dorado

[boegel]

• link to support tickets: #2023090860000662 + #2023102360000756 + #2023120660000516 + #2023121360002966
• website: https://github.com/nanoporetech/dorado
• installation docs: https://github.com/nanoporetech/dorado
• toolchain: foss/2022a
• easyblock to use: (see existing easyconfigs)
• required dependencies:
  • (see existing easyconfigs)
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: no
  • container image: no
  • pre-built binaries (RHEL8 Linux x86_64): yes (https://github.com/nanoporetech/dorado#installation)
  • easyconfig outside EasyBuild: no

[boegel]

trivial update of dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb didn't work, build failed, see nanoporetech/dorado#364

[branfosj]

At the point this happens it is logging information. I traced this to requested_bytes being added for PyTorch 2.0. I used a sed to replace it with logging reserved_bytes a second time instead.

# requested_bytes not in PyTorch 1.13.1
preconfigopts += "sed -i 's/requested_bytes/reserved_bytes/g' ../dorado/dorado/nn/CudaCRFModel.cpp && 

I've not PR-ed this as I am having issues with linking related to SSL. I bypassed that issue with a hack, as I only needed dorado for a test I was doing locally.

dorado-0.3.4-foss-2022a-CUDA-11.7.0.eb

easyblock = 'CMakeMake'

name = 'dorado'
version = '0.3.4'
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': '2022a'}
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_GZ,
}]
checksums = [None]

builddependencies = [
    ('binutils', '2.38'),
    ('CMake', '3.24.3'),
]

dependencies = [
    ('CUDA', '11.7.0', '', SYSTEM),
    # ('OpenSSL', '1.1', '', SYSTEM),
    ('PyTorch', '1.13.1', '-CUDA-%(cudaver)s'),
    ('HDF5', '1.12.2'),
    ('zstd', '1.5.2'),
    ('HTSlib', '1.15.1'),
    ('kineto', '0.4.0'),
    ('libaec', '1.0.6'),
]

# 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 's/OPENSSL_USE_STATIC_LIBS TRUE/OPENSSL_USE_STATIC_LIBS FALSE/' ../dorado/cmake/OpenSSL.cmake && "
preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && "
# link in the ssl and crypto libs
preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/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 '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
# link with -lhts, not -lhtslib
preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "

# requested_bytes not in PyTorch 1.13.1
preconfigopts += "sed -i 's/requested_bytes/reserved_bytes/g' ../dorado/dorado/nn/CudaCRFModel.cpp && "

configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python "
configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc "
configopts += "-DDORADO_LIBTORCH_DIR=$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'
configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" '

sanity_check_paths = {
    'files': ['bin/dorado'],
    'dirs': [],
}

sanity_check_commands = ["dorado basecaller --help"]

moduleclass = 'bio'

[laraPPr]

The same users is also asking to install v0.4.1 #2023102360000756

[laraPPr]

Other people are now also asking for v0.5.0 #2023120660000516 + #2023121360002966

[boegel]

working easyconfig for dorado v0.5.1: easybuilders/easybuild-easyconfigs#19489

[boegel]

dorado 0.5.1 installed on all HPC-UGent Tier-2 GPU clusters (incl. donphan) + Tier-1 GPU partition, so closing...