Merge branch 'easybuilders:develop' into 20250108170217_new_pr_whispe…

…r-ctranslate2052

easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0-foss-2023a-CUDA-12.6.0.eb

@@ -0,0 +1,88 @@
+easyblock = 'CMakeMake'
+
+name = 'CTranslate2'
+version = '4.5.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://opennmt.net/CTranslate2/'
+description = "Fast inference engine for Transformer models."
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['https://github.com/OpenNMT/CTranslate2/archive/']
+sources = [{
+    "download_filename": "v%(version)s.tar.gz",
+    "filename": SOURCE_TAR_GZ,
+}]
+patches = [
+    'CTranslate2-4.5.0_fix-third-party.patch',
+    'CTranslate2-4.5.0_fix-tests.patch',
+    'CTranslate2-4.5.0_replace-cxxopts.patch',
+]
+checksums = [
+    {'CTranslate2-4.5.0.tar.gz': 'f3040c7c3da5dde022fdc16906c279f3f936c6e79f3df8f998c908bb01a77cfe'},
+    {'CTranslate2-4.5.0_fix-third-party.patch': '45ab6d19954010dc5d515498a0827f0b13992d88b9691ab73ab27fee1114e3e3'},
+    {'CTranslate2-4.5.0_fix-tests.patch': '73123eafe612538354be5aa96c750199e1a219a5316800848c3894c1cc6ca2ad'},
+    {'CTranslate2-4.5.0_replace-cxxopts.patch': 'e378969c2968e2fd57863956a4d2f267731a49d1b890dcc45593d6a310531271'},
+]
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('pybind11', '2.11.1'),
+    ('cxxopts', '3.0.0', '', SYSTEM),
+    ('spdlog', '1.11.0'),
+    ('cpu_features', '0.9.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('googletest', '1.13.0'),
+    ('PyYAML', '6.0'),
+    ('cuDNN', '9.5.0.50', versionsuffix, SYSTEM),
+]
+
+# make sure that CTranslate2 libraries are linked to FlexiBLAS, not OpenBLAS
+preconfigopts = "export CMAKE_INCLUDE_PATH=$EBROOTFLEXIBLAS/include/flexiblas:${CMAKE_INCLUDE_PATH} && "
+preconfigopts += "sed -i 's/openblas/flexiblas/g' %(start_dir)s/CMakeLists.txt && "
+
+configopts = '-DOPENMP_RUNTIME=COMP -DWITH_CUDA=ON -DWITH_MKL=OFF '
+configopts += '-DOPENBLAS_INCLUDE_DIR="$EBROOTFLEXIBLAS/include" -DWITH_OPENBLAS=ON '
+configopts += '-DWITH_CUDNN=ON '
+configopts += '-DENABLE_CPU_DISPATCH=OFF '
+
+prebuildopts = 'export CT2_VERBOSE=3 && '
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'installopts': '',
+    'runtest': False,
+}
+
+exts_list = [
+    ('ctranslate2', version, {
+        'sources': ['CTranslate2-%(version)s.tar.gz'],
+        'start_dir': 'python',
+        'checksums': ['f3040c7c3da5dde022fdc16906c279f3f936c6e79f3df8f998c908bb01a77cfe'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ct2-translator', 'lib/libctranslate2.%s' % SHLIB_EXT],
+    'dirs': ['include/ctranslate2', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "ct2-translator --help",
+    "python -c 'import ctranslate2'",
+    "python -m pip check",
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'ai'

easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-tests.patch

@@ -0,0 +1,21 @@
+Author: Pavel Tománek (pavelToman)
+Fix compilation of tests + replace third_party GTest by one from EB.
+--- tests/CMakeLists.txt.orig	2025-01-03 16:35:23.243495904 +0100
++++ tests/CMakeLists.txt	2025-01-03 17:34:04.044755825 +0100
+@@ -2,7 +2,7 @@
+
+ option(BUILD_GMOCK "" OFF)
+ option(INSTALL_GTEST "" OFF)
+-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../third_party/googletest ${CMAKE_CURRENT_BINARY_DIR}/googletest)
++find_package(GTest)
+
+ add_executable(ctranslate2_test
+   batching_test.cc
+@@ -21,6 +21,7 @@
+ target_link_libraries(ctranslate2_test
+   ${PROJECT_NAME}
+   gtest_main
++  gtest
+   )
+
+ add_executable(benchmark_ops

easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_fix-third-party.patch

@@ -0,0 +1,42 @@
+Author: Pavel Tománek (pavelToman)
+Replace recursively downloaded third party sw with programs from EB.
+--- CMakeLists.txt.orig	2025-01-03 16:15:51.023557000 +0100
++++ CMakeLists.txt	2025-01-08 15:50:57.345502000 +0100
+@@ -95,7 +95,7 @@
+ endif()
+
+ find_package(Threads)
+-add_subdirectory(third_party/spdlog EXCLUDE_FROM_ALL)
++find_package(spdlog)
+
+ set(PRIVATE_INCLUDE_DIRECTORIES
+   ${CMAKE_CURRENT_SOURCE_DIR}/src
+@@ -246,7 +246,7 @@
+   set(BUILD_SHARED_LIBS_SAVED "${BUILD_SHARED_LIBS}")
+   set(BUILD_SHARED_LIBS OFF)
+   set(BUILD_TESTING OFF)
+-  add_subdirectory(third_party/cpu_features EXCLUDE_FROM_ALL)
++  find_package(CpuFeatures)
+   set(BUILD_SHARED_LIBS "${BUILD_SHARED_LIBS_SAVED}")
+   list(APPEND LIBRARIES cpu_features)
+ endif()
+@@ -498,19 +498,6 @@
+   message(STATUS "NVCC host compiler: ${CUDA_HOST_COMPILER}")
+   message(STATUS "NVCC compilation flags: ${CUDA_NVCC_FLAGS}")
+
+-  # We should ensure that the Thrust include directories appear before
+-  # -I/usr/local/cuda/include for both GCC and NVCC, so that the headers
+-  # are coming from the submodule and not the system.
+-  set(THRUST_INCLUDE_DIRS
+-    ${CMAKE_CURRENT_SOURCE_DIR}/third_party/thrust/dependencies/cub
+-    ${CMAKE_CURRENT_SOURCE_DIR}/third_party/thrust
+-    )
+-  cuda_include_directories(${THRUST_INCLUDE_DIRS})
+-  list(APPEND PRIVATE_INCLUDE_DIRECTORIES ${THRUST_INCLUDE_DIRS})
+-
+-  set(CUTLASS_INCLUDE_DIRS
+-    ${CMAKE_CURRENT_SOURCE_DIR}/third_party/cutlass/include
+-  )
+   cuda_include_directories(${CUTLASS_INCLUDE_DIRS})
+   list(APPEND PRIVATE_INCLUDE_DIRECTORIES ${CUTLASS_INCLUDE_DIRS})
+

easybuild/easyconfigs/c/CTranslate2/CTranslate2-4.5.0_replace-cxxopts.patch

@@ -0,0 +1,22 @@
+Author: Pavel Tománek (pavelToman)
+Replace recursively downloaded third party cxxopts with cxxopts from EB.
+--- cli/CMakeLists.txt.orig	2025-01-03 16:47:35.863270652 +0100
++++ cli/CMakeLists.txt	2025-01-03 16:52:02.988342754 +0100
+@@ -1,15 +1,9 @@
+-if (NOT IS_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/../third_party/cxxopts/include")
+-  message(FATAL_ERROR "The client dependency repository (cxxopts) is missing! "
+-    "You probably didn't clone the project with --recursive. You can include it "
+-    "by calling \"git submodule update --init --recursive\"")
+-endif()
+-
+ add_executable(translator
+   translator.cc
+   )
+ target_include_directories(translator
+-  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/../third_party/cxxopts/include
+-  )
++  PRIVATE "$ENV{EBROOTCXXOPTS}/include"
++)
+ target_link_libraries(translator
+   PRIVATE ${PROJECT_NAME}
+ )

easybuild/easyconfigs/c/CastXML/CastXML-0.6.10-GCCcore-13.2.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'CastXML'
+version = '0.6.10'
+
+homepage = 'https://github.com/CastXML/CastXML'
+description = """CastXML is a C-family abstract syntax tree XML output tool."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+github_account = 'CastXML'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['d8498b39b4cf3d57671254056013de177f47fc7a2683f1a53049ab854d85ad55']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('Clang', '17.0.6'),
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/castxml'],
+    'dirs': ['share/castxml'],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/c/cpu_features/cpu_features-0.9.0-GCCcore-12.3.0.eb

