{ai}[foss/2024a] AlphaFold3 v3.0.1-20250908, dm-haiku v0.0.14, Flax v0.10.2, ... w/ CUDA 12.6.0

easybuild/easyconfigs/a/AlphaFold3/AlphaFold3-3.0.0.20250109_data_path.patch

@@ -0,0 +1,95 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/01
+# - additionally search libciffpp components.cif in path definded by 
+#   environment variable LIBCIFPP_DATA_DIR
+# - allow to set default model dir and public databases dir by environment
+#   variables AF3_MODEL_DIR and DB_DIR, respectively. 
+diff -ru alphafold3-ea040346e10db1759170e723ef263316e64aa768/run_alphafold.py alphafold3-ea040346e10db1759170e723ef263316e64aa768_data_path/run_alphafold.py
+--- alphafold3-ea040346e10db1759170e723ef263316e64aa768/run_alphafold.py	2025-01-09 13:59:41.000000000 +0100
++++ alphafold3-ea040346e10db1759170e723ef263316e64aa768_data_path/run_alphafold.py	2025-01-15 18:48:19.060274236 +0100
+@@ -55,8 +55,14 @@
+
+
+ _HOME_DIR = pathlib.Path(os.environ.get('HOME'))
+-_DEFAULT_MODEL_DIR = _HOME_DIR / 'models'
+-_DEFAULT_DB_DIR = _HOME_DIR / 'public_databases'
++_DEFAULT_MODEL_DIR = os.environ.get('AF3_MODEL_DIR')
++if _DEFAULT_MODEL_DIR == None:
++  _DEFAULT_MODEL_DIR = _HOME_DIR / 'models'
++else: _DEFAULT_MODEL_DIR = pathlib.Path(_DEFAULT_MODEL_DIR)
++_DEFAULT_DB_DIR = os.environ.get('DB_DIR')
++if _DEFAULT_DB_DIR == None:
++  _DEFAULT_DB_DIR = _HOME_DIR / 'public_databases'
++else: _DEFAULT_DB_DIR = pathlib.Path(_DEFAULT_DB_DIR)
+
+
+ # Input and output paths.
+diff -ru alphafold3-ea040346e10db1759170e723ef263316e64aa768/src/alphafold3/build_data.py alphafold3-ea040346e10db1759170e723ef263316e64aa768_data_path/src/alphafold3/build_data.py
+--- alphafold3-ea040346e10db1759170e723ef263316e64aa768/src/alphafold3/build_data.py	2025-01-09 13:59:41.000000000 +0100
++++ alphafold3-ea040346e10db1759170e723ef263316e64aa768_data_path/src/alphafold3/build_data.py	2025-01-15 18:04:26.440308446 +0100
+@@ -17,16 +17,21 @@
+ import alphafold3.constants.converters
+ from alphafold3.constants.converters import ccd_pickle_gen
+ from alphafold3.constants.converters import chemical_component_sets_gen
+-
++from os import getenv
+
+ def build_data():
+   """Builds intermediate data."""
+-  for site_path in site.getsitepackages():
+-    path = pathlib.Path(site_path) / 'share/libcifpp/components.cif'
+-    if path.exists():
+-      cif_path = path
+-      break
++  cif_path = None
++  if getenv('LIBCIFPP_DATA_DIR'):
++    path = getenv('LIBCIFPP_DATA_DIR') + '/components.cif'
++    cif_path = path
+   else:
++    for site_path in site.getsitepackages():
++      path = pathlib.Path(site_path) / 'share/libcifpp/components.cif'
++      if path.exists():
++        cif_path = path
++        break
++  if (not cif_path):
+     raise ValueError('Could not find components.cif')
+
+   out_root = resources.files(alphafold3.constants.converters)
+diff -ru alphafold3-ea040346e10db1759170e723ef263316e64aa768/src/alphafold3/model/mkdssp_pybind.cc alphafold3-ea040346e10db1759170e723ef263316e64aa768_data_path/src/alphafold3/model/mkdssp_pybind.cc
+--- alphafold3-ea040346e10db1759170e723ef263316e64aa768/src/alphafold3/model/mkdssp_pybind.cc	2025-01-09 13:59:41.000000000 +0100
++++ alphafold3-ea040346e10db1759170e723ef263316e64aa768_data_path/src/alphafold3/model/mkdssp_pybind.cc	2025-01-15 14:34:35.267983665 +0100
+@@ -27,20 +27,23 @@
+ void RegisterModuleMkdssp(pybind11::module m) {
+   py::module site = py::module::import("site");
+   py::list paths = py::cast<py::list>(site.attr("getsitepackages")());
++  const char* libcifpp_data_dir_p = std::getenv("LIBCIFPP_DATA_DIR");
++  if (!libcifpp_data_dir_p) {
+   // Find the first path that contains the libcifpp components.cif file.
+-  bool found = false;
+-  for (const auto& py_path : paths) {
+-    auto path_str =
+-        std::filesystem::path(py::cast<absl::string_view>(py_path)) /
+-        "share/libcifpp/components.cif";
+-    if (std::filesystem::exists(path_str)) {
+-      setenv("LIBCIFPP_DATA_DIR", path_str.parent_path().c_str(), 0);
+-      found = true;
+-      break;
++     bool found = false;
++     for (const auto& py_path : paths) {
++       auto path_str =
++           std::filesystem::path(py::cast<absl::string_view>(py_path)) /
++           "share/libcifpp/components.cif";
++       if (std::filesystem::exists(path_str)) {
++       setenv("LIBCIFPP_DATA_DIR", path_str.parent_path().c_str(), 0);
++       found = true;
++       break;
++     }
++    }
++    if (!found) {
++      throw py::type_error("Could not find the libcifpp components.cif file.");
+     }
+-  }
+-  if (!found) {
+-    throw py::type_error("Could not find the libcifpp components.cif file.");
+   }
+   m.def(
+       "get_dssp",

