# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-"""
+"""Building block based Dockerfile generation for CI testing images.
+
Generates a set of docker images used for running GROMACS CI on Gitlab.
The images are prepared according to a selection of build configuration targets
that hope to cover a broad enough scope of different possible systems,
Based on the example script provided by the NVidia HPCCM repository.
+Reference:
+ `NVidia HPC Container Maker <https://github.com/NVIDIA/hpc-container-maker>`__
+
Authors:
* Paul Bauer <paul.bauer.q@gmail.com>
* Eric Irrgang <ericirrgang@gmail.com>
$ python3 scripted_gmx_docker_builds.py --format docker > Dockerfile && docker build .
$ python3 scripted_gmx_docker_builds.py | docker build -
+See Also:
+ :file:`buildall.sh`
+
"""
import argparse
'ccache',
'git',
'gnupg',
+ 'gpg-agent',
'libfftw3-dev',
'libhwloc-dev',
'liblapack-dev',
'wget',
'xsltproc']
+_opencl_extra_packages = [
+ 'nvidia-opencl-dev',
+ # The following require apt_ppas=['ppa:intel-opencl/intel-opencl']
+ 'intel-opencl-icd',
+ 'ocl-icd-libopencl1',
+ 'ocl-icd-opencl-dev',
+ 'opencl-headers',
+ # The following require
+ # apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
+ # apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
+ 'libelf1',
+ 'rocm-opencl',
+ 'rocm-dev',
+ 'clinfo'
+]
+
# Extra packages needed to build Python installations from source.
_python_extra_packages = ['build-essential',
'ca-certificates',
'linkchecker',
'mscgen',
'm4',
+ 'openssh-client',
'texinfo',
'texlive-latex-base',
'texlive-latex-extra',
'texlive-fonts-recommended',
'texlive-fonts-extra']
-# Supported Python versions for maintained branches.
-# TODO: Remove '3.5.9' from defaults in master once script in release-2020 diverges.
-_python_versions = ['3.5.9', '3.6.10', '3.7.7', '3.8.2']
-
# Parse command line arguments
-parser = argparse.ArgumentParser(description='GROMACS CI image creation script', parents=[utility.parser])
+parser = argparse.ArgumentParser(description='GROMACS CI image creation script',
+ parents=[utility.parser])
parser.add_argument('--format', type=str, default='docker',
choices=['docker', 'singularity'],
help='Container specification format (default: docker)')
-parser.add_argument('--venvs', nargs='*', type=str, default=_python_versions,
- help='List of Python versions ("major.minor.patch") for which to install venvs. '
- 'Default: {}'.format(' '.join(_python_versions)))
def base_image_tag(args) -> str:
# If we use the package version of LLVM, we need to install extra packages for it.
if (args.llvm is not None) and (args.tsan is None):
return ['libomp-dev',
+ 'libomp5',
'clang-format-' + str(args.llvm),
'clang-tidy-' + str(args.llvm)]
else:
return []
+def get_opencl_packages(args) -> typing.Iterable[str]:
+ if (args.doxygen is None) and (args.oneapi is None):
+ return _opencl_extra_packages
+ else:
+ return []
def get_compiler(args, compiler_build_stage: hpccm.Stage = None) -> bb_base:
# Compiler
else:
compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
+ elif args.oneapi is not None:
+ if compiler_build_stage is not None:
+ compiler = compiler_build_stage.runtime(_from='oneapi')
+ # Prepare the toolchain (needed only for builds done within the Dockerfile, e.g.
+ # OpenMPI builds, which don't currently work for other reasons)
+ oneapi_toolchain = hpccm.toolchain(CC='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icc',
+ CXX='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icpc')
+ setattr(compiler, 'toolchain', oneapi_toolchain)
+
+ else:
+ raise RuntimeError('No oneAPI compiler build stage!')
+
elif args.gcc is not None:
compiler = hpccm.building_blocks.gnu(extra_repository=True,
version=args.gcc,
use_cuda = True
if hasattr(compiler, 'toolchain'):
+ if args.oneapi is not None:
+ raise RuntimeError('oneAPI building OpenMPI is not supported')
return hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
else:
raise RuntimeError('compiler is not an HPCCM compiler building block!')
elif args.mpi == 'impi':
+ # TODO Intel MPI from the oneAPI repo is not working reliably,
+ # reasons are unclear. When solved, add packagages called:
+ # 'intel-oneapi-mpi', 'intel-oneapi-mpi-devel'
+ # during the compiler stage.
