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{bio,perf}[GCC/14.2.0,foss/2025a] dorado v1.4.0, kineto v20260317 w/ CUDA 12.8.0 #25641
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84 changes: 84 additions & 0 deletions
84
easybuild/easyconfigs/d/dorado/dorado-1.4.0-foss-2025a-CUDA-12.8.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| easyblock = 'CMakeMake' | ||
|
|
||
| name = 'dorado' | ||
| version = '1.4.0' | ||
| 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': '2025a'} | ||
| toolchainopts = {'usempi': False} | ||
|
|
||
| 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 = [ | ||
| 'dorado-1.4.0_fix-hts-cmake.patch', | ||
| 'dorado-1.4.0_fix-TestUtils.h.patch', | ||
| ] | ||
| checksums = [ | ||
| {'dorado-1.4.0.tar.xz': 'b65aaaeacd9169ecf3722b4e37956f74ae4ac9ce09827d3bb4cdef1ec82e6965'}, | ||
| {'dorado-1.4.0_fix-hts-cmake.patch': 'b99f268086650462437cc252040bb8636dfe1e1bbb566e65590fd3401d63f2a0'}, | ||
| {'dorado-1.4.0_fix-TestUtils.h.patch': 'f99f0de9506ad9e58be508ae353546e94eb77c6ae5b085637060ec83331ad5ed'}, | ||
| ] | ||
|
|
||
| builddependencies = [ | ||
| ('CMake', '3.31.3'), | ||
| ('git', '2.49.0'), | ||
| ] | ||
|
|
||
| dependencies = [ | ||
| ('CUDA', '12.8.0', '', SYSTEM), | ||
| ('Python', '3.13.1'), | ||
| ('OpenSSL', '3', '', SYSTEM), | ||
| ('PyTorch', '2.9.1', versionsuffix), | ||
| ('HDF5', '1.14.6'), | ||
| ('zstd', '1.5.6'), | ||
| ('HTSlib', '1.22.1'), | ||
| ('kineto', '20260317', versionsuffix), | ||
| ('libaec', '1.1.4'), | ||
| ] | ||
|
|
||
| # 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 += r"sed -i 's/OpenSSL::SSL/ssl\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " | ||
| # replace dont_install_external_libraries.patch by sed cmd - use system CUDA | ||
| preconfigopts += "sed -i '/install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)/d' " | ||
| preconfigopts += "../dorado/cmake/InstallRedistLibs.cmake && " | ||
| # disable treating warnings like errors by stripping out -Werror | ||
| # cfr. https://github.com/nanoporetech/dorado/issues/779 | ||
| preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && " | ||
|
|
||
| local_torch_root_py = 'import torch, pathlib; print(pathlib.Path(torch.__file__).resolve().parent)' | ||
| configopts = ' '.join([ | ||
| "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA", | ||
| "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc", | ||
| '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL', | ||
| '-DCMAKE_C_FLAGS="$CFLAGS -pthread"', | ||
| '-DCMAKE_CXX_FLAGS="$CXXFLAGS -pthread"', | ||
| # let torch find its files - different paths for PyTorch from sources and wheels | ||
| rf'''-DDORADO_LIBTORCH_DIR="$(python -c '{local_torch_root_py}')"''', | ||
| r'''-DCMAKE_PREFIX_PATH="$(python -c 'import torch; print(torch.utils.cmake_prefix_path)')"''', | ||
| ]) + ' ' | ||
|
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| runtest = True | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/dorado'], | ||
| 'dirs': [], | ||
| } | ||
|
|
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| sanity_check_commands = ["dorado basecaller --help"] | ||
|
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| moduleclass = 'bio' | ||
23 changes: 23 additions & 0 deletions
23
easybuild/easyconfigs/d/dorado/dorado-1.4.0_fix-TestUtils.h.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| Replace std::filesystem::remove_all with rm -rf in test temp-dir cleanup to avoid | ||
| segfault with PyTorch 2.9.1-loaded filesystem symbols | ||
| Author: Pavel Tomanek (Inuits/Ugent) with help of ChatGPT5.4 | ||
| --- tests/TestUtils.h.orig 2026-03-27 16:30:29.957036727 +0100 | ||
| +++ tests/TestUtils.h 2026-03-27 16:31:17.700602831 +0100 | ||
