e23ba80575dd6eedb3529a']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('tcsh', '6.24.10'),
+    ('Python', '3.11.3'),
+    ('X11', '20230603'),
+    ('motif', '2.3.8'),
+    ('R', '4.3.2'),
+    ('PyQt5', '5.15.10'),
+    ('expat', '2.5.0'),
+    ('libpng', '1.6.39'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('GSL', '2.7'),
+    ('GLib', '2.77.1'),
+    ('zlib', '1.2.13'),
+    ('freeglut', '3.4.0'),
+    ('Pillow', '10.0.0'),
+    ('matplotlib', '3.7.2'),
+    ('SciPy-bundle', '2023.07'),
+    ('Xvfb', '21.1.8'),
+    ('FFmpeg', '6.0'),  # required for running the program
+]
+
+# Make sure stuff does not get installed in .local
+configopts = '-DSTANDARD_PYTHON_INSTALL=OFF '
+
+# Changing permissions of some files
+postinstallcmds = ['chmod a+x %(installdir)s/bin/afni_system_check.py ;']
+postinstallcmds += ['chmod a+x %(installdir)s/bin/uber_subject.py ; ']
+postinstallcmds += ['chmod a+x %(installdir)s/bin/init_user_dotfiles.py ; ']
+# Copying apparently missing files over
+postinstallcmds += ['cp -f %(start_dir)s/src/discoraj/ClusterExplorer/ClustExp_HistTable.py %(installdir)s/bin ; ']
+postinstallcmds += ['cp -f %(start_dir)s/src/discoraj/ClusterExplorer/ClustExp_StatParse.py %(installdir)s/bin ; ']
+postinstallcmds += ['cp -rf %(start_dir)s/src/scripts_for_r %(installdir)s/bin ; ']
+postinstallcmds += ['cp -rf %(start_dir)s/src/R_scripts %(installdir)s/bin/scripts_for_r ; ']
+
+sanity_check_commands = ["afni -help"]
+
+sanity_check_paths = {
+    'files': ['bin/afni', 'lib/libgts.%s' % SHLIB_EXT, 'lib/libnifti2.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+modextrapaths = {'PATH': ['bin/scripts_for_r']}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AMGX/AMGX-2.4.0-foss-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,114 @@
+easyblock = 'CMakeMake'
+
+name = 'AMGX'
+version = '2.4.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/NVIDIA/AMGX'
+
+description = """Distributed multigrid linear solver library on GPU"""
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+github_account = 'NVIDIA'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'AMGX-%(version)s_external-thrust.patch',
+    'AMGX-%(version)s_fix-openmp-linking.patch',
+]
+checksums = [
+    {'v2.4.0.tar.gz': 'b030b8c2e58c4c9987444e5d28fd61e1c5dcd65d484a290d6a18ae0bc5c0e9db'},
+    {'AMGX-2.4.0_external-thrust.patch': '90e4be09615a26bd7ebce68ced63d9d3b52141f7b480e8cedb17b05003656e16'},
+    {'AMGX-2.4.0_fix-openmp-linking.patch': '10046d5d9fff48cb4902797525d43963855c4834f262bdc3c341bbc2cb1f6f76'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('UCX-CUDA', '1.14.1', versionsuffix),
+    ('magma', '2.7.2', versionsuffix),
+    ('CCCL', '2.3.0', versionsuffix),
+]
+
+cuda_compute_capabilities = ['7.0', '8.0', '9.0']  # AMGX defaults for CUDA 12
+
+configopts = '-DCUDA_ARCH="%(cuda_cc_cmake)s" '
+
+# Can't run all tests (55 failing); many fail due to mixed precision not being supported
+# some fail due to missing external data files, many unknown issues
+# All tests can be attempted with "amgx_tests_launcher --all"
+local_tests = [
+    'AggregatesCoarseGeneratorTest',
+    'AggregatesCoarseningFactor',
+    'AggregatesDeterminism',
+    'AggregatesDiagonalOutside',
+    'AmgLevelsReuse',
+    'CAPIFailure',
+    'CAPIVersionCheck',
+    'ClassicalStrengthAffinityTest',
+    'ClassicalStrengthTest',
+    'ConfigStringParsing',
+    'CsrMultiplyTests_Poisson27_100_100',
+    'CsrMultiplyTests_Poisson27_10_10',
+    'CsrMultiplyTests_Poisson5_100_100',
+    'CsrMultiplyTests_Poisson5_10_1',
+    'CsrMultiplyTests_Poisson7_100_100',
+    'CsrMultiplyTests_Poisson7_10_10',
+    'CsrMultiplyTests_Poisson9_100_100',
+    'CsrMultiplyTests_Poisson9_10_10',
+    'CsrSparsityILU1Tests_Poisson27_100_100',
+    'CsrSparsityILU1Tests_Poisson27_10_10',
+    'CsrSparsityILU1Tests_Poisson5_100_100',
+    'CsrSparsityILU1Tests_Poisson5_10_10',
+    'CsrSparsityILU1Tests_Poisson7_100_100',
+    'CsrSparsityILU1Tests_Poisson7_10_10',
+    'CsrSparsityILU1Tests_Poisson9_100_100',
+    'CsrSparsityILU1Tests_Poisson9_10_10',
+    'CsrSparsityTests_Poisson27_100_100',
+    'CsrSparsityTests_Poisson27_10_10',
+    'CsrSparsityTests_Poisson5_100_100',
+    'CsrSparsityTests_Poisson5_10_10',
+    'CsrSparsityTests_Poisson7_100_100',
+    'CsrSparsityTests_Poisson7_10_10',
+    'CsrSparsityTests_Poisson9_100_100',
+    'CsrSparsityTests_Poisson9_10_10',
+    'DenseLUSolverTest_Factorization_Id_256',
+    'DenseLUSolverTest_Factorization_Id_32',
+    'DenseLUSolverTest_Solve_Id_256',
+    'DenseLUSolverTest_Solve_Id_32',
+    'DenseLUSolverTest_Solve_Poisson3D',
+    'FactoriesTest',
+    'FGMRESConvergencePoisson',
+    'GenericSpMVTest',
+    'IDRConvergencePoisson',
+    'IDRmsyncConvergencePoisson',
+    'LargeMatricesSupport',
+    'LowDegDeterminism',
+    'MatrixTests',
+    'MatrixVectorMultiplyTests',
+    'MinMaxColoringTest',
+    'Nested_AMG_equivalence',
+    'NestedSolvers',
+    'NormTests',
+    'ObjectDestructionSequence',
+    'PermuteTests',
+    'RandomMatrix',
+    'SmootherBlockPoissonTest',
+    'TemplateConfigTest',
+    'TemplateTest',
+    'truncateCountTest',
+    'VectorTests',
+]
+
+runtest = "amgx_tests_launcher && src/amgx_tests_launcher " + ' '.join(local_tests)
+
+sanity_check_paths = {
+    'files': ['include/amgx_c.h', 'lib/libamgx.a', 'lib/libamgxsh.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