easybuild/easyconfigs/a/AlphaFold3/AlphaFold3-3.0.0_disable_fetch.patch

@@ -0,0 +1,20 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/01
+# disable FetchContent for pybind11, abseil-cpp, pybind11_abseil, cifpp and dssp
+# use find_package instead.
+diff -ru alphafold3-3.0.0/CMakeLists.txt alphafold3-3.0.0_disable_fetch/CMakeLists.txt
+--- alphafold3-3.0.0/CMakeLists.txt	2024-11-11 11:42:47.000000000 +0100
++++ alphafold3-3.0.0_disable_fetch/CMakeLists.txt	2025-01-14 17:14:41.925312870 +0100
+@@ -54,8 +54,11 @@
+   GIT_TAG 57560472b4260dc41f457706bc45fc6ef0bc0f10 # v4.4.7
+   EXCLUDE_FROM_ALL)
+
+-FetchContent_MakeAvailable(pybind11 abseil-cpp pybind11_abseil cifpp dssp)
+-
++#FetchContent_MakeAvailable(pybind11 abseil-cpp pybind11_abseil cifpp dssp)
++find_package(pybind11 CONFIG REQUIRED)
++find_package(absl CONFIG REQUIRED)
++find_package(pybind11_abseil CONFIG REQUIRED)
++find_package(dssp CONFIG REQUIRED)
+ find_package(
+   Python3
+   COMPONENTS Interpreter Development NumPy

