easybuilders · WilleBell · Oct 27, 2023 · Oct 27, 2023
diff --git a/easybuild/easyconfigs/d/DGL/DGL-1.1.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/DGL/DGL-1.1.1-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,163 @@
+easyblock = 'CMakeMake'
+
+name = 'DGL'
+version = '1.1.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://www.dgl.ai'
+description = """DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs.
+DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest
+of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+github_account = 'dmlc'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = [
+    {
+        'download_filename': '%(version)s.tar.gz',
+        'filename': '%(namelower)s-%(version)s.tar.gz',
+    },
+    {
+        'source_urls': ['https://github.com/KarypisLab/METIS/archive'],
+        'download_filename': 'v5.1.1-DistDGL-v0.5.tar.gz',
+        'filename': 'metis-5.1.1-DistDGL-v0.5.tar.gz',
+        'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/METIS --strip-components=1 -xf %s",
+    },
+    {
+        'source_urls': ['https://github.com/KarypisLab/GKlib/archive'],
+        'download_filename': 'METIS-v5.1.1-DistDGL-0.5.tar.gz',
+        'filename': 'GKlib-METIS-v5.1.1-DistDGL-0.5.tar.gz',
+        'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/METIS/GKlib --strip-components=1 -xf %s",
+    },
+    {
+        'filename': 'tensorpipe-20230206.tar.gz',
+        'git_config': {
+            'url': 'https://github.com/pytorch',
+            'repo_name': 'tensorpipe',
+            'commit': '6042f1a4cbce8eef997f11ed0012de137b317361',
+            'recursive': True,
+        },
+        'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/tensorpipe --strip-components=1 -xf %s",
+    },
+    {
+        'filename': 'pcg-20220408.tar.gz',
+        'git_config': {
+            'url': 'https://github.com/imneme',
+            'repo_name': 'pcg-cpp',
+            'commit': '428802d1a5634f96bcd0705fab379ff0113bcf13',
+            'recursive': True,
+        },
+        'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/pcg --strip-components=1 -xf %s",
+    },
+    # requires commit 8009060 due to LIBXSMM_MELTW_FLAG_OPREDUCE_VECS_REDOP_MAX 
+    #   -> do not use outdated dependency ver 1.17
+    {
+        'filename': 'libxsmm-20230504.tar.gz',
+        'git_config': {
+            'url': 'https://github.com/libxsmm',
+            'repo_name': 'libxsmm',
+            'commit': '80090603e43f6ddc870cc42e1403dd0af07744cc',
+            'recursive': True,
+        },
+        'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/libxsmm --strip-components=1 -xf %s",
+    },
+    # DGL really needs cub >= 1.17, cub version in CUDA 11.7.0 is only 1.15
+    {
+        'source_urls': ['https://github.com/NVIDIA/thrust/archive'],
+        'download_filename': '1.17.0.tar.gz',
+        'filename': 'thrust-1.17.0.tar.gz',
+        'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/thrust --strip-components=1 -xf %s",
+    },
+    {
+        'source_urls': ['https://github.com/NVIDIA/cub/archive'],
+        'download_filename': '1.17.0.tar.gz',
+        'filename': 'cub-1.17.0.tar.gz',
+        'extract_cmd':
+            "tar -C %(namelower)s-%(version)s/third_party/thrust/dependencies/cub --strip-components=1 -xf %s",
+    },
+]
+patches = [
+    '%(name)s-%(version)s_use_externals_instead_of_submodules.patch',
+    '%(name)s-%(version)s_nanoflanSearchParams.patch'
