#357 Monai-full deps

vscentrum · Nov 27, 2024 · b82cbeb · b82cbeb
1 parent 247274b
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diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/CharLS-2023b.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/CharLS-2023b.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'CharLS'
+version = '2.4.2'
+
+homepage = 'https://github.com/team-charls/charls'
+description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image
+compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000
+compression ratios."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/team-charls/charls/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['d1c2c35664976f1e43fec7764d72755e6a50a80f38eca70fcc7553cad4fe19d9']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+
+sanity_check_paths = {
+    'files': ['lib/libcharls.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'
diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/ITK_v3-2023b-5.4.0-WHL.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/ITK_v3-2023b-5.4.0-WHL.eb
@@ -0,0 +1,208 @@
+# Contributors:
+# Fenglai Liu ([email protected]) - Vanderbilt University
+# Alex Domingo ([email protected]) - Vrije Universiteit Brussel (VUB)
+# Denis Kristak (INUITS), Pavel Tománek (INUITS)
+
+easyblock = 'PythonBundle'
+
+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'}
+# toolchainopts = {'pic': True, 'cstd': 'c++11'}
+# toolchainopts = {'pic': True, 'cstd': 'gnu++14'}
+# toolchainopts = {
+#     'extra_cxxflags': '-U_Float128 -U_Float32 -U_Float64 -U_Float32x -U_Float64x',
+#     'extra_cflags': '-U_Float128 -U_Float32 -U_Float64 -U_Float32x -U_Float64x',
+# }
+
+# 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'},
+# ]
+
+# DEPS:
+    # SWIG minimal version is 4.2.0 - https://github.com/InsightSoftwareConsortium/ITK/blob/v5.4.0/Wrapping/Generators/SwigInterface/CMakeLists.txt#L16
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('Bison', '3.8.2'),
+    ('Eigen', '3.4.0'),
+    ('SWIG', '4.2.1'),
+    ('Perl', '5.38.0'),
+    ('git', '2.42.0'),
+]
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),  # NumPy
+    ('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', '0.6.8'),
+]
+
+# # 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=$EBROOTSWIG '
+# configopts += '-DPY_SITE_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages '
+# Dependencies from EB
+local_sys_deps = [
+    'CASTXML',
+    'DOUBLECONVERSION',
+    'EIGEN',
+    'EXPAT',
+    'FFTW',
+    'HDF5',
+    'JPEG',
+    'PNG',
+    'SWIG',
+    'TIFF',
+    'ZLIB'
+]
+local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps]
+# configopts += ' '.join(local_sys_cmake)
+
+# prebuildopts = 'LC_ALL=C '
+# prebuildopts = 'LC_ALL=C CXXFLAGS="$CXXFLAGS -U_Float128 -U_Float32 -U_Float64 -U_Float32x -U_Float64x" ' # not working
+# buildopts = 'CXXFLAGS="$CXXFLAGS -U_Float128 -U_Float32 -U_Float64 -U_Float32x -U_Float64x"' # not working
+
+# 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' % (l, SHLIB_EXT) for l in local_lib_names],
+#     'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'],
+# }
+
+# download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+exts_default_options = {
+    'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+    'modulename': False,
+}
+exts_list = [
+    ('itk_segmentation', version, {
+        'checksums': ['ff2ca7cdf42c8c32b20e1ecf7ee0a0be68e885ce673c565e72a4876b28d2e2f3'],
+    }),
+    ('itk_registration', version, {
+        'checksums': ['3f41cff2136f69ae5c2ce6166191dff86e4722097411aaaba07a74884d36ff73'],
+    }),
+    ('itk_numerics', version, {
+        'checksums': ['e2dcda0a07ccb6b9b518d3cc4413387a44c30a313c22e15bf818af06c7da8bfd'],
+    }),
+    ('itk_io', version, {
+        'checksums': ['393d711f9edb248aed402e7fc9613045536dbd6b45fc8db638a28d0a409fe974'],
+    }),
+    ('itk_filtering', version, {
+        'checksums': ['86026c853f1fd0b13e282f952cff7455df0ac131cc608df8669ce335633eef0a'],
+    }),
+    ('itk_core', version, {
+        'checksums': ['8ca83de9c269e6b20648f2391aa2bf96903b8ed645c3d8cd40d90b939dda439e'],
+    }),
+    ('itk', version, {
+        'modulename': 'itk',
+        'checksums': ['0f0dcce9df862831e705eebf0ffa95de554b17027f69d67b31b30dcb8d838019'],
+    }),
+]
+
+# exts_list = [
+#     ('itk_segmentation', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#     }),
+#     ('itk_registration', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#     }),
+#     ('itk_numerics', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#     }),
+#     ('itk_io', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#     }),
+#     ('itk_filtering', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#     }),
+#     ('itk_core', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#     }),
+#     ('itk', version, {
+#         'source_tmpl': '%(name)s-%(version)s-cp311-abi3-manylinux_2_28_x86_64.whl',