easybuild/easyconfigs/a/AlphaFold3/AlphaFold3-3.0.1-20250908-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,111 @@
+# Author: Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2025/02
+# Update: Pavel Tomanek (Inuits)
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold3'
+version = '3.0.1-20250908'
+versionsuffix = '-CUDA-%(cudaver)s'
+local_commit = 'a8ecdb2'
+
+homepage = 'https://deepmind.google/technologies/alphafold'
+description = """This package provides an implementation of the inference pipeline of AlphaFold3.
+See below for how to access the model parameters. You may only use AlphaFold3
+model parameters if received directly from Google. Use is subject to these
+terms of use:
+https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+github_account = 'google-deepmind'
+
+builddependencies = [
+    ('scikit-build', '0.17.6'),
+    ('poetry', '1.8.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('scikit-build-core', '0.10.6'),
+    ('pybind11', '2.12.0'),
+    ('pybind11_abseil', '202402.0'),
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('jax', '0.6.2', versionsuffix),
+    ('jax-triton', '0.3.0', versionsuffix),
+    ('jaxtyping', '0.2.38', versionsuffix),
+    ('dm-haiku', '0.0.14', versionsuffix),
+    ('dm-tree', '0.1.9'),
+    ('RDKit', '2025.03.3'),
+    ('tqdm', '4.66.5'),
+    ('dssp', '4.4.10'),
+    ('Abseil', '20240722.0'),
+    ('HMMER', '3.4'),
+]
+
+exts_list = [
+    ('zstandard', '0.23.0', {
+        'checksums': ['b2d8c62d08e7255f68f7a740bae85b3c9b8e5466baa9cbf7f57f1cde0ac6bc09'],
+    }),
+    ('typeguard', '2.13.3', {
+        'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'],
+    }),
+    (name, version, {
+        # unpin dependencies versions
+        'preinstallopts': """sed -i 's/==.*/",/g' %(start_dir)s/pyproject.toml && """,
+        'patches': [
+            '%(name)s-3.0.0_disable_fetch.patch',
+            '%(name)s-3.0.0.20250109_data_path.patch',
+        ],
+        'postinstallcmds': [
+            'cp run_alphafold.py %(installdir)s/bin',
+            'cp run_alphafold_data_test.py %(installdir)s/bin',
+            'cp run_alphafold_test.py %(installdir)s/bin',
+            'cp fetch_databases.sh %(installdir)s',
+            'chmod +x %(installdir)s/bin/run_alphafold.py',
+            '%(installdir)s/bin/build_data',
+        ],
+        'source_urls': ['https://github.com/%(github_account)s/%(namelower)s/archive'],
+        'sources': [{'download_filename': 'a8ecdb2.tar.gz', 'filename': '%(name)s-%(version)s-a8ecdb2.tar.gz'}],
+        'checksums': [
+            {'AlphaFold3-3.0.1-20250908-a8ecdb2.tar.gz':
+             '77cc1ee5e9d111bafd4cd6af01d43eee01059cb3f7fd2d19fd6c38d81082246d'},
+            {'AlphaFold3-3.0.0_disable_fetch.patch':
+             '041a35a09f783405f40e3ba47566ad6d063a10cfd98f0efd2e2a04c78e2c155e'},
+            {'AlphaFold3-3.0.0.20250109_data_path.patch':
+             'a06a971460df5e4cbe7a59042100512d2f96755d6dcdef01d4bc4e8c55122287'},
+        ],
+    }),
+]
+
+fix_python_shebang_for = ['bin/run_alphafold.py']
+
+sanity_check_paths = {
+    'files': ['bin/run_alphafold.py'],
+    'dirs': ['lib'],
+}
+sanity_check_commands = [
+    ('run_alphafold.py --help|grep "AlphaFold 3 structure prediction script"')
+]
+
+modextravars = {
+    # Compilation Time Workaround with XLA Flags
+    'XLA_FLAGS': '--xla_gpu_enable_triton_gemm=false ',
+    # Unified memory:
+    'XLA_PYTHON_CLIENT_PREALLOCATE': 'false',
+    'TF_FORCE_UNIFIED_MEMORY': 'true',
+    'XLA_CLIENT_MEM_FRACTION': '3.2',
+}
+
+modextrapaths = {'PYTHONPATH': 'bin'}  # to be able 'import run_alphafold'
+
+modloadmsg = """
+To let AF3 works properly you need to have Google models parameters (weights), then set:
+export AF3_MODEL_DIR="/path/to/the/dir/with/models"
+Also you should have databases dowloaded - use fetch_databases.sh to download them and set:
+export DB_DIR="/path/to/fetched/databases"
+You can test your installation by:
+1) python bin/run_alphafold_data_test.py (works without models)
+2) python bin/run_alphafold_test.py --model_dir="$AF3_MODEL_DIR" (only with models)
+"""
+
+moduleclass = 'bio'

easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.14-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,35 @@
+# update 0.0.12: Thomas Hoffmann (EMBL)
+easyblock = 'PythonBundle'
+
+name = 'dm-haiku'
+version = '0.0.14'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/deepmind/dm-haiku'
+description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural
+network library for TensorFlow."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [('poetry', '1.8.3')]
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('jax', '0.6.2', versionsuffix),
+    ('Flax', '0.10.2', versionsuffix),
+    ('absl-py', '2.1.0'),
+]
+
+exts_list = [
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm_haiku', version, {
+        'modulename': 'haiku',
+        'checksums': ['0c1d56ef20e1e04d8551f788ff8964167092c5d8051b7c17ed3f9ce60c0b0a59'],
+    }),
+]
+
+moduleclass = 'lib'

easybuild/easyconfigs/f/Flax/Flax-0.10.2-gfbf-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'Flax'
+version = '0.10.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://flax.readthedocs.io'
+description = """Flax is a high-performance neural network library and ecosystem for JAX that is
+designed for flexibility: Try new forms of training by forking an example and
+by modifying the training loop, not by adding features to a framework."""
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+
+builddependencies = [('hatchling', '1.24.2')]
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('jax', '0.6.2', versionsuffix),
+    ('Optax', '0.2.4', versionsuffix),
+    ('protobuf-python', '5.28.0'),
+    ('PyYAML', '6.0.2'),
+    ('tensorstore', '0.1.72'),
+]
+
+exts_list = [
+    ('nest_asyncio', '1.6.0', {
+        'checksums': ['6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe'],
+    }),
+    ('humanize', '4.11.0', {
+        'checksums': ['e66f36020a2d5a974c504bd2555cf770621dbdbb6d82f94a6857c0b1ea2608be'],
+    }),
+    ('orbax_checkpoint', version, {
+        'modulename': 'orbax.checkpoint',
+        'checksums': ['e575ebe1f94e5cb6353ab8c9df81de0ca7cddc118645c3bfc17b8344f19d42f1'],
+    }),
+    ('%(namelower)s', version, {
+        'checksums': ['6f831350026ad48182ba6588bb4dd72dc1084985d9aca923254cb3e4c78d75f3'],
+    }),
+]
+
+moduleclass = 'ai'

easybuild/easyconfigs/j/jax-triton/jax-triton-0.3.0-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,32 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/12
+
+easyblock = 'PythonBundle'
+
+name = 'jax-triton'
+version = '0.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pypi.org/project/jax-triton'
+description = """The jax-triton repository contains integrations between JAX and Triton."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('jax', '0.6.2', versionsuffix),
+    ('Triton', '3.3.1', versionsuffix),
+]
+
+exts_list = [
+    ('jax_triton', version, {
+        'checksums': ['da7b9cd8f784de50b26d104a3f4c417c0afcdd894f98442bc815a822900033e6'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'ai'

easybuild/easyconfigs/j/jaxtyping/jaxtyping-0.2.38-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,39 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/12
+
+easyblock = 'PythonBundle'
+
+name = 'jaxtyping'
+version = '0.2.38'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/patrick-kidger/jaxtyping'
+description = """Type annotations and runtime type-checking for:
+1. shape and dtype of JAX arrays;
+   (Now also supports PyTorch, NumPy, and TensorFlow!)
+2. PyTrees.  """
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+builddependencies = [
+    ('poetry', '1.8.3')
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('jax', '0.6.2', versionsuffix),
+]
+
+exts_list = [
+    ('wadler_lindig', '0.1.3', {
+        'checksums': ['476fb7015135f714cef8f8eac7c44b164c8b993345e651a9b6f25b7b112440c9'],
+    }),
+    (name, version, {
+        'checksums': ['84d509341437189e82d7dbb59a2970435724851ca79fd8550e886cd37c048333'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'ai'