# TODO also consider hpccm's intel_mpi package if that doesn't need
# a license to run.
raise RuntimeError('Intel MPI recipe not implemented yet.')
return None
-def get_opencl(args):
- # Add OpenCL environment if needed
- if (args.opencl is not None):
- if args.opencl == 'nvidia':
- if (args.cuda is None):
- raise RuntimeError('Need Nvidia environment for Nvidia OpenCL image')
-
- return hpccm.building_blocks.packages(ospackages=['nvidia-opencl-dev'])
-
- elif args.opencl == 'intel':
- return hpccm.building_blocks.packages(
- apt_ppas=['ppa:intel-opencl/intel-opencl'],
- ospackages=['opencl-headers', 'ocl-icd-libopencl1',
- 'ocl-icd-opencl-dev', 'intel-opencl-icd'])
-
- elif args.opencl == 'amd':
- # libelf1 is a necessary dependency for something in the ROCm stack,
- # which they should set up, but seem to have omitted.
- return hpccm.building_blocks.packages(
- apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
- apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main'],
- ospackages=['ocl-icd-libopencl1', 'ocl-icd-opencl-dev', 'opencl-headers', 'libelf1', 'rocm-opencl'])
- else:
- return None
-
-
def get_clfft(args):
if (args.clfft is not None):
return hpccm.building_blocks.generic_cmake(
'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
output_stages['compiler_build'] = tsan_stage
+def oneapi_runtime(_from='0'):
+ oneapi_runtime_stage = hpccm.Stage()
+ oneapi_runtime_stage += hpccm.primitives.copy(_from='oneapi-build',
+ files={"/opt/intel": "/opt/intel",
+ "/etc/bash.bashrc": "/etc/bash.bashrc"})
+ return oneapi_runtime_stage
+
+def add_oneapi_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
+ """Isolate the oneAPI preparation stage.
+
+ This stage is isolated so that its installed components are minimized in the
+ final image (chiefly /opt/intel) and its environment setup script can be
+ sourced. This also helps with rebuild time and final image size.
+
+ Note that the ICC compiler inside oneAPI on linux also needs
+ gcc to build other components and provide libstdc++.
+ """
+ if not isinstance(output_stages, collections.abc.MutableMapping):
+ raise RuntimeError('Need output_stages container.')
+ oneapi_stage = hpccm.Stage()
+ oneapi_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='oneapi-build')
+
+ version = str(input_args.oneapi)
+
+ # Add required components for the next stage (both for hpccm and Intel's setvars.sh script)
+ oneapi_stage += hpccm.building_blocks.packages(ospackages=['wget', 'gnupg2', 'ca-certificates', 'lsb-release'])
+ oneapi_stage += hpccm.building_blocks.packages(
+ apt_keys=['https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB'],
+ apt_repositories=['deb https://apt.repos.intel.com/oneapi all main'],
+ # Add minimal packages (not the whole HPC toolkit!)
+ ospackages=['intel-oneapi-dpcpp-cpp-compiler-pro-{}'.format(version),
+ 'intel-oneapi-openmp-{}'.format(version),
+ 'intel-oneapi-mkl-{}'.format(version),
+ 'intel-oneapi-mkl-devel-{}'.format(version)]
+ )
+ # Ensure that all bash shells on the final container will have access to oneAPI
+ oneapi_stage += hpccm.primitives.shell(
+ commands=['echo "source /opt/intel/oneapi/setvars.sh" >> /etc/bash.bashrc']
+ )
+ setattr(oneapi_stage, 'runtime', oneapi_runtime)
+
+ output_stages['compiler_build'] = oneapi_stage
+
def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
"""Get shell commands to set up the venv for the requested Python version."""
