{bio}[foss/2024a] Rapids-SingleCell v0.10.11, RAPIDS v24.10.0, ucx-py v0.40.00, update CUDA-Python v12.6.2.post1 w/ CUDA 12.6.0

easybuild/easyconfigs/c/CUDA-wheel-bundle/CUDA-wheel-bundle-12.6.0-gfbf-2024a-RAPIDS-24.10.0.eb

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+easyblock = 'PythonBundle'
+
+name = 'CUDA-wheel-bundle'
+version = '12.6.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://developer.nvidia.com/cuda'
+description = "Repackaging of NVIDIA CUDA libraries as Python packages"
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+
+dependencies = [
+    ('CUDA', version, '', SYSTEM),
+    ('cuDNN', '9.5.1.17', versionsuffix, SYSTEM),
+    ('cuSPARSELt', '0.6.3.2', versionsuffix, SYSTEM),
+    ('UCX-CUDA', '1.16.0', versionsuffix),
+    ('NCCL', '2.26.2', versionsuffix),
+    ('ucx-py', '0.40.00'),
+    ('Python', '3.12.3'),
+]
+
+dummy_package = True
+
+exts_list = [
+    # the following package list is based on the requirements of PyTorch 2.7.1
+    # provided by CUDA
+    ('nvidia-cublas-cu12', '12.6.4.1'),
+    ('nvidia-cuda-cupti-cu12', '12.6.80'),
+    ('nvidia-cuda-nvrtc-cu12', '12.6.77'),
+    ('nvidia-cuda-runtime-cu12', '12.6.77'),
+    ('nvidia-cufft-cu12', '11.3.0.4'),
+    ('nvidia-curand-cu12', '10.3.7.77'),
+    ('nvidia-cusolver-cu12', '11.7.1.2'),
+    ('nvidia-cusparse-cu12', '12.5.4.2'),
+    ('nvidia-nvjitlink-cu12', '12.6.85'),
+    ('nvidia-nvtx-cu12', '12.6.77'),
+    # provided by cuDNN
+    ('nvidia-cudnn-cu12', '9.5.1.17'),
+    # provided by cuSPARSELt
+    ('nvidia-cusparselt-cu12', '0.6.3'),
+    # provided by NCCL
+    ('nvidia-nccl-cu12', '2.26.2.post1'),
+    # provided by UCX-CUDA
+    ('libucx-cu12', '1.16.0.post2'),
+    # provided by ucx-py
+    ('ucx-py-cu12', '0.40.0')
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/r/RAPIDS/RAPIDS-24.10.0-foss-2024a-CUDA-12.6.0.eb

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+easyblock = 'PythonBundle'
+
+name = 'RAPIDS'
+version = '24.10.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://rapids.ai/'
+description = """RAPIDS provides unmatched speed with familiar APIs that match the most popular
+PyData libraries. Built on state-of-the-art foundations like NVIDIA CUDA and
+Apache Arrow, it unlocks the speed of GPUs with code you already know."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('hatchling', '1.24.2'),
+    ('Cython', '3.0.10'),
+    ('CMake', '3.31.8'),
+]
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.12.3'),
+    ('CUDA-Python', '12.6.2.post1', versionsuffix),
+    # provides nvidia-nccl-cu12-2.26.2.post1, libucx-cu12, ucx-py-cu12, nvidia-cublas-cu12,...
