Merge pull request #20476 from lexming/5.0.x-sync

sync with develop (20240506)

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

@@ -0,0 +1,17 @@
+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
+
+download_instructions = "Manually obtain (ELECTRONICS_%(version)s_LINX64.tgz) from your ANSYS vendor"
+sources = ['ELECTRONICS_%(version)s_LINX64.tgz']
+checksums = ['7b131adf981ebca1e2f4fe8e607e50323167b69e77180a0ab61b2759d57abca5']
+
+moduleclass = 'phys'

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/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb

@@ -19,7 +19,7 @@ checksums = ['eb939471f5f4218e6cfd62f58ccd2a0a5283d4a19a2902741c7fb25e2f016eaf']
 
 dependencies = [
     ('R', '4.2.2'),
-    ('Arrow', '11.0.0'),
+    ('Arrow', '11.0.0'),  # arrow-R x.y.z[.N] only works with Arrow x.y.z
 ]
 
 preinstallopts = "export LIBARROW_BINARY=true && "

easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb → easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.1-foss-2023a-R-4.3.2.eb

@@ -1,7 +1,7 @@
 easyblock = 'RPackage'
 
 name = 'arrow-R'
-version = '14.0.0.2'
+version = '14.0.1'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://cran.r-project.org/web/packages/arrow'
@@ -13,16 +13,18 @@ source_urls = [
     'https://cran.r-project.org/src/contrib/Archive/arrow',  # package archive
     'https://cran.r-project.org/src/contrib/',  # current version of packages
     'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    'https://archive.apache.org/dist/arrow/arrow-%(version)s',  # full Arrow source tarballs
 ]
-sources = ['arrow_%(version)s.tar.gz']
-checksums = ['7138a52d66f1b94ec31c25e8929d6f92b1640df852a10817600a82ab68ba8ab7']
+sources = ['apache-arrow-%(version)s.tar.gz']
+checksums = ['5c70eafb1011f9d124bafb328afe54f62cc5b9280b7080e1e3d668f78c0e407e']
 
 dependencies = [
     ('R', '4.3.2'),
     ('R-bundle-CRAN', '2023.12'),
-    ('Arrow', '14.0.1'),
+    ('Arrow', '14.0.1'),  # arrow-R x.y.z[.N] only works with Arrow x.y.z
 ]
 
+start_dir = 'r'
 preinstallopts = "export LIBARROW_BINARY=true && "
 
 sanity_check_paths = {

easybuild/easyconfigs/a/assembly-stats/assembly-stats-1.0.1-GCCcore-11.3.0.eb

@@ -0,0 +1,43 @@
+# Author: Ehsan Moravveji (VSCentrum, KU Leuven)
+
+easyblock = 'CMakeMake'
+
+name = 'assembly-stats'
+version = '1.0.1'
+
+homepage = 'https://github.com/sanger-pathogens/assembly-stats'
+description = 'Get assembly statistics from FASTA and FASTQ files.'
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'sanger-pathogens'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-1.0.1_fix_str_cast.patch']
+checksums = [
+    {'v1.0.1.tar.gz': '02be614da4d244673bcd0adc6917749681d52a58cb0a039c092d01cdeabd8575'},
+    {'assembly-stats-1.0.1_fix_str_cast.patch': '2c1d63e7b1246b290ddfeea2604076ae892dfe337e5092e83575c2c3cbcfd7fd'},
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+    ('pkgconf', '1.8.0'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+]
+
+configopts = '-DINSTALL_DIR=%(installdir)s/bin'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/assembly-stats'],
+    'dirs': []
+}
+
+sanity_check_commands = ['assembly-stats -v']
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/assembly-stats/assembly-stats-1.0.1_fix_str_cast.patch