+#         'checksums': ['0f0dcce9df862831e705eebf0ffa95de554b17027f69d67b31b30dcb8d838019'],
+#     }),
+# ]
+# sanity_check_commands = ["python -c 'import itk'"]
+
+# modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'data'
+
+# E1:
+    # rebuild CastXML-0.6.8 with cstd gnu++14 -> ok -> ITK failed with the same error
+    # rebuild CastXML-0.6.8 with cstd c++11 -> ok -> ITK failed -> log3.txt (errors a little bit different)
+    # -> delete all confingopts except -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF -> OK
+        # -> add next line: -DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON + VTK dep -> OK
+        # -> add next line: -DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python -> ERROR
+            # -> add buildopts CXXFLAGS="$CXXFLAGS -U_Float128 -U_Float32 -U_Float64 -U_Float32x -U_Float64x" -> NO
+                # -> try add cxx flags to buildopts -> NO
+                    # try put it into 'extra_cxxflags' and 'extra_cflags' -> NO
+    # -> delete all ITK_USE_SYSTEM...-> still same error
+        # cmake:
+            # == 2024-11-25 16:55:45,484 run.py:714 WARNING Found 33 potential errors (some may be harmless) in output of  cmake  
+            # -DCMAKE_INSTALL_PREFIX=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ITK/5.4.0-foss-2023b -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DPYTHON_EXECUTABLE=/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/bin/python -DPython_EXECUTABLE=/apps/gent/RHEL8/cascadelake-ib/software/Python/3.11.5-GCCcore-13.2.0/bin/python -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF -DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON -DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python -DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig -DSWIG_DIR=$EBROOTSWIG -DPY_SITE_PACKAGES_PATH=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/ITK/5.4.0-foss-2023b/lib/python3.11/site-packages  /tmp/vsc47063/easybuild/build/ITK/5.4.0/foss-2023b/ITK-5.4.0/:
+            # -- Performing Test C_HAS_WARNING-Wno-uninitialized - Failed
+            # -- Performing Test C_HAS_WARNING-Wno-unused-parameter - Failed
+            # -- Performing Test C_HAS_WARNING-Wall - Failed
+            # -- Performing Test C_HAS_WARNING-Wno-long-double - Failed
+            # -- Performing Test C_HAS_WARNING-Wcast-align - Failed
+            # -- Performing Test C_HAS_WARNING-Wdisabled-optimization - Failed
+            # -- Performing Test C_HAS_WARNING-Wextra - Failed
+            # -- Performing Test C_HAS_WARNING-Wformat_2 - Failed
+            # -- Performing Test C_HAS_WARNING-Winvalid-pch - Failed
+            # -- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Failed
+            # -- Performing Test C_HAS_WARNING-Wpointer-arith - Failed
+            # -- Performing Test C_HAS_WARNING-Wshadow - Failed
+            # -- Performing Test C_HAS_WARNING-Wunused - Failed
+            # -- Performing Test C_HAS_WARNING-Wwrite-strings - Failed
+            # -- Performing Test C_HAS_WARNING-Wno-strict-overflow - Failed
+            # -- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed
+            # -- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Failed
+            # -- Performing Test C_HAS_WARNING-mtune_generic - Failed
+            # -- Performing Test C_HAS_WARNING-march_corei7 - Failed
+            # -- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
+            # -- Performing Test VXL_HAS_DBGHELP_H - Failed
+            # -- Performing Test VXL_HAS_ALIGNED_MALLOC - Failed
+            # -- Performing Test VXL_HAS_MINGW_ALIGNED_MALLOC - Failed
+            # -- Performing Test VXL_HAS_POSIX_MEMALIGN - Failed
+            # -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
+            # -- Performing Test GDCM_HAVE_WCHAR_IFSTREAM - Failed
+            # -- Performing Test Iconv_IS_BUILT_IN - Failed
+            # -- Check size of __int64 - failed
+            # -- Performing Test H5_HAVE___TM_GMTOFF - Failed
+            # -- Performing Test H5_HAVE_STRUCT_TIMEZONE - Failed
+            # -- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG - Failed
+            # -- Performing Test H5_HAVE_STRUCT_TEXT_INFO - Failed
+            # -- Check size of _Quad - failed
+    # -> try create SWIG-4.2.1 - the v4.2.0 is minimal version -> not help
+    # problem during make:
+        # same as E1_old
diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/OpenSlide-2023b.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/OpenSlide-2023b.eb
@@ -2,7 +2,6 @@ easyblock = 'MesonNinja'
 
 name = 'OpenSlide'
 version = '4.0.0'
-# versionsuffix = '-largefiles'
 
 homepage = 'https://openslide.org/'
 description = """OpenSlide is a C library that provides a simple interface to
@@ -14,14 +13,9 @@ source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
 checksums = ['0845f3bc5db660ccff890602efc0167524f6269dd20c49a9a5b469658dbb603c']
 