+    ('CUDA-wheel-bundle', '%(cudaver)s', versionsuffix),
+    ('SciPy-bundle', '2024.05'),
+    ('Arrow', '17.0.0'),
+    ('numba', '0.60.0'),
+    ('dask', '2024.9.1'),
+]
+
+exts_default_options = {'source_urls': [PYPI_SOURCE, 'https://pypi.nvidia.com/%(name)s-cu%(cudamajver)s']}
+_rapids_whl_name = '%(name)s_cu%(cudamajver)s-%(version)s-'
+_rapids_whl_cp_version = 'cp%(pymajver)s%(pyminver)s-cp%(pymajver)s%(pyminver)s'
+_rapids_tmpl = _rapids_whl_name + _rapids_whl_cp_version
+
+# fix treelite sources
+local_treelite_fix = (
+    "sed -i 's/os.cpu_count()/%(parallel)s/' packager/nativelib.py && "
+    "sed -i '1i #include <cstdint>' cpp_src/src/gtil/postprocessor.h && "
+)
+
+exts_list = [
+    ('zict', '3.0.0', {
+        'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'],
+    }),
+    ('treelite', '4.3.0', {
+        'preinstallopts': local_treelite_fix,
+        'checksums': ['7d0f4cf89826fbf9556b39c9fff2e82ab071b1b16adb98de4e98fcbaf860bc27'],
+    }),
+    ('cachetools', '5.5.0', {
+        'checksums': ['2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a'],
+    }),
+    ('fastrlock', '0.8.3', {
+        'checksums': ['4af6734d92eaa3ab4373e6c9a1dd0d5ad1304e172b1521733c6c3b3d73c8fa5d'],
+    }),
+    ('cupy_cuda12x', '13.6.0', {
+        'modulename': 'cupy',
+        'source_tmpl': f'%(name)s-%(version)s-{_rapids_whl_cp_version}-manylinux2014_%(arch)s.whl',
+        'checksums': ['79b0cacb5e8b190ef409f9e03f06ac8de1b021b0c0dda47674d446f5557e0eb1'],
+    }),
+    ('libucxx', '0.40.0', {
+        'modulename': False,
+        'source_tmpl': f'{_rapids_whl_name}py3-none-manylinux_2_24_%(arch)s.manylinux_2_28_%(arch)s.whl',
+        'checksums': ['eb00c16bea61814456a92307f36e7b8b6746c4a04b31a3f28d89bbb4025bc120'],
+    }),
+    ('ucxx', '0.40.0', {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_27_%(arch)s.manylinux_2_28_%(arch)s.whl',
+        'modulename': 'ucxx',
+        'checksums': ['8d12a50952027e609a952f12153e794cd4cb636b7cbde211047ad5f3e8eff801'],
+    }),
+    ('distributed-ucxx', '0.40.0', {
+        'modulename': False,
+        'source_tmpl': 'distributed_ucxx_cu%(cudamajver)s-%(version)s-py3-none-any.whl',
+        'checksums': ['07d05b85e8449840e157c35b25131f6b7678ff33c5294d2cafbf7fc9968750be'],
+    }),
+    ('nvtx', '0.2.14', {
+        'source_tmpl': (
+            f'%(name)s-%(version)s-{_rapids_whl_cp_version}-manylinux_2_17_%(arch)s.manylinux2014_%(arch)s.whl'
+        ),
+        'checksums': ['17efe5d903996bceb0c8a12cae80fa9b66bee7ee895923bd9d8ec2a5af1aabd8'],
+    }),
+    ('pynvjitlink_cu12', '0.4.0', {
+        'source_tmpl': (
+            f'%(name)s-%(version)s-{_rapids_whl_cp_version}-manylinux_2_27_%(arch)s.manylinux_2_28_%(arch)s.whl'
+        ),
+        'modulename': 'pynvjitlink',
+        'checksums': ['8f6834d84e0fba15b8c0ee39d8c4397e631708f97a8196c2f7b3082f2f35f465'],
+    }),
+    ('rmm', version, {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_24_%(arch)s.manylinux_2_28_%(arch)s.whl',
+        'modulename': 'rmm',
+        'checksums': ['e6141f0356afdd2a422da4b8e48a44c929928c78f7e005c648df02d6ef9c7740'],
+    }),
+    ('dask_cuda', version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'checksums': ['3666ba38169c6c4448c698c0fe05d3fe5bb9b1c13b6de86030c7e6ad3e2dc2be'],
+    }),
+    ('dask-cudf', '24.10.1', {
+        'source_tmpl': 'dask_cudf_cu%(cudamajver)s-%(version)s-py3-none-any.whl',
+        'modulename': False,
+        'checksums': ['9f04be126ffc5921298c51d2888572ac0e31ac77a9dd67920ecec1a1b40978e8'],