| @@ -2,6 +2,7 @@ | ||
|
|
||
| #include <spdlog/spdlog.h> | ||
|
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||
| +#include <cstdlib> | ||
| #include <cstring> | ||
| #include <filesystem> | ||
| #include <string> | ||
| @@ -44,7 +45,8 @@ | ||
| while (!deleted && tries < 5) { | ||
| try { | ||
| tries++; | ||
| - deleted = std::filesystem::remove_all(m_path); | ||
| + std::string cmd = "rm -rf -- \"" + m_path.string() + "\""; | ||
| + deleted = (std::system(cmd.c_str()) == 0) ? 1 : 0; | ||
| } catch (std::exception& e) { | ||
| std::string what = e.what(); | ||
| spdlog::warn(what); |
118 changes: 118 additions & 0 deletions
118
easybuild/easyconfigs/d/dorado/dorado-1.4.0_fix-hts-cmake.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,118 @@ | ||
| Replace vendored HTSlib CMake integration with system HTSlib target | ||
| Author: Pavel Tomanek (Inuits/Ugent) with help of ChatGPT5.4 | ||
| --- cmake/Htslib.cmake.orig 2026-03-27 16:02:28.928335000 +0100 | ||
| +++ cmake/Htslib.cmake 2026-03-27 16:03:27.115524695 +0100 | ||
| @@ -1,100 +1,14 @@ | ||
| -if(NOT TARGET htslib) # lazy include guard | ||
| - if(WIN32) | ||
| - message(STATUS "Fetching htslib") | ||
| - download_and_extract( | ||
| - ${DORADO_CDN_URL}/htslib-win-v1.22.1.tar.gz | ||
| - htslib-win | ||
| - "8cedc027d0c796e6fe6c8e30fe8ec161c46122d9ab66d5d6339f039ffc91b2ea" | ||
| - ) | ||
| - set(HTSLIB_DIR ${DORADO_3RD_PARTY_DOWNLOAD}/htslib-win CACHE STRING | ||
| - "Path to htslib repo") | ||
| - add_library(htslib SHARED IMPORTED) | ||
| - set_target_properties(htslib PROPERTIES | ||
| - "IMPORTED_IMPLIB" ${HTSLIB_DIR}/hts-3.lib | ||
| - "IMPORTED_LOCATION" ${HTSLIB_DIR}/hts-3.dll | ||
| - "INTERFACE_INCLUDE_DIRECTORIES" ${HTSLIB_DIR}) | ||
| - target_link_directories(htslib INTERFACE ${HTSLIB_DIR}) | ||
| - else() | ||
| - message(STATUS "Setting up htslib build") | ||
| - set(HTSLIB_DIR ${DORADO_3RD_PARTY_SOURCE}/htslib CACHE STRING "Path to htslib repo") | ||
| - set(htslib_PREFIX ${CMAKE_BINARY_DIR}/3rdparty/htslib) | ||
| - | ||
| - find_program(MAKE_COMMAND make REQUIRED) | ||
| - find_program(AUTOCONF_COMMAND autoconf REQUIRED) | ||
| - find_program(AUTOHEADER_COMMAND autoheader REQUIRED) | ||
| - execute_process( | ||
| - COMMAND bash -c "${AUTOCONF_COMMAND} -V | sed 's/.* //; q'" | ||
| - OUTPUT_VARIABLE AUTOCONF_VERS | ||
| - COMMAND_ERROR_IS_FATAL ANY | ||
| - ) | ||
| - if (AUTOCONF_VERS VERSION_GREATER_EQUAL 2.70 AND NOT CMAKE_GENERATOR STREQUAL "Xcode") | ||
| - set(AUTOCONF_COMMAND autoreconf --install) | ||
| - endif() | ||
| - | ||
| - # htslib will only try to build the .so as PIC, but ont_core needs it all as PIC. | ||
| - unset(hts_cflags) | ||
| - if (LINUX) | ||
| - set(hts_cflags "-fPIC") | ||
| - endif() | ||
| - | ||
| - # If we're building with sanitizers then we need to build htslib the same way. | ||
| - if (ECM_ENABLE_SANITIZERS MATCHES "address") | ||
| - set(hts_cflags "${hts_cflags} -g -fsanitize=address") | ||
| - endif() | ||
| - if (ECM_ENABLE_SANITIZERS MATCHES "undefined") | ||
| - set(hts_cflags "${hts_cflags} -g -fsanitize=undefined") | ||
| - endif() | ||
| - if (ECM_ENABLE_SANITIZERS MATCHES "thread") | ||
| - set(hts_cflags "${hts_cflags} -g -fsanitize=thread") | ||
| - endif() | ||
| - | ||
| - unset(hts_configure_flags) | ||
| - if (hts_cflags) | ||
| - set(hts_configure_flags "CPPFLAGS=${hts_cflags}" "LDFLAGS=${hts_cflags}") | ||
| - endif() | ||
| - | ||
| - # Parallelise the htslib build too, though not enough to compete with the main build. | ||
| - include(ProcessorCount) | ||
| - ProcessorCount(nproc) | ||
| - math(EXPR htslib_build_jobs "${nproc} / 4") | ||
| - if (htslib_build_jobs EQUAL 0) | ||
| - set(htslib_build_jobs 1) | ||
| - endif() | ||
