{ai}[gfbf/2024a] jax v0.4.34, ml_dtypes v0.5.0 w/ CUDA 12.6.0 WIP

easybuild/easyconfigs/b/Bazel/Bazel-6.5.0-GCCcore-13.3.0.eb

@@ -0,0 +1,31 @@
+name = 'Bazel'
+version = '6.5.0'
+
+homepage = 'https://bazel.io/'
+description = """Bazel is a build tool that builds code quickly and reliably.
+It is used to build the majority of Google's software."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s']
+sources = ['%(namelower)s-%(version)s-dist.zip']
+patches = ['Bazel-6.5.0_py3.12_pytest_assertEqual.patch']
+checksums = [
+    {'bazel-6.5.0-dist.zip': 'fc89da919415289f29e4ff18a5e01270ece9a6fe83cb60967218bac4a3bb3ed2'},
+    {'Bazel-6.5.0_py3.12_pytest_assertEqual.patch': '2670dd5c393970ba20db2c98cf0208df7190ff339ccb66fee9a6d48aaaf3ede6'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('Python', '3.12.3'),
+    ('Zip', '3.0'),
+]
+
+dependencies = [
+    ('Java', '11.0.20', '', SYSTEM),
+]
+
+runtest = True
+testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..."
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/Bazel/Bazel-6.5.0_py3.12_pytest_assertEqual.patch

@@ -0,0 +1,31 @@
+# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2025/01
+# replace assertEquals by assertEqual
+# https://docs.python.org/3/whatsnew/3.12.html#id3
+diff -ru bazel-6.5.0/examples/py_native/fail.py bazel-6.5.0_pytest_assertEqual/examples/py_native/fail.py
+--- bazel-6.5.0/examples/py_native/fail.py	1980-01-01 00:00:00.000000000 +0100
++++ bazel-6.5.0_pytest_assertEqual/examples/py_native/fail.py	2025-01-24 14:27:22.973336188 +0100
+@@ -6,7 +6,7 @@
+ class TestGetNumber(unittest.TestCase):
+
+   def test_fail(self):
+-    self.assertEquals(GetNumber(), 0)
++    self.assertEqual(GetNumber(), 0)
+
+
+ if __name__ == '__main__':
+diff -ru bazel-6.5.0/examples/py_native/test.py bazel-6.5.0_pytest_assertEqual/examples/py_native/test.py
+--- bazel-6.5.0/examples/py_native/test.py	1980-01-01 00:00:00.000000000 +0100
++++ bazel-6.5.0_pytest_assertEqual/examples/py_native/test.py	2025-01-24 14:27:22.973336188 +0100
+@@ -8,10 +8,10 @@
+ class TestGetNumber(unittest.TestCase):
+
+   def test_ok(self):
+-    self.assertEquals(GetNumber(), 42)
++    self.assertEqual(GetNumber(), 42)
+
+   def test_fib(self):
+-    self.assertEquals(Fib(5), 8)
++    self.assertEqual(Fib(5), 8)
+
+ if __name__ == '__main__':
+   unittest.main()