+    }),
+    ('dask_expr', '1.1.14', {
+        'preinstallopts': "sed -i 's/2024.9.0/2024.9.1/' pyproject.toml && ",
+        'checksums': ['c67c0c190d933e253f85674da71615f23ed8ba08f3abcc0cd160080643feb40a'],
+    }),
+    ('rapids_dask_dependency', version, {
+        'source_tmpl': SOURCE_PY3_WHL,
+        'modulename': False,
+        'checksums': ['25242e0b1264e18e97d53b3fa96256d1e75f13865b84ea989f730b54c86d9023'],
+    }),
+    ('raft-dask', version, {
+        'source_tmpl': f'raft_dask_cu%(cudamajver)s-%(version)s-{_rapids_whl_cp_version}-manylinux_2_28_%(arch)s.whl',
+        'modulename': False,
+        'checksums': ['bdc1fecf821b6b77e2692b2504bad0c9a3b4d75596732c53d454345941927779'],
+    }),
+    ('pylibraft', version, {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_28_%(arch)s.whl',
+        'modulename': 'pylibraft',
+        'checksums': ['88014c4ad7cf49b8ae5979051b571f838621954460c7898c4ef49488d446fffc'],
+    }),
+    ('libcudf', '24.10.1', {
+        'modulename': False,
+        'source_tmpl': f'{_rapids_whl_name}py3-none-manylinux_2_28_%(arch)s.whl',
+        'checksums': ['59eaabf315efb7da8e3d6add14806d4f41b4fd664a9d636d72c1638c9574882a'],
+    }),
+    ('pylibcudf', '24.10.1', {
+        'modulename': 'pylibcudf',
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_24_%(arch)s.manylinux_2_28_%(arch)s.whl',
+        'checksums': ['717987c16cc8774c8326fc3c94bd2ad1c58acf41e52586052e38dd00ba1bc7e4'],
+    }),
+    ('pylibcugraph', version, {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_28_%(arch)s.whl',
+        'modulename': 'pylibcugraph',
+        'checksums': ['fa2b2c2b03322afa21bf9160ac0ed185ca258486f39a6a20d7714041ba3b4cc8'],
+    }),
+    ('cuvs', version, {
+        'modulename': 'cuvs',
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_28_%(arch)s.whl',
+        'checksums': ['730fe5c9fc8ea9b3a985101ccab51707c94ddd2e4358f6e9178c01c728f09eea'],
+    }),
+    ('cudf', '24.10.1', {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_24_%(arch)s.manylinux_2_28_%(arch)s.whl',
+        'checksums': ['fb1934d908e33b61a4ded6c33f8305b78947d01149ed5c37b07e0c581ebbc136'],
+    }),
+    ('cuml', version, {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_28_%(arch)s.whl',
+        'checksums': ['47647af4bc997cb2bc8f5713b2c4187f7b427c5d2bc745468697711544c26e76'],
+    }),
+    ('cugraph', version, {
+        'source_tmpl': f'{_rapids_tmpl}-manylinux_2_28_%(arch)s.whl',
+        'checksums': ['64f7c683d186066726ebdd5e061fcc7e6cb739c6d3dce1accdda46265d7b92c7'],
+    }),
+]
+
+# update dask and distributed pinned version in rapids-dask-dependency dist METADATA
+postinstallcmds = [
+    "sed -i 's/2024.9.0/2024.9.1/' "
+    "%(installdir)s/lib/python%(pyshortver)s/site-packages/rapids_dask_dependency-%(version)s.dist-info/METADATA",
+]
+
+modextravars = {
+    'RAPIDS_LIBUCX_PREFER_SYSTEM_LIBRARY': 'true',
+    'NUMBA_CUDA_USE_NVIDIA_BINDING': '1',
+}
+
+sanity_check_commands = [
+    "python -sc 'from numba import cuda'",
+    "python -sc 'import cupy as cp; x=cp.arange(10); print(int(x.sum()))' | grep 45",
+]
+
+moduleclass = 'ai'

easybuild/easyconfigs/r/rapids-singlecell/rapids-singlecell-0.10.11-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,66 @@
+easyblock = 'PythonBundle'
+
+name = 'rapids-singlecell'
+version = '0.10.11'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/scverse/rapids_singlecell'
+description = """rapids-singlecell provides GPU-accelerated single-cell analysis with an AnnData-first API.