@@ -0,0 +1,43 @@
+# Author: Ehsan Moravveji (VSCentrum, KU Leuven)
+# Purpose: This patch prevents the compile-time error "taking address of rvalue [-fpermissive]"
+#          by redefining a simple casting from integer to string. Consequently, the additional
+#          "-fpermissive" compiler flag need not be included to supress the error.
+diff -ruN assembly-stats-original/fasta_unittest.cpp assembly-stats/fasta_unittest.cpp
+--- assembly-stats-original/fasta_unittest.cpp	2024-04-03 11:45:32.230992000 +0200
++++ assembly-stats/fasta_unittest.cpp	2024-04-03 11:50:08.868140000 +0200
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <string>
+ #include "fasta.h"
+ #include "gtest/gtest.h"
+
+@@ -94,8 +95,7 @@
+     while (fa.fillFromFile(inStream))
+     {
+         counter++;
+-        string expectedName = static_cast<ostringstream*>( &(ostringstream() << counter) )->str();
+-        EXPECT_EQ(0, fa.name().compare(expectedName));
++        EXPECT_EQ(0, fa.name().compare(std::to_string(counter)));
+         EXPECT_EQ(0, fa.seq().compare("ACGT"));
+     }
+
+diff -ruN assembly-stats-original/fastq_unittest.cpp assembly-stats/fastq_unittest.cpp
+--- assembly-stats-original/fastq_unittest.cpp	2024-04-03 11:45:32.226036000 +0200
++++ assembly-stats/fastq_unittest.cpp	2024-04-03 12:29:04.830873000 +0200
+@@ -1,5 +1,6 @@
+ #include <list>
+ #include <iostream>
++#include <string>
+ #include <sstream>
+ #include "fastq.h"
+ #include "gtest/gtest.h"
+@@ -50,8 +51,7 @@
+     while (fq.fillFromFile(inStream))
+     {
+         counter++;
+-        string expectedName = static_cast<ostringstream*>( &(ostringstream() << counter) )->str();
+-        EXPECT_EQ(0, fq.name().compare(expectedName));
++        EXPECT_EQ(0, fq.name().compare(std::to_string(counter)));
+         EXPECT_EQ(0, fq.seq().compare("ACGT"));
+     }
+ }

easybuild/easyconfigs/a/astropy/astropy-5.1.1-intel-2022a.eb

@@ -0,0 +1,34 @@
+easyblock = "PythonBundle"
+
+name = 'astropy'
+version = '5.1.1'
+
+homepage = 'https://www.astropy.org/'
+description = """The Astropy Project is a community effort to develop a common 
+core package for Astronomy in Python and foster an ecosystem of interoperable 
+astronomy packages."""
+
+docurls = 'https://docs.astropy.org'
+
+toolchain = {'name': 'intel', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+]
+
+exts_list = [
+    ('pyerfa', '2.0.0.1', {
+        'modulename': 'erfa',
+        'checksums': ['2fd4637ffe2c1e6ede7482c13f583ba7c73119d78bef90175448ce506a0ede30'],
+    }),
+    ('extension-helpers', '1.0.0', {
+        'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'],
+    }),
+    (name, version, {
+        'checksums': ['ba4bd696af7090fd399b464c704bf27b5633121e461785edc70432606a94bd81'],
+    }),
+]
+
+moduleclass = 'astro'

easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-12.3.0.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonBundle'
+
+name = 'attrdict3'
+version = '2.0.2'
+
+homepage = 'https://github.com/pirofti/AttrDict3'
+description = """AttrDict is a Python library that provides mapping objects that allow their elements
+ to be accessed both as keys and as attributes."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+]
+
+exts_list = [
+    (name, version, {
+        'modulename': 'attrdict',
+        'checksums': ['004c171ca1120cc1755701db99d7fa4944afb1e68950434efdaa542513335fe8'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/b/BCFtools/BCFtools-1.19-GCC-13.2.0.eb

@@ -0,0 +1,39 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Author: Jonas Demeulemeester
+# The Francis Crick Insitute, London, UK
+
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.19'
+
+homepage = 'https://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence
+ variants"""
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['782b5f1bc690415192231e82213b3493b047f45e630dc8ef6f154d6126ab3e68']
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('HTSlib', '1.19.1'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.4'),
+    ('GSL', '2.7'),
+]
+
+configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl"
+
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'],
+    'dirs': ['libexec/%(namelower)s'],
+}
+
+moduleclass = 'bio'