easybuild/easyconfigs/a/AMGX/AMGX-2.4.0_external-thrust.patch

@@ -0,0 +1,13 @@
+Forces AMGX to use external dependencies, avoiding needing the git submodule
+the entire (deprecated) thrust library and all its dependencies.
+author: [email protected]
+--- CMakeLists.txt.orig	2024-03-30 01:54:34.469780980 +0100
++++ CMakeLists.txt	2024-03-30 01:54:46.491884432 +0100
+@@ -251,7 +251,6 @@
+ ENDIF()
+
+ # We depend on a specific version of thrust now so include the submodule
+-add_subdirectory("thrust")
+ find_package(Thrust REQUIRED CONFIG)
+ thrust_create_target(Thrust)
+

easybuild/easyconfigs/a/AMGX/AMGX-2.4.0_fix-openmp-linking.patch

@@ -0,0 +1,15 @@
+Adds missing link option necessary for openmp linking.
+The target_link_libraries used for amgx are not sufficient as CMake haven't
+sorted this out yet, thus manually adding the flag for GCC.
+author: [email protected]
+--- CMakeLists.txt.orig	2024-03-30 03:27:22.354168764 +0100
++++ CMakeLists.txt	2024-03-30 03:28:00.397486779 +0100
+@@ -291,6 +291,8 @@
+ ELSE (WIN32)
+   target_link_libraries(amgx CUDA::cublas CUDA::cusparse CUDA::cusolver CUDA::nvToolsExt m pthread)
+   target_link_libraries(amgxsh CUDA::cublas CUDA::cusparse CUDA::cusolver CUDA::nvToolsExt m pthread)
++  target_link_options(amgx INTERFACE "-fopenmp")
++  target_link_options(amgxsh INTERFACE "-fopenmp")
+ ENDIF(WIN32)
+
+ if(MPI_FOUND)

easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb

@@ -0,0 +1,30 @@
+easyblock = 'CmdCp'
+
+name = 'AMICA'
+version = '2024.1.19'
+local_commit = 'e0db55f07c8c410641cd5b0df5498a5a53129ce6'
+
+homepage = 'https://github.com/sccn/amica'
+description = """Code for AMICA: Adaptive Mixture ICA with shared components"""
+
+toolchain = {'name': 'intel', 'version': '2023a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/sccn/amica/archive/']
+sources = [{'download_filename': '%s.zip' % local_commit, 'filename': '%(name)s-%(version)s.zip'}]
+checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b']
+
+# original command: 
+# $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90
+cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp  -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")]
+
+test_cmd = "./amica17 ./amicadefs.param"
+
+files_to_copy = [(['amica17', 'amicadefs.param'], 'bin')]
+
+sanity_check_paths = {
+    'files': ["bin/amica17", "bin/amicadefs.param"],
+    'dirs': [],
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb

@@ -0,0 +1,52 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <[email protected]>, Fotis Georgatos <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'AMOS'
+version = '3.1.0'
+
+homepage = 'http://amos.sourceforge.net'
+description = """The AMOS consortium is committed to the development of open-source whole genome assembly software"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True, 'cstd': 'c++98'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'AMOS-%(version)s_GCC-4.7.patch',
+    'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch',
+    'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch',
+]
+checksums = [
+    {'amos-3.1.0.tar.gz': '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b'},
+    {'AMOS-3.1.0_GCC-4.7.patch': '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844'},
+    {'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch':
+     '80379cee8e8c8228590af89d37ea3fdb734c7e0ebe5bb357eaf2af71d1399fc6'},
+    {'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch':
+     'e291d87b8cd27752474ee0e1f3acb44f9657cac50d5d6dcceca0efc6436f1fe1'},
+]
+
+dependencies = [
+    ('expat', '2.5.0'),
+    ('MUMmer', '4.0.0rc1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'],
+    'dirs': []
+}
+
+parallel = 1  # make crashes otherwise
+
+moduleclass = 'bio'