{bio}[foss/2022a] warp v2.0.0dev8, dotNET-SDK v8.0.204, PyTorch v2.0.1, AreTomo2 v1.0.0, torchvision v0.15.2, w/ CUDA 11.8.0

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-11.3.0-CUDA-11.8.0.eb

@@ -0,0 +1,60 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/10
+easyblock = 'MakeCp'
+
+name = 'AreTomo2'
+version = '1.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/czimaginginstitute/AreTomo2'
+
+description = """AreTomo2, a multi-GPU accelerated software package that fully automates motion- 
+corrected marker-free tomographic alignment and reconstruction, now includes    
+robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single  
+package. AreTomo2 is part of our endeavor to build a fully-automated high-      
+throughput processing pipeline that enables real-time reconstruction of         
+tomograms in parallel with tomographic data collection. It strives to be fast   
+and accurate, as well as provides for easy integration into subtomogram         
+processing workflows by generating IMod compatible files containing alignment   
+and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also 
+be used for on-the-fly reconstruction of tomograms and CTF estimation in        
+parallel with tilt series collection, enabling real-time assessment of sample   
+quality and adjustment of collection parameters"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_makefile.patch']
+checksums = [
+    {'v1.0.0.tar.gz': '5518cd5d7bc13a6dbb6d9310b22c301e73a0c91dc059da403445d79ca0ff8892'},
+    {'AreTomo2-1.0.0_makefile.patch': '8595b2fc55e0b5e1bf7c077c93c09503b4e8f95123c6aaf0a5fbe44dda871c73'},
+]
+
+github_account = 'czimaginginstitute'
+
+build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"'
+
+builddependencies = [
+    ('binutils', '2.38')
+]
+
+dependencies = [
+    ('CUDA', '11.8.0', '', SYSTEM),
+]
+
+files_to_copy = [(['AreTomo2'], 'bin')]
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/compat/bin',
+    'cd %(installdir)s/compat/bin && ln -s ../../bin/AreTomo2 AreTomo'
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s', 'compat/bin/AreTomo'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = ['%(name)s -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-8.0.204-linux-x64.eb

@@ -0,0 +1,35 @@
+##
+# Authors::	Robert Qiao <rob.qiao@flinders.edu.au>
+#               Robert Mijakovic <robert.mijakovic@lxp.lu>
+# update 8.0.204 THEMBL
+# License:: MIT
+# Notes::   requires glibc v2.14 or higher
+##
+easyblock = 'Tarball'
+
+name = 'dotNET-SDK'
+version = '8.0.204'
+versionsuffix = '-linux-x64'
+
+homepage = 'https://www.microsoft.com/net/'
+description = """.NET is a free, cross-platform, open source developer platform for building many different types
+ of applications."""
+
+toolchain = SYSTEM
+source_urls = ['https://dotnetcli.azureedge.net/dotnet/Sdk/%(version)s/']
+sources = ['dotnet-sdk-%(version)s%(versionsuffix)s.tar.gz']
+checksums = ['0ec834dc0f11a994057cd05d84c6250db726457f2fe308091d50543a5285dd15']
+
+sanity_check_paths = {
+    'files': ['dotnet'],
+    'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'],
+}
+
+sanity_check_commands = ["dotnet --help"]
+
+modextrapaths = {
+    'PATH': [''],
+    'DOTNET_ROOT': [''],
+}
+
+moduleclass = 'lang'

easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.8.0.eb

@@ -0,0 +1,44 @@
+easyblock = 'CMakeMake'
+
+name = 'magma'
+version = '2.6.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://icl.cs.utk.edu/magma/'
+description = """The MAGMA project aims to develop a dense linear algebra library similar to
+ LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/']
+sources = [SOURCE_TAR_GZ]
+patches = ['%(name)s-%(version_major_minor)s.1_allow-all-sms.patch']
+checksums = [
+    '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71',  # %(name)s-%(version)s.tar.gz
+    # %(name)s-%(version_major_minor)s.1_allow-all-sms.patch
+    'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738',
+]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+dependencies = [
+    ('CUDA', '11.8.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', versionsuffix),
+]
+
+# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
+cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0']
+
+# make sure both static and shared libs are built
+configopts = [
+    '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF')
+]
+
+sanity_check_paths = {
+    'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'

easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-11.3.0-CUDA-11.8.0.eb

@@ -0,0 +1,26 @@
+name = 'NCCL'
+version = '2.15.5'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://developer.nvidia.com/nccl'
+description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective
+communication primitives that are performance optimized for NVIDIA GPUs."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'NVIDIA'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s-1.tar.gz']
+checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('CUDA', '11.8.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', versionsuffix),
+]
+
+# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
+cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0']
+
+moduleclass = 'lib'

easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a-CUDA-11.8.0.eb

@@ -0,0 +1,171 @@
+name = 'PyTorch'
+version = '2.0.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pytorch.org/'
+description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration.
+PyTorch is a deep learning framework that puts Python first."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [GITHUB_RELEASE]
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+patches = [
+    'PyTorch-1.7.0_disable-dev-shm-test.patch',
+    'PyTorch-1.11.1_skip-test_init_from_local_shards.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
+    'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
+    'PyTorch-1.12.1_fix-TestTorch.test_to.patch',
+    'PyTorch-1.12.1_skip-test_round_robin.patch',
+    'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch',
+    'PyTorch-1.13.1_fix-protobuf-dependency.patch',
+    'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch',
+    'PyTorch-1.13.1_skip-failing-singular-grad-test.patch',
+    'PyTorch-1.13.1_skip-tests-without-fbgemm.patch',
+    'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch',
+    'PyTorch-2.0.1_avoid-test_quantization-failures.patch',
+    'PyTorch-2.0.1_disable-test-sharding.patch',
+    'PyTorch-2.0.1_fix-numpy-compat.patch',
+    'PyTorch-2.0.1_fix-shift-ops.patch',
+    'PyTorch-2.0.1_fix-skip-decorators.patch',
+    'PyTorch-2.0.1_fix-test_memory_profiler.patch',
+    'PyTorch-2.0.1_fix-test-ops-conf.patch',
+    'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch',
+    'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch',
+    'PyTorch-2.0.1_fix-vsx-loadu.patch',
+    'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch',
+    'PyTorch-2.0.1_no-cuda-stubs-rpath.patch',
+    'PyTorch-2.0.1_remove-test-requiring-online-access.patch',
+    'PyTorch-2.0.1_skip-diff-test-on-ppc.patch',
+    'PyTorch-2.0.1_skip-failing-gradtest.patch',
+    'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch',
+    'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch',
+]
+checksums = [
+    {'pytorch-v2.0.1.tar.gz': '9c564ca440265c69400ef5fdd48bf15e28af5aa4bed84c95efaad960a6699998'},
+    {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'},
+    {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch':
+     '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'},
+    {'PyTorch-1.12.1_add-hypothesis-suppression.patch':
+     'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'},
+    {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch':
+     '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'},
+    {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'},
+    {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'},
+    {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch':
+     '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'},
+    {'PyTorch-1.13.1_fix-protobuf-dependency.patch':
+     '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'},
+    {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch':
+     'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'},
+    {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch':
+     '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'},
+    {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch':
+     '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'},
+    {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch':
+     'da44961d6c204403ba0c4b88cedccf06a7a3d24f29c4398545f96efae7a45c95'},
+    {'PyTorch-2.0.1_avoid-test_quantization-failures.patch':
+     '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'},
+    {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'},