-# patches = ['%(name)s-%(version)s_large_file_support.patch']
-
 builddependencies = [
     ('Meson', '1.2.3'),
     ('Ninja', '1.11.1'),
-    # ('Autotools', '20220317'),
-    # ('M4', '1.4.19'),
-    # ('pkgconf', '1.9.5'),
     ('binutils', '2.40'),
 ]
 
@@ -38,18 +32,11 @@ dependencies = [
     ('GLib', '2.78.1'),
 ]
 
-# configure_cmd = 'meson setup'
-# build_cmd = 'meson compile'
-# install_cmd = 'meson install'
-
-# preconfigopts = "autoreconf -f -i && "
-
 sanity_check_paths = {
     'files': [
         'bin/openslide-quickhash1sum',
         'bin/openslide-show-properties',
         'bin/openslide-write-png',
-        # 'lib/libopenslide.la',
         'lib/libopenslide.%s' % SHLIB_EXT
     ],
     'dirs': ['include/openslide']

diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/clearml-2023b.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/clearml-2023b.eb
@@ -0,0 +1,76 @@
+easyblock = 'PythonBundle'
+
+name = 'clearml'
+version = '1.16.5'
+
+homepage = 'https://github.com/allegroai/clearml'
+description = """Auto-Magical CI/CD to streamline your AI workload. 
+Experiment Management, Data Management, Pipeline, Orchestration, Scheduling & Serving in one MLOps/LLMOps solution."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+#DEPS:
+    # OK attrs>=18.0
+    # ok furl>=2.0.0
+    # OK jsonschema>=2.6.0
+    # OK numpy>=1.10
+    # OK pathlib2>=2.3.0
+    # OK Pillow>=4.1.1
+    # OK psutil>=3.4.2
+    # OK pyparsing>=2.0.3
+    # OK python-dateutil>=2.6.1
+    # ok pyjwt>=2.4.0,<2.9.0 ; python_version > '3.5'
+    # OK PyYAML>=3.12
+    # ok referencing<0.40 ; python_version >= '3.8'
+    # OK requests>=2.20.0
+    # OK six>=1.16.0
+    # OK urllib3>=1.21.1
+    # ok referencing 0.35.1 requires rpds-py, which is not installed.
+    # ok furl 2.1.3 requires orderedmultidict, which is not installed.
+
+
+builddependencies = [
+    ('hatchling', '1.18.0'),
+    ('maturin', '1.3.1'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('SciPy-bundle', '2023.11'),
+    ('PyYAML', '6.0.1'),
+    ('Pillow', '10.2.0'),
+#     ('networkx', '3.2.1'),
+#     ('dask', '2024.5.1'),
+#     ('imageio', '2.34.1'),
+#     ('scikit-learn', '1.3.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('orderedmultidict', '1.0.1', {
+        'checksums': ['04070bbb5e87291cc9bfa51df413677faf2141c73c61d2a5f7b26bea3cd882ad'],
+    }),
+    ('rpds_py', '0.18.0', {
+        'modulename': 'rpds',
+        'checksums': ['42821446ee7a76f5d9f71f9e33a4fb2ffd724bb3e7f93386150b61a43115788d'],
+    }),
+    ('referencing', '0.35.1', {
+        'checksums': ['25b42124a6c8b632a425174f24087783efb348a6f1e0008e63cd4466fedf703c'],
+    }),
+    ('PyJWT', '2.8.0', {
+        'modulename': 'jwt',
+        'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'],
+    }),
+    ('furl', '2.1.3', {
+        'checksums': ['5a6188fe2666c484a12159c18be97a1977a71d632ef5bb867ef15f54af39cc4e'],
+    }),
+    (name, version, {
+        'source_tmpl': 'clearml-1.16.5-py2.py3-none-any.whl',
+        'checksums': ['3caa00914e039cb2b62ca90795c3ca17077042ae1edcefc17bf13f695653480f'],
+    }),
+]
+
+moduleclass = 'ai'