| - | ||
| - # The Htslib build apparently requires BUILD_IN_SOURCE=1, which is a problem when | ||
| - # switching between build targets because htscodecs object files aren't regenerated. | ||
| - # To avoid this, copy the source tree to a build-specific directory and do the build there. | ||
| - set(HTSLIB_BUILD ${CMAKE_BINARY_DIR}/htslib_build) | ||
| - file(COPY ${HTSLIB_DIR} DESTINATION ${HTSLIB_BUILD}) | ||
| - | ||
| - include(ExternalProject) | ||
| - ExternalProject_Add(htslib_project | ||
| - PREFIX ${HTSLIB_BUILD} | ||
| - SOURCE_DIR ${HTSLIB_BUILD}/htslib | ||
| - BUILD_IN_SOURCE 1 | ||
| - CONFIGURE_COMMAND ${AUTOHEADER_COMMAND} | ||
| - COMMAND ${AUTOCONF_COMMAND} | ||
| - COMMAND ./configure --disable-bz2 --disable-lzma --disable-libcurl --disable-s3 --disable-gcs --without-libdeflate ${hts_configure_flags} | ||
| - BUILD_COMMAND ${MAKE_COMMAND} -j${htslib_build_jobs} install prefix=${htslib_PREFIX} | ||
| - COMMAND ${INSTALL_NAME} | ||
| - INSTALL_COMMAND "" | ||
| - BUILD_BYPRODUCTS ${htslib_PREFIX}/lib/libhts.a | ||
| - LOG_CONFIGURE 0 | ||
| - LOG_BUILD 0 | ||
| - LOG_TEST 0 | ||
| - LOG_INSTALL 0 | ||
| - ) | ||
| - | ||
| - add_library(htslib STATIC IMPORTED) | ||
| - # Need to ensure this directory exists before we can add it to INTERFACE_INCLUDE_DIRECTORIES | ||
| - file(MAKE_DIRECTORY ${htslib_PREFIX}/include) | ||
| - set_target_properties(htslib | ||
| - PROPERTIES | ||
| - "IMPORTED_LOCATION" ${htslib_PREFIX}/lib/libhts.a | ||
| - "INTERFACE_INCLUDE_DIRECTORIES" ${htslib_PREFIX}/include) | ||
| - message(STATUS "Done configuring htslib") | ||
| - | ||
| - # Make sure that the project is built before any targets try to use it. | ||
| - add_dependencies(htslib htslib_project) | ||
| - endif() | ||
| +if(NOT TARGET htslib) | ||
| + find_package(htslib QUIET NO_MODULE) | ||
| + if(htslib_FOUND AND TARGET htslib::hts) | ||
| + add_library(htslib INTERFACE IMPORTED) | ||
| + target_link_libraries(htslib INTERFACE htslib::hts) | ||
| + message(STATUS "Using system htslib via config package") | ||
| + else() | ||
| + find_package(PkgConfig REQUIRED) | ||
| + pkg_check_modules(HTSLIB REQUIRED IMPORTED_TARGET htslib) | ||
| + add_library(htslib INTERFACE IMPORTED) | ||
| + target_link_libraries(htslib INTERFACE PkgConfig::HTSLIB) | ||
| + message(STATUS "Using system htslib via pkg-config") | ||
| + endif() | ||
| endif() |
38 changes: 38 additions & 0 deletions
38
easybuild/easyconfigs/k/kineto/kineto-20260317-GCC-14.2.0-CUDA-12.8.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| easyblock = 'CMakeMake' | ||
|
|
||
| name = 'kineto' | ||
| version = '20260317' | ||
| local_commit = '7d860f2' | ||
| versionsuffix = '-CUDA-%(cudaver)s' | ||
|
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| homepage = 'https://github.com/pytorch/kineto' | ||
| description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters" | ||
|
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| toolchain = {'name': 'GCC', 'version': '14.2.0'} | ||
|
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| 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 = ['015ad66abc07c4120be0789168d34f5537dc8b87b0ad96775a3ba70a18894c96'] | ||
|
|
||
| builddependencies = [ | ||
| ('CMake', '3.31.3'), | ||
| ('Python', '3.13.1'), | ||
| ] | ||
| dependencies = [('CUDA', '12.8.0', '', SYSTEM)] | ||
|
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| start_dir = 'libkineto' | ||
|
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| sanity_check_paths = { | ||
| 'files': ['lib/libkineto.a'], | ||
| 'dirs': ['include/kineto'], | ||
| } | ||
|
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| moduleclass = 'perf' |
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