+]
+checksums = [
+    {'dgl-1.1.1.tar.gz': '076026a7818f2396056252269d7960c561840bb0fe89494e11f8d6c524891c49'},
+    {'metis-5.1.1-DistDGL-v0.5.tar.gz': 'cedf0b32d32a8496bac7eb078b2b8260fb00ddb8d50c27e4082968a01bc33331'},
+    {'GKlib-METIS-v5.1.1-DistDGL-0.5.tar.gz': '52aa0d383d42360f4faa0ae9537ba2ca348eeab4db5f2dfd6343192d0ff4b833'},
+    {'tensorpipe-20230206.tar.gz': 'fc0a4f914c3496539fbb5db8948d629b3d2b64e019c5204345ca0b427eb46f6b'},
+    {'pcg-20220408.tar.gz': 'e4612f432d4e03dcd86ee49d863c2453c00fe9bac3fe6fbbac1e92ae1675467b'},
+    {'libxsmm-20230504.tar.gz': 'c72972c05ea30908c072f9bf3f9f4f7e510fa9bd85dc42b0710f3b0a4640b98e'},
+    {'thrust-1.17.0.tar.gz': 'b02aca5d2325e9128ed9d46785b8e72366f758b873b95001f905f22afcf31bbf'},
+    {'cub-1.17.0.tar.gz': '16fd4860ae3196bc3eb08bf5754fa2a9697951ddae36dc9721e6614388893618'},
+    {'DGL-1.1.1_use_externals_instead_of_submodules.patch':
+     'b98bb1b90ea5cb64e492fee3b2390eff4d9901a37c954c39326ce667a0ecdd8e'},
+    {'DGL-1.1.1_nanoflanSearchParams.patch': '3538bf470d2457f24b44636ca2422b0df8f5bd5f6157ca8ffc94f0c022844d57'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('googletest', '1.11.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+    ('tqdm', '4.64.0'),
+    ('DLPack', '0.8'),
+    ('DMLC-Core', '0.5'),
+    ('Parallel-Hashmap', '1.36'),
+    ('nanoflann', '1.5.0'),
+    # ('libxsmm', '1.17'),  # requires commit 8009060 due to LIBXSMM_MELTW_FLAG_OPREDUCE_VECS_REDOP_MAX
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('NCCL', '2.12.12', versionsuffix),
+    ('PyTorch', '1.12.0', versionsuffix),
+]
+
+_copts = [
+    '-DUSE_AVX=OFF',  # AVX + LIBXSMM requires libxsmm tag 1.eol
+    '-DBUILD_CPP_TEST=ON',
+    '-DUSE_CUDA=ON',  # Must be "ON", as opposed to "1" or so, due to bad CMake code in DGL
+    '-DUSE_NCCL=ON',
+    '-DUSE_SYSTEM_NCCL=ON',
+    '-DBUILD_WITH_SHARED_NCCL=ON',
+    '-DUSE_FP16=ON',
+]
+configopts = ' '.join(_copts)
+
+# Must not build shared libs, DGL uses internal versions of, among others, METIS
+# but it doesn't install these internal libraries and simply assumes that everything is
+# statically linked.
+build_shared_libs = False
+
+runtest = 'test'
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'easyblock': 'PythonPackage',
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'runtest': True,
+}
+
+exts_list = [
+    ('dgl', version, {
+        'installopts': "--use-feature=in-tree-build ",
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'start_dir': 'python',
+        'checksums': ['076026a7818f2396056252269d7960c561840bb0fe89494e11f8d6c524891c49'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libdgl.%s' % SHLIB_EXT],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {
+    'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/d/DGL/DGL-1.1.1_nanoflanSearchParams.patch b/easybuild/easyconfigs/d/DGL/DGL-1.1.1_nanoflanSearchParams.patch
@@ -0,0 +1,14 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/07
+# allow using nanoflann 1.5.0, which provides nanoflann::SearchParameters(), but not nanoflann::SearchParams()
+diff -ru dgl-1.1.1/src/graph/transform/cpu/kdtree_ndarray_adapter.h dgl-1.1.1_nanoflanSearchParams/src/graph/transform/cpu/kdtree_ndarray_adapter.h
+--- dgl-1.1.1/src/graph/transform/cpu/kdtree_ndarray_adapter.h	2023-06-23 07:00:04.000000000 +0200
++++ dgl-1.1.1_nanoflanSearchParams/src/graph/transform/cpu/kdtree_ndarray_adapter.h	2023-07-06 12:17:16.433558692 +0200