easybuild/easyconfigs/j/jax/jax-0.4.34-gfbf-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,229 @@
+# 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: Pavel Tománek (INUITS)
+# Updated by: Thomas Hoffmann (EMBL Heidelberg)
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.4.34'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://jax.readthedocs.io/'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'gfbf', 'version': '2024a'}
+cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6", "9.0"]
+
+builddependencies = [
+    # ('Bazel', '7.4.1'),  TODO: problems with @@local_config_python//:py3_runtime:
+    # Error in fail: interpreter_path must be an absolute path
+    # Bazel 6.5.0 (download) works.
+    ('pybind11', '2.13.6'),
+    ('pytest-xdist', '3.6.1'),
+    ('git', '2.45.1'),  # bazel uses git to fetch repositories
+    ('matplotlib', '3.9.2'),  # required for tests/lobpcg_test.py
+    ('poetry', '1.8.3'),
+    ('Clang', '18.1.8', versionsuffix)
+]
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),  # 12.6.2 ?
+    ('cuDNN', '9.5.0.50', versionsuffix, SYSTEM),
+    ('NCCL', '2.22.3', versionsuffix),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),  # 2024.11 ?
+    ('absl-py', '2.1.0'),
+    ('flatbuffers-python', '24.3.25'),
+    ('ml_dtypes', '0.5.0'),
+    ('zlib', '1.3.1'),
+]
+
+# downloading xla and other tarballs to avoid that Bazel downloads it during the build
+local_extract_cmd = 'mkdir -p %(builddir)s/archives && cp %s %(builddir)s/archives'
+# note: following commits *must* be the exact same onces used upstream
+# XLA_COMMIT from jax-jaxlib: third_party/xla/workspace.bzl
+local_xla_commit = 'cd6e808c59f53b40a99df1f1b860db9a3e598bff'
+# TFRT_COMMIT from xla: third_party/tsl/third_party/tf_runtime/workspace.bzl
+local_tfrt_commit = '0aeefb1660d7e37964b2bb71b1f518096bda9a25'  # TODO: still required?
+# TODO: add other downloads
+
+# Use sources downloaded by EasyBuild
+_jaxlib_buildopts = '--bazel_options="--distdir=%(builddir)s/archives" '
+# Use dependencies from EasyBuild
+_jaxlib_buildopts += '--bazel_options="--action_env=TF_SYSTEM_LIBS=pybind11" '
+_jaxlib_buildopts += '--bazel_options="--action_env=CPATH=$EBROOTPYBIND11/include:$EBROOTCUDA/extras/CUPTI/include" '
+# Avoid warning (treated as error) in upb/table.c
+_jaxlib_buildopts += '--bazel_options="--copt=-Wno-maybe-uninitialized" '  # TODO: still required?
+# _jaxlib_buildopts += '--nouse_clang '  #TODO: avoid clang (?)
+_jaxlib_buildopts += '--cuda_version=%(cudaver)s '
+_jaxlib_buildopts += '--python_bin_path=$EBROOTPYTHON/bin/python3 '
+# Do not use hermetic CUDA/cuDNN/NCCL: (requires action_env=CPATH=$EBROOTCUDA/extras/CUPTI/include";
+# requires patch of external/xla/xla/tsl/cuda/cupti_stub.cc and jaxlib/gpu/vendor.h (#include <cupti.h>): 
+_jaxlib_buildopts += """--bazel_options=--repo_env=LOCAL_CUDNN_PATH="$EBROOTCUDNN" """
+_jaxlib_buildopts += """--bazel_options=--repo_env=LOCAL_NCCL_PATH="$EBROOTNCCL" """
+_jaxlib_buildopts += """--bazel_options=--repo_env=LOCAL_CUDA_PATH="$EBROOTCUDA" """
+_jaxlib_buildopts += """--bazel_options="--copt=-Ithird_party/gpus/cuda/extras/CUPTI/include" """
+
+_plugins_buildopts = """--enable_cuda """
+_plugins_buildopts += """--build_gpu_plugin """
+# _plugins_buildopts +="""--gpu_plugin_cuda_version=12 """
+_plugins_buildopts += """--build_gpu_pjrt_plugin """
+_plugins_buildopts += """--build_gpu_kernel_plugin=cuda """
+
+# get rid of .devDate versionsuffix:  TODO: find a better way
+# _no_devtag = """ export JAX_RELEASE && export JAXLIB_RELEASE && """  does not work (?)
+_no_devtag = """ sed -i "s/version=__version__/version='%(version)s'/g" setup.py && """
+_jaxlib_buildopts += """--bazel_options="--action_env=JAXLIB_RELEASE=1" """  # required?
+
+components = [
+    ('jaxlib', version, {
+        'sources': [
+            {
+                'source_urls': ['https://github.com/google/jax/archive/'],
+                'filename': 'jax-v%(version)s.tar.gz',
+            },
+            {
+                'source_urls': ['https://github.com/openxla/xla/archive'],
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit[:8],
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'source_urls': ['https://github.com/tensorflow/runtime/archive'],
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8],
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'patches': [
+            'jax-0.4.35_easyblock_compat.patch',
+            'jax-0.4.35_fix-pybind11-systemlib_cupti.patch',
+            'jax-0.4.35_version.patch',
+        ],
+        'checksums': [
+            {'jax-v0.4.34.tar.gz':
+             'd3a75ad667772309ade81350fa70c4a78028a920028800282e46d8383c0ee6bb'},
+            {'xla-cd6e808c.tar.gz':
+             '65cb6d63ef4083b35775052636cb9c629f86db6947c8b91711923ba31dbdcde8'},
+            {'tf_runtime-0aeefb16.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+            {'jax-0.4.35_easyblock_compat.patch':
+             'cbf4ad92b8438c4ce2a975efce1c47c57d4c3b117bceee071ab660f964057223'},
