{tools}[gfbf/2023a] jax v0.4.25 w/ CUDA 12.1.1

easybuild/easyconfigs/j/jax/jax-0.4.25-gfbf-2023a-CUDA-12.1.1.eb

@@ -0,0 +1,144 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Updated by: Alex Domingo (Vrije Universiteit Brussel)
+# Updated by: Thomas Hoffmann (EMBL Heidelberg)
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.4.25'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pypi.python.org/pypi/jax'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'gfbf', 'version': '2023a'}
+cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9.0"]
+
+builddependencies = [
+    ('Bazel', '6.3.1'),
+    ('pytest-xdist', '3.3.1'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.41.0', '-nodocs'),
+    ('matplotlib', '3.7.2'),  # required for tests/lobpcg_test.py
+    ('poetry', '1.5.1'),
+    ('pybind11', '2.11.1'),
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM),
+    ('NCCL', '2.18.3', versionsuffix),
+    ('zlib', '1.2.13'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('flatbuffers-python', '23.5.26'),
+    ('ml_dtypes', '0.3.2'),
+]
+
+# downloading xla and other tarballs to avoid that Bazel downloads it during the build
+# note: this *must* be the exact same commit as used in third_party/{xla,"other"}/workspace.bzl
+local_xla_commit = '4ccfe33c71665ddcbca5b127fefe8baa3ed632d4'
+local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'
+
+local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives'
+local_repo_opt = '--bazel_options="--distdir=%(builddir)s/archives" '
+local_repo_opt += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+local_repo_opt += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include" '
+
+
+# Some tests require an isolated run:
+local_isolated_tests = [
+    'tests/host_callback_test.py::HostCallbackTapTest::test_tap_scan_custom_jvp',
+    'tests/host_callback_test.py::HostCallbackTapTest::test_tap_transforms_doc',
+    'tests/lax_scipy_special_functions_test.py::LaxScipySpcialFunctionsTest' +
+    '::testScipySpecialFun_gammainc_s_2x1x4_float32_float32',
+]
+# deliberately not testing in parallel, as that results in (additional) failing tests;
+# use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing,
+# see https://github.com/google/jax/issues/7323 and
+# https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst;
+# use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs;
+# use NVIDIA_TF32_OVERRIDE=0 to avoid loosing numerical precision by disabling TF32 Tensor Cores;
+local_test_exports = [
+    "NVIDIA_TF32_OVERRIDE=0",
+    "CUDA_VISIBLE_DEVICES=0",
+    "XLA_PYTHON_CLIENT_ALLOCATOR=platform",
+    "JAX_ENABLE_X64=true",
+]
+local_test = ''.join(['export %s;' % x for x in local_test_exports])
+# run all tests at once except for local_isolated_tests:
+local_test += "pytest -vv tests %s && " % ' '.join(['--deselect %s' % x for x in local_isolated_tests])
+# run remaining local_isolated_tests separately: 
+local_test += ' && '.join(['pytest -vv %s' % x for x in local_isolated_tests])
+
+use_pip = True
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '2.1.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'],
+    }),
+    ('jaxlib', version, {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit,
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/runtime/archive',
+            'https://github.com/openxla/xla/archive'
+        ],
+        'patches': ['jax-0.4.25_fix-pybind11-systemlib.patch'],
+        'checksums': [
+            {'jaxlib-v0.4.25.tar.gz':
+             'fc1197c401924942eb14185a61688d0c476e3e81ff71f9dc95e620b57c06eec8'},
+            {'xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4.tar.gz':
+             '8a59b9af7d0850059d7043f7043c780066d61538f3af536e8a10d3d717f35089'},
+            {'tf_runtime-0aeefb1660d7e37964b2bb71b1f518096bda9a25.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.25_fix-pybind11-systemlib.patch':
+             'daad5b726d1a138431b05eb60ecf4c89c7b5148eb939721800bdf43d804ca033'},
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        # Avoid warning (treated as error) in upb/table.c
+        'buildopts': local_repo_opt + ' --bazel_options="--copt=-Wno-maybe-uninitialized"'
+    }),
+]
+
+exts_list = [
+    (name, version, {
+        'patches': ['jax-0.4.25_fix_env_test_no_log_spam.patch'],
+        'runtest': local_test,
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'checksums': [
+            {'jax-v0.4.25.tar.gz': '8b30af49688c0c13b82c6f5ce992727c00b5fc6d04a4c6962012f4246fa664eb'},
+            {'jax-0.4.25_fix_env_test_no_log_spam.patch':
+             'a18b5f147569d9ad41025124333a0f04fd0d0e0f9e4309658d7f6b9b838e2e2a'},
+        ],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/j/jax/jax-0.4.25_fix-pybind11-systemlib.patch

@@ -0,0 +1,38 @@
+Add missing value for System Pybind11 Bazel config
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/third_party/xla/fix-pybind11-systemlib.patch b/third_party/xla/fix-pybind11-systemlib.patch
+new file mode 100644
+index 000000000..68bd2063d
+--- /dev/null
++++ b/third_party/xla/fix-pybind11-systemlib.patch
+@@ -0,0 +1,13 @@
++--- xla-orig/third_party/tsl/third_party/systemlibs/pybind11.BUILD
+++++ xla-4ccfe33c71665ddcbca5b127fefe8baa3ed632d4/third_party/tsl/third_party/systemlibs/pybind11.BUILD
++@@ -6,3 +6,10 @@
++         "@tsl//third_party/python_runtime:headers",
++     ],
++ )
+++
+++# Needed by pybind11_bazel.
+++config_setting(
+++    name = "osx",
+++    constraint_values = ["@platforms//os:osx"],
+++)
+++
+diff --git a/third_party/xla/workspace.bzl b/third_party/xla/workspace.bzl
+index ebc8d9838..125e1c173 100644
+--- a/third_party/xla/workspace.bzl
++++ b/third_party/xla/workspace.bzl
+@@ -29,6 +29,9 @@ def repo():
+         sha256 = XLA_SHA256,
+         strip_prefix = "xla-{commit}".format(commit = XLA_COMMIT),
+         urls = tf_mirror_urls("https://github.com/openxla/xla/archive/{commit}.tar.gz".format(commit = XLA_COMMIT)),
++        patch_file = [
++            "//third_party/xla:fix-pybind11-systemlib.patch",
++        ],
+     )
+
+     # For development, one often wants to make changes to the TF repository as well
+

easybuild/easyconfigs/j/jax/jax-0.4.25_fix_env_test_no_log_spam.patch

@@ -0,0 +1,18 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/03
+# avoid overriding LD_LIBRARY_PATH, which would lead to test error: error while loading shared libraries: libpython3.11.so.1.0: cannot open shared object file: No such file or directory'
+diff -ru jax-jax-v0.4.25/tests/logging_test.py jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py
+--- jax-jax-v0.4.25/tests/logging_test.py	2024-02-24 19:25:17.000000000 +0100
++++ jax-jax-v0.4.25_fix_env_test_no_log_spam/tests/logging_test.py	2024-03-15 12:00:34.133022613 +0100
+@@ -72,8 +72,11 @@
+     python = sys.executable
+     assert "python" in python
+     # Make sure C++ logging is at default level for the test process.
++    import os
++    tmp_env=os.environ.copy()
++    tmp_env['TF_CPP_MIN_LOG_LEVEL']='1'
+     proc = subprocess.run([python, "-c", program], capture_output=True,
+-                          env={"TF_CPP_MIN_LOG_LEVEL": "1"})
++                          env=tmp_env)
+
+     lines = proc.stdout.split(b"\n")
+     lines.extend(proc.stderr.split(b"\n"))