+@@ -74,7 +74,7 @@
+       FloatType* out_dists) const {
+     nanoflann::KNNResultSet<FloatType, IdType> resultSet(num_closest);
+     resultSet.init(out_idxs, out_dists);
+-    index_->findNeighbors(resultSet, query_pt, nanoflann::SearchParams());
++    index_->findNeighbors(resultSet, query_pt, nanoflann::SearchParameters());
+   }
+
+   /** @brief Interface expected by KDTreeSingleIndexAdaptor */
diff --git a/easybuild/easyconfigs/d/DGL/DGL-1.1.1_use_externals_instead_of_submodules.patch b/easybuild/easyconfigs/d/DGL/DGL-1.1.1_use_externals_instead_of_submodules.patch
@@ -0,0 +1,64 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/07
+# based on DGL-0.9.1_use_externals_instead_of_submodules.patch,
+# but build libxsmm because LIBXSMM_MELTW_FLAG_OPREDUCE_VECS_REDOP_MAX is required from commit 8009060 > v1.17
+diff -ru dgl-1.1.1/CMakeLists.txt dgl-1.1.1_use_externals_instead_of_submodules/CMakeLists.txt
+--- dgl-1.1.1/CMakeLists.txt	2023-06-23 07:00:04.000000000 +0200
++++ dgl-1.1.1_use_externals_instead_of_submodules/CMakeLists.txt	2023-07-06 11:08:46.258340318 +0200
+@@ -176,12 +176,12 @@
+
+ # include directories
+ target_include_directories(dgl PRIVATE "include")
+-target_include_directories(dgl PRIVATE "third_party/dlpack/include")
+-target_include_directories(dgl PRIVATE "third_party/dmlc-core/include")
+-target_include_directories(dgl PRIVATE "third_party/phmap/")
++#target_include_directories(dgl PRIVATE "third_party/dlpack/include")
++#target_include_directories(dgl PRIVATE "third_party/dmlc-core/include")
++#target_include_directories(dgl PRIVATE "third_party/phmap/")
+ target_include_directories(dgl PRIVATE "third_party/METIS/include/")
+ target_include_directories(dgl PRIVATE "tensoradapter/include")
+-target_include_directories(dgl PRIVATE "third_party/nanoflann/include")
++#target_include_directories(dgl PRIVATE "third_party/nanoflann/include")
+ target_include_directories(dgl PRIVATE "third_party/libxsmm/include")
+ target_include_directories(dgl PRIVATE "third_party/pcg/include")
+
+@@ -189,7 +189,7 @@
+ if (USE_HDFS)
+   option(DMLC_HDFS_SHARED "dgl has to build with dynamic hdfs library" ON)
+ endif()
+-add_subdirectory("third_party/dmlc-core")
++#add_subdirectory("third_party/dmlc-core")
+ list(APPEND DGL_LINKER_LIBS dmlc)
+ set(GOOGLE_TEST 0) # Turn off dmlc-core test
+
+@@ -220,6 +220,7 @@
+   endif(REBUILD_LIBXSMM)
+   add_dependencies(dgl libxsmm)
+   list(APPEND DGL_LINKER_LIBS -L${CMAKE_SOURCE_DIR}/third_party/libxsmm/lib/ xsmm.a)
++  list(APPEND DGL_LINKER_LIBS  flexiblas)
+ endif((NOT MSVC) AND USE_LIBXSMM)
+
+ if(NOT MSVC)
+@@ -305,15 +306,18 @@
+ # Testing
+ if(BUILD_CPP_TEST)
+   message(STATUS "Build with unittest")
+-  add_subdirectory(./third_party/googletest)
++  #add_subdirectory(./third_party/googletest)
+   enable_testing()
+   include_directories(${gtest_SOURCE_DIR}/include ${gtest_SOURCE_DIR})
+   include_directories("include")
+-  include_directories("third_party/dlpack/include")
+-  include_directories("third_party/dmlc-core/include")
+-  include_directories("third_party/phmap")
++  #include_directories("third_party/dlpack/include")
++  #include_directories("third_party/dmlc-core/include")
++  #include_directories("third_party/phmap")
+   include_directories("third_party/libxsmm/include")
+   include_directories("third_party/pcg/include")
++  if (USE_AVX)     #TH?
++    include_directories("third_party/xbyak")    #TH ?
++  endif(USE_AVX)   #TH ?