+            {'jax-0.4.35_fix-pybind11-systemlib_cupti.patch':
+             '51369589193be60dc94ec2de1b35d0a9268288578903fb05d41b6d1a8c9df460'},
+            {'jax-0.4.35_version.patch':
+             'cd2139a7802abf14b4b2cecee331aed80fff2ef91e16fa105093aea0795455e8'},
+        ],
+        'start_dir': 'jax-jax-v%(version)s',
+        'buildopts': _jaxlib_buildopts,
+        'prebuildopts': ' mkdir third_party/gpus/cuda/extras/ -p && ' +
+                        'ln -s $EBROOTCUDA/extras/CUPTI third_party/gpus/cuda/extras --relative &&' +
+                        _no_devtag
+    }),
+    # build jaxlib first and then plugins in 2nd interation:
+    ('jaxlib', version, {
+        'sources': [
+            {
+                'source_urls': ['https://github.com/google/jax/archive/'],
+                'filename': 'jax-v%(version)s.tar.gz',
+            },
+            {
+                'source_urls': ['https://github.com/openxla/xla/archive'],
+                'download_filename': '%s.tar.gz' % local_xla_commit,
+                'filename': 'xla-%s.tar.gz' % local_xla_commit[:8],
+                'extract_cmd': local_extract_cmd,
+            },
+            {
+                'source_urls': ['https://github.com/tensorflow/runtime/archive'],
+                'download_filename': '%s.tar.gz' % local_tfrt_commit,
+                'filename': 'tf_runtime-%s.tar.gz' % local_tfrt_commit[:8],
+                'extract_cmd': local_extract_cmd,
+            },
+        ],
+        'checksums': [
+            {'jax-v0.4.34.tar.gz':
+             'd3a75ad667772309ade81350fa70c4a78028a920028800282e46d8383c0ee6bb'},
+            {'xla-cd6e808c.tar.gz':
+             '65cb6d63ef4083b35775052636cb9c629f86db6947c8b91711923ba31dbdcde8'},
+            {'tf_runtime-0aeefb16.tar.gz':
+             'a3df827d7896774cb1d80bf4e1c79ab05c268f29bd4d3db1fb5a4b9c2079d8e3'},
+        ],
+        'start_dir': 'jax-jax-v%(version)s',
+        'buildopts': _jaxlib_buildopts + _plugins_buildopts,
+        'prebuildopts': _no_devtag
+    }),
+
+]
+# failing:
+# tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_expm1_complex128 FAILED [ 98%]
+# tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_expm1_complex64 FAILED [ 98%]
+# tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_tan_complex128 FAILED [ 99%]
+# tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_tan_complex64 FAILED [ 99%]
+# FAILED tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_expm1_complex128 - AssertionError: 
+# FAILED tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_expm1_complex64 - AssertionError: 
+# FAILED tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_tan_complex128 - AssertionError: 
+# FAILED tests/lax_test.py::FunctionAccuracyTest::testSuccessOnComplexPlane_tan_complex64 - AssertionError: 
+# tests/nn_test.py::NNFunctionsTest::testDotProductAttentionMask7 FAILED   [ 10%]
+# FAILED tests/nn_test.py::NNFunctionsTest::testDotProductAttentionMask7 - AssertionError: 
+# 
+
+# Some tests require an isolated run:  TODO: still required?
+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
+
+exts_list = [
+    (name, version, {
+        'patches': ['jax-0.4.35_version.patch'],
+        'preinstallopts': _no_devtag,
+        'runtest': False,
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'checksums': [
+            {'jax-v0.4.34.tar.gz': 'd3a75ad667772309ade81350fa70c4a78028a920028800282e46d8383c0ee6bb'},
+            {'jax-0.4.35_version.patch': 'cd2139a7802abf14b4b2cecee331aed80fff2ef91e16fa105093aea0795455e8'},
+        ],
+    }),
+]
+sanity_check_commands = [
+    """python -c "import jax_cuda"$(echo $EBVERSIONCUDA|awk -F '.' '{print $1}')"_plugin" """
+]
+sanity_pip_check = True
+
+# TODO: patch to set default XLA_FLAGS
+modluafooter = """
+setenv("XLA_FLAGS", "--xla_gpu_cuda_data_dir=" .. os.getenv("CUDA_HOME"));
+"""
+
+modtclfooter = """
+setenv XLA_FLAGS --xla_gpu_cuda_data_dir=$::env(CUDA_HOME)
+"""
+
+# TODO: sanity check paths
+
+
+moduleclass = 'ai'

easybuild/easyconfigs/j/jax/jax-0.4.35_easyblock_compat.patch

@@ -0,0 +1,21 @@
+# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2024/11
+# add dummy parameters to build/build.py for cudnn_path and cuda_path, which are set by default by the jaxlib easyblock.
+diff -ru jax-jax-v0.4.35/build/build.py jax-jax-v0.4.35_easyblockcompat/build/build.py
+--- jax-jax-v0.4.35/build/build.py	2024-10-22 21:00:23.000000000 +0200
++++ jax-jax-v0.4.35_easyblockcompat/build/build.py	2024-11-19 12:35:46.524479324 +0100
+@@ -549,6 +549,15 @@
+       help_str="Same as update_requirements, but will consider dev, nightly "
+                "and pre-release versions of packages.")
+
++  parser.add_argument(
++      "--cuda_path",
++      default="dummy",
++      help="compatibility with jaxlib.py easyblock")
++  parser.add_argument(
++      "--cudnn_path",
++      default="dummy",
++      help="compatibility with jaxlib.py easyblock")
++
+   args = parser.parse_args()
+
+   logging.basicConfig()