+    {'PyTorch-2.0.1_fix-numpy-compat.patch': 'f3e5798193e0909a415d824f13772973200965db84476c1737824f2735f2db94'},
+    {'PyTorch-2.0.1_fix-shift-ops.patch': '5ee655d5dba56d801d5618543b6ca299fa874939a3471f7b5449bfcb7f3f18c7'},
+    {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'},
+    {'PyTorch-2.0.1_fix-test_memory_profiler.patch':
+     'fd03117c46f59c1c62227d31c410c4cdd98fd35410976758cb9e7ec947582ddb'},
+    {'PyTorch-2.0.1_fix-test-ops-conf.patch': '0f995e4f89baf3cbeb8666cbfe694666a2ef2bc53d97d6301f768b3ff9001fa4'},
+    {'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch':
+     '20f9172ae696da0c5c7b3bae6f0bf1221192cb1cbac3a44526a415087834bee7'},
+    {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch':
+     '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'},
+    {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'},
+    {'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch':
+     '57e2985a5b7085c2786e4b0c4a5f0c81f6b2ae9d5804bbd552b06e8b1570f4c4'},
+    {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'},
+    {'PyTorch-2.0.1_remove-test-requiring-online-access.patch':
+     '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'},
+    {'PyTorch-2.0.1_skip-diff-test-on-ppc.patch': 'f6e39cd774e5663df25507a73d37ad598157c2eadb2f47ca20a537dbe4b3e14f'},
+    {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'},
+    {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch':
+     '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'},
+    {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch':
+     '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'},
+]
+
+osdependencies = [OS_PKG_IBVERBS_DEV]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('hypothesis', '6.46.7'),
+    # For tests
+    ('pytest-rerunfailures', '11.1'),
+    ('pytest-shard', '0.1.2'),
+]
+
+dependencies = [
+    ('CUDA', '11.8.0', '', SYSTEM),
+    ('Ninja', '1.10.2'),  # Required for JIT compilation of C++ extensions
+    ('Python', '3.10.4'),
+    ('protobuf', '3.19.4'),
+    ('protobuf-python', '3.19.4'),
+    ('pybind11', '2.9.2'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('MPFR', '4.1.0'),
+    ('GMP', '6.2.1'),
+    ('numactl', '2.0.14'),
+    ('FFmpeg', '4.4.2'),
+    ('Pillow', '9.1.1'),
+    ('expecttest', '0.1.3'),
+    ('networkx', '2.8.4'),
+    ('sympy', '1.10.1'),
+    ('cuDNN', '8.7.0.84', '-CUDA-%(cudaver)s', SYSTEM),
+    ('magma', '2.6.2', '-CUDA-%(cudaver)s'),
+    ('NCCL', '2.15.5', '-CUDA-%(cudaver)s'),
+]
+
+# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
+cuda_compute_capabilities = [
+    '3.5',
+    '3.7',
+    '5.2',
+    '6.0',
+    '6.1',
+    '7.0',
+    '7.2',
+    '7.5',
+    '8.0',
+    '8.6',
+    '9.0',
+]
+
+custom_opts = ['USE_CUPTI_SO=1']
+
+
+excluded_tests = {
+    '': [
+        # This test seems to take too long on NVIDIA Ampere at least.
+        'distributed/test_distributed_spawn',
+        # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375
+        'distributions/test_constraints',
+        # no xdoctest
+        'doctests',
+        # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712
+        'test_native_mha',
+        # intermittent failures on various systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712
+        'distributed/rpc/test_tensorpipe_agent',
+    ]
+}
+
+runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error  --verbose %(excluded_tests)s'
+
+# Especially test_quantization has a few corner cases that are triggered by the random input values,
+# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030
+# So allow a low number of tests to fail as the tests "usually" succeed
+max_failed_tests = 2
+
+tests = ['PyTorch-check-cpp-extension.py']
+
+moduleclass = 'ai'
+#

easybuild/easyconfigs/t/torchvision/torchvision-0.15.2-foss-2022a-CUDA-11.8.0.eb

@@ -0,0 +1,22 @@
+name = 'torchvision'
+version = '0.15.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+homepage = 'https://github.com/pytorch/vision'
+description = " Datasets, Transforms and Models specific to Computer Vision"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/pytorch/vision/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['1efcb80e0a6e42c54f07ee16167839b4d302aeeecc12839cc47c74b06a2c20d4']
+
+builddependencies = [('CMake', '3.23.1')]
+
+dependencies = [
+    ('CUDA', '11.8.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('Pillow-SIMD', '9.2.0'),
+    ('PyTorch', '2.0.1', versionsuffix),
+]
+
+moduleclass = 'vis'