{bio}[foss/2024a] dorado v1.0.2 w/ CUDA 12.6.0

easybuild/easyconfigs/d/dorado/dorado-1.0.0_dont_install_external_libraries.patch

@@ -0,0 +1,11 @@
+--- cmake/InstallRedistLibs.cmake.orig	2025-06-03 10:40:42.830160000 +0200
++++ cmake/InstallRedistLibs.cmake	2025-06-03 10:41:52.532350000 +0200
+@@ -54,7 +54,7 @@
+         else()
+             # bundle the libraries from the cuda toolkit
+             file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}")
+-            install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
++            #install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
+         endif()
+     endforeach()
+

easybuild/easyconfigs/d/dorado/dorado-1.0.2-foss-2024a-CUDA-12.6.0.eb

@@ -0,0 +1,116 @@
+easyblock = 'CMakeMake'
+
+name = 'dorado'
+version = '1.0.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/nanoporetech/dorado'
+description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/nanoporetech/dorado/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/nanoporetech',
+        'repo_name': name,
+        'tag': 'v%(version)s',
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_XZ,
+}]
+patches = [
+    '%(name)s-1.0.0_dont_install_external_libraries.patch',
+]
+checksums = [
+    {'dorado-1.0.2.tar.xz':
+     '6c07feb001de20f4d6bfc5b6199ecde159c836f67ac9e11002c89833a9d10bd6'},
+    {'dorado-1.0.0_dont_install_external_libraries.patch':
+     'feaaf0144e4e1c4fc2b6eff55254491b0d0da83833a8e72451b91a7df142f2dd'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('CMake', '3.29.3'),
+    ('patchelf', '0.18.0'),
+    ('git', '2.45.1'),
+]
+
+dependencies = [
+    ('CUDA', '12.6.0', '', SYSTEM),
+    ('PyTorch', '2.6.0', '-CUDA-%(cudaver)s'),
+    ('HDF5', '1.14.5'),
+    ('zstd', '1.5.6'),
+    ('HTSlib', '1.21'),
+    ('kineto', '20250715'),
+    ('libaec', '1.1.3'),
+]
+
+# don't link to OpenSSL static libraries
+# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
+preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
+# link in the ssl and crypto libs, to fix:
+# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
+preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
+
+# don't use vendored HTSlib, use provided HTSlib dependency
+preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
+# link with -lhts, not -lhtslib
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/secondary/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# disable treating warnings like errors by stripping out -Werror
+# cfr. https://github.com/nanoporetech/dorado/issues/779
+preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//g' ../dorado/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/modbase/CMakeLists.txt && "
+preconfigopts += "sed -i 's/enable_warnings_as_errors.*//' ../dorado/dorado/torch_utils/CMakeLists.txt && "
+
+# skip including a nonexistant file
+preconfigopts += "head -442 ../dorado/cmake/Torch.cmake > /tmp/a && "
+preconfigopts += "tail -31 ../dorado/cmake/Torch.cmake >> /tmp/a && "
+preconfigopts += "mv /tmp/a ../dorado/cmake/Torch.cmake && "
+
+_copts = [
+    "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
+    "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc",
+    '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL',
+    "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
+    # add -pthread flag (in addition to -lpthread) to avoid linking error:
+    # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread -lcublas"',
+]
+
+configopts = ' '.join(_copts) + ' '
+
+# disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking
+configopts += "$(if %(rpath_enabled)s; then "
+configopts += "echo '-DCMAKE_SKIP_INSTALL_RPATH=YES -DCMAKE_SKIP_RPATH=YES'; fi) "
+
+# CUDA libraries that are copied to installdir need to be patched to have an RPATH section
+# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check);
+# by default, CMake sets RUNPATH to '$ORIGIN' rather than RPATH (but that's disabled above)
+postinstallcmds = [
+    "if %(rpath_enabled)s; then "
+    "  for lib in $(ls %(installdir)s/lib/lib{cu,nv}*.so*); do "
+    "    echo setting RPATH in $lib;"
+    "    patchelf --force-rpath --set-rpath '$ORIGIN' $lib;"
+    "  done;"
+    "fi",
+]
+
+sanity_check_paths = {
+    'files': ['bin/dorado'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["dorado basecaller --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/k/kineto/kineto-20250715-GCC-13.3.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'kineto'
+version = '20250715'
+local_commit = '16e2a56'
+
+homepage = 'https://github.com/pytorch/kineto'
+description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters"
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/pytorch/kineto/archive/']
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/pytorch',
+        'repo_name': name,
+        'commit': local_commit,
+        'recursive': True,
+    },
+    'filename': SOURCE_TAR_XZ,
+}]
+checksums = ['65e986bfc7664257b09563dceddb1dd0f4c0857af4696597d73b3bf970728db4']
+
+builddependencies = [
+    ('CMake', '3.29.3'),
+    ('Python', '3.12.3'),
+    ('CUDA', '12.6.0', '', SYSTEM),
+]
+
+start_dir = 'libkineto'
+
+sanity_check_paths = {
+    'files': ['lib/libkineto.a'],
+    'dirs': ['include/kineto'],
+}
+
+moduleclass = 'perf'