+   file(GLOB_RECURSE TEST_SRC_FILES ${PROJECT_SOURCE_DIR}/tests/cpp/*.cc)
+   add_executable(runUnitTests ${TEST_SRC_FILES})
+   target_link_libraries(runUnitTests gtest gtest_main)
+Only in dgl-1.1.1_use_externals_instead_of_submodules: .CMakeLists.txt.swp
diff --git a/easybuild/easyconfigs/d/DLPack/DLPack-0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DLPack/DLPack-0.8-GCC-11.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeMake'
+
+name = 'DLPack'
+version = '0.8'
+
+homepage = 'https://dmlc.github.io/dlpack/latest/'
+description = """DLPack is a stable in-memory data structure for an ndarray
+system to interact with a variety of frameworks."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'dmlc'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['cf965c26a5430ba4cc53d61963f288edddcd77443aa4c85ce722aaf1e2f29513']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/dlpack/dlpack.h', 'lib/cmake/dlpack/dlpackConfig.cmake'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'DMLC-Core'
+version = '0.5'
+
+homepage = 'https://dmlc-core.readthedocs.io/en/latest'
+description = """DMLC-Core is the backbone library to support all DMLC
+projects, offers the bricks to build efficient and scalable distributed
+machine learning libraries."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'dmlc'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['cd97475ae1ecf561a1cb1129552f9889d52b11b3beb4c56e5345d007d5020ece']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('googletest', '1.11.0'),
+]
+
+_copts = [
+    '-DUSE_CXX14_IF_AVAILABLE=ON',
+    '-DGOOGLE_TEST=ON',
+]
+configopts = ' '.join(_copts)
+
+build_shared_libs = True
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['include/dmlc/common.h', 'lib/cmake/dmlc/dmlc-config.cmake', 'lib/libdmlc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.5.0-GCCcore-11.3.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'CMakeMake'
+
+name = 'nanoflann'
+version = '1.5.0'
+
+homepage = 'https://github.com/jlblancoc/nanoflann'
+description = "nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies."
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'optarch': False}  # optarch causes test error on zen2
+
+github_account = 'jlblancoc'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    '%(name)s-%(version)s_use_external_googletest.patch',
+]
+checksums = [
+    {'v1.5.0.tar.gz': '89aecfef1a956ccba7e40f24561846d064f309bc547cc184af7f4426e42f8e65'},
+    {'nanoflann-1.5.0_use_external_googletest.patch':
+     '5f0b99b0558bdf76c19d52eb82d10cdcc104eb6c2fb1891e033b5c96fb47f7b9'},
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+    ('googletest', '1.11.0'),
+]
+
+configopts = '-DNANOFLANN_BUILD_TESTS=ON'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['include/nanoflann.hpp', 'lib/pkgconfig/nanoflann.pc'],
+    'dirs': ['share/nanoflann/cmake'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.5.0_use_external_googletest.patch b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.5.0_use_external_googletest.patch
@@ -0,0 +1,46 @@
+Use external googletest
+
+Åke Sandgren, 20230213
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index fc84430..31ab273 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -90,6 +90,10 @@ endif()
+ # Tests
+ option(NANOFLANN_BUILD_TESTS "Build unit tests" ON)
+ if(NANOFLANN_BUILD_TESTS)
++        find_package(GTest)
++        if (NOT GTEST_FOUND)
++            message(ERROR "Testing requires googletest.")
++        endif()
+ 	enable_testing()
+ 	add_subdirectory(tests)
+ endif()
+diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
+index 2e593da..9c3b443 100644
+--- a/tests/CMakeLists.txt
++++ b/tests/CMakeLists.txt
+@@ -8,17 +8,6 @@ if(MSVC)
+ 	add_definitions(-D_VARIADIC_MAX=10)
+ endif(MSVC)
+
+-if(NOT TARGET gtest)
+-	# Treat this directory as "system" to ignore pedantic warnings.
+-	if(CMAKE_COMPILER_IS_GNUCXX)
+-		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -isystem gtest-1.8.0/include")
+-	endif()
+-
+-	# Compile gtest from sources:
+-	add_subdirectory(gtest-1.8.0)
+-	INCLUDE_DIRECTORIES("gtest-1.8.0/include/")
+-endif()
+-
+ set(EXECUTABLE_OUTPUT_PATH "${${PROJECT_NAME}_BINARY_DIR}")
+
+ # Tests based on Google gtest:
+@@ -37,4 +26,4 @@ ADD_TEST(unit_tests_run ${EXECUTABLE_OUTPUT_PATH}/unit_tests)
+ set_tests_properties(unit_tests_run PROPERTIES DEPENDS unit_tests_build)
+
+ # Add the required libraries for linking:
+-TARGET_LINK_LIBRARIES(unit_tests mygtest nanoflann)
++TARGET_LINK_LIBRARIES(unit_tests ${GTEST_LIBRARIES} nanoflann)