@@ -0,0 +1,32 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak, update: Pavel Tománek
+easyblock = 'CMakeMake'
+
+name = 'cpu_features'
+version = '0.9.0'
+
+homepage = 'https://github.com/google/cpu_features'
+description = """A cross-platform C library to retrieve CPU features (such as available instructions) at runtime."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/google/cpu_features/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['bdb3484de8297c49b59955c3b22dba834401bc2df984ef5cfc17acbe69c5018e']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+modextrapaths = {'CPATH': 'include/cpu_features'}
+
+sanity_check_paths = {
+    'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'],
+    'dirs': ['include/cpu_features/']
+}
+
+sanity_check_commands = ['list_cpu_features']
+
+moduleclass = 'tools'

easybuild/easyconfigs/i/ITK/ITK-5.4.0-foss-2023b.eb

@@ -0,0 +1,90 @@
+# Contributors:
+# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University
+# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB)
+# Denis Kristak (INUITS), Pavel Tománek (INUITS)
+
+easyblock = 'CMakeMake'
+
+name = 'ITK'
+version = '5.4.0'
+
+homepage = 'https://itk.org'
+description = """Insight Segmentation and Registration Toolkit (ITK) provides
+ an extensive suite of software tools for registering and segmenting
+ multidimensional imaging data."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+github_account = 'InsightSoftwareConsortium'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'ITK-5.3.0_add-vtk-include-dir.patch',
+]
+checksums = [
+    {'v5.4.0.tar.gz': 'd71a36fc0aee2c9257fe128f7657feb1e671461bd48561b620619f290c71795e'},
+    {'ITK-5.3.0_add-vtk-include-dir.patch': 'df7e834a024db5d1a1459d898bd43a044351e29759ab0bf69ce03d64da95b3f7'},
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Bison', '3.8.2'),
+    ('Eigen', '3.4.0'),
+    ('SWIG', '4.3.0'),
+    ('Perl', '5.38.0'),
+    ('git', '2.42.0'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('double-conversion', '3.3.0'),
+    ('expat', '2.5.0'),
+    ('HDF5', '1.14.3'),
+    ('libjpeg-turbo', '3.0.1'),
+    ('libpng', '1.6.40'),
+    ('LibTIFF', '4.6.0'),
+    ('VTK', '9.3.0'),
+    ('zlib', '1.2.13'),
+    ('CastXML', '0.6.10'),
+]
+
+# Features
+configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
+configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON '
+# Enable Python bindings
+configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG '
+configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages '
+# Dependencies from EB
+local_sys_deps = [
+    'CASTXML',
+    'DOUBLECONVERSION',
+    'EIGEN',
+    'EXPAT',
+    'FFTW',
+    'HDF5',
+    'JPEG',
+    'PNG',
+    'SWIG',
+    'TIFF',
+    'ZLIB'
+]
+local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps]
+configopts += ' '.join(local_sys_cmake)
+
+prebuildopts = 'LC_ALL=C '
+
+local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF',
+                   'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters']
+
+sanity_check_paths = {
+    'files': ['bin/itkTestDriver'] +
+             ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (lname, SHLIB_EXT) for lname in local_lib_names],
+    'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'],
+}
+
+sanity_check_commands = ["python -c 'import itk'"]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'data'

easybuild/easyconfigs/s/SWIG/SWIG-4.3.0-GCCcore-13.2.0.eb

@@ -0,0 +1,27 @@
+name = 'SWIG'
+version = '4.3.0'
+
+homepage = 'http://www.swig.org/'
+description = """SWIG is a software development tool that connects programs written in C and C++ with
+ a variety of high-level programming languages."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f7203ef796f61af986c70c05816236cbd0d31b7aa9631e5ab53020ab7804aa9e']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Bison', '3.8.2'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('PCRE2', '10.42'),
+]
+
+configopts = '--without-alllang --with-boost=no'
+
+moduleclass = 'devel'