+It is largely compatible with Scanpy and includes selected functionality from Squidpy, decoupler, and pertpy.
+Computations use CuPy and NVIDIA RAPIDS for performance on large datasets."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [('hatchling', '1.24.2')]
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.12.3'),
+    ('CUDA-Python', '12.6.2.post1', versionsuffix),
+    ('RAPIDS', '24.10.0', versionsuffix),
+    ('SciPy-bundle', '2024.05'),
+    ('anndata', '0.11.4'),
+    ('scanpy', '1.10.4'),
+    ('scikit-misc', '0.5.1'),
+    ('matplotlib', '3.9.2'),
+    ('tqdm', '4.66.5'),
+    ('statsmodels', '0.14.4'),
+    ('scikit-image', '0.25.0'),
+]
+
+local_test_cmd = (
+    'pytest -v tests '
+    # Dask tests spawn processes and open TCP ports
+    '--ignore=tests/dask '
+    # Multi-GPU neighbor tests
+    '--ignore=tests/test_mg_neighbors.py '
+    # Harmony tests download data at runtime
+    '--ignore=tests/test_harmony.py '
+    # Wrong API calls to scanpy from test_neighbors
+    # from scanpy.neighbors._connectivity import jaccard as scanpy_jaccard
+    '--ignore=tests/test_neighbors.py '
+    # problem on A2 gpu
+    # '-k "not float64 and not test_block_size_consistency" '
+)
+
+exts_list = [
+    ('natsort', '8.4.0', {
+        'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'],
+    }),
+    ('rapids_singlecell', version, {
+        'testinstall': True,
+        'runtest': local_test_cmd,
+        # .git dir required
+        'sources': [{
+            'git_config': {
+                'url': 'https://github.com/scverse',
+                'repo_name': '%(name)s',
+                'tag': 'v%(version)s',
+                'keep_git_dir': True,
+            },
+            'filename': SOURCE_TAR_XZ,
+        }],
+        'checksums': ['c7d63fcd780ada30ad9569158bbd2f1452bc6b5d071124d1b25794d8a71cf28c'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/u/ucx-py/ucx-py-0.40.00-gfbf-2024a.eb

@@ -0,0 +1,49 @@
+easyblock = 'PythonBundle'
+
+name = 'ucx-py'
+version = '0.40.00'
+
+github_account = 'rapidsai'
+
+homepage = "https://ucx-py.readthedocs.io"
+description = """UCX-Py is the Python interface for UCX, a low-level high-performance networking library.
+UCX and UCX-Py supports several transport methods including InfiniBand and NVLink
+while still using traditional networking protocols like TCP."""
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [('Cython', '3.0.10')]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('PyYAML', '6.0.2'),
+    ('SciPy-bundle', '2024.05'),
+    ('UCX', '1.16.0'),
+]
+
+exts_list = [
+    ('pynvml', '11.4.1', {
+        'preinstallopts': (
+            "sed -i -e 's/SafeConfigParser()/ConfigParser()/' -e 's/readfp(/read_file(/' versioneer.py && "
+        ),
+        'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'],
+    }),
+    ('rapids-dependency-file-generator', '1.16.0', {
+        'source_urls': ['https://github.com/%(github_account)s/dependency-file-generator/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['b49989947a8e9e7f722762758d536f74cc2f72d680d3939da225d58a36c235df'],
+    }),
+    ('rapids-build-backend', '0.3.2', {
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['11ed069adf2b6b70b8f45e5d8e3947ed8f669e4cd7e7245f491b86f0c1f0a01d'],
+    }),
+    (name, version, {
+        'modulename': 'ucp',
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['283692e775202995d7a3326e4de17d4b728635a71ee1e7a12d330680dadcc8c4'],
+    }),
+]
+
+moduleclass = 'lib'