major = version.version[0]
- minor = version.version[1]
+ minor = version.version[1] # type: int
pyenv = '$HOME/.pyenv/bin/pyenv'
# WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
# TODO: Get requirements.txt from an input argument.
commands.append("""{path}/bin/python -m pip install --upgrade \
- 'cmake>=3.9.6' \
+ 'cmake>=3.13' \
'flake8>=3.7.7' \
- 'mpi4py>=2' \
+ 'mpi4py>=3.0.3' \
'networkx>=2.0' \
'numpy>=1' \
'pip>=10.1' \
'pytest>=3.9' \
- 'setuptools>=28.0.0' \
- 'scikit-build>=0.7'""".format(path=venv_path))
+ 'setuptools>=42' \
+ 'scikit-build>=0.10'""".format(path=venv_path))
+
+ # TODO: Remove 'importlib_resources' dependency when Python >=3.7 is required.
+ if minor == 6:
+ commands.append("""{path}/bin/python -m pip install --upgrade \
+ 'importlib_resources'""".format(path=venv_path))
return commands
output_stages['pyenv'] = pyenv_stage
+def add_documentation_dependencies(input_args,
+ output_stages: typing.MutableMapping[str, hpccm.Stage]):
+ """Add appropriate layers according to doxygen input arguments."""
+ if input_args.doxygen is None:
+ return
+ output_stages['main'] += hpccm.primitives.shell(
+ commands=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
+ output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1', 'gcovr'])
+ if input_args.doxygen == '1.8.5':
+ doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
+ output_stages['main'] += hpccm.building_blocks.generic_autotools(
+ repository='https://github.com/westes/flex.git',
+ commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
+ prefix='/tmp/install-of-flex',
+ configure_opts=['--disable-shared'],
+ preconfigure=['./autogen.sh'])
+ output_stages['main'] += hpccm.building_blocks.generic_autotools(
+ repository='https://github.com/doxygen/doxygen.git',
+ commit=doxygen_commit,
+ prefix='',
+ configure_opts=[
+ '--flex /tmp/install-of-flex/bin/flex',
+ '--static'])
+ else:
+ version = input_args.doxygen
+ archive_name = 'doxygen-{}.linux.bin.tar.gz'.format(version)
+ archive_url = 'https://sourceforge.net/projects/doxygen/files/rel-{}/{}'.format(
+ version,
+ archive_name
+ )
+ binary_path = 'doxygen-{}/bin/doxygen'.format(version)
+ commands = [
+ 'mkdir doxygen && cd doxygen',
+ 'wget {}'.format(archive_url),
+ 'tar xf {} {}'.format(archive_name, binary_path),
+ 'cp {} /usr/local/bin/'.format(binary_path),
+ 'cd .. && rm -rf doxygen'
+ ]
+ output_stages['main'] += hpccm.primitives.shell(commands=commands)
+
+
def build_stages(args) -> typing.Iterable[hpccm.Stage]:
"""Define and sequence the stages for the recipe corresponding to *args*."""
# installed.
if args.llvm is not None and args.tsan is not None:
add_tsan_compiler_build_stage(input_args=args, output_stages=stages)
+ if args.oneapi is not None:
+ add_oneapi_compiler_build_stage(input_args=args, output_stages=stages)
# Building blocks are chunks of container-builder instructions that can be
# copied to any build stage with the addition operator.
building_blocks = collections.OrderedDict()
+ building_blocks['base_packages'] = hpccm.building_blocks.packages(
+ ospackages=_common_packages)
# These are the most expensive and most reusable layers, so we put them first.
building_blocks['compiler'] = get_compiler(args, compiler_build_stage=stages.get('compiler_build'))
building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
+ for i, cmake in enumerate(args.cmake):
+ building_blocks['cmake' + str(i)] = hpccm.building_blocks.cmake(
+ eula=True,
+ prefix='/usr/local/cmake-{}'.format(cmake),
+ version=cmake)
# Install additional packages early in the build to optimize Docker build layer cache.
- os_packages = _common_packages + get_llvm_packages(args)
+ os_packages = list(get_llvm_packages(args)) + get_opencl_packages(args)
if args.doxygen is not None:
os_packages += _docs_extra_packages
- building_blocks['ospackages'] = hpccm.building_blocks.packages(ospackages=os_packages)
+ if args.oneapi is not None:
+ os_packages += ['lsb-release']
+ building_blocks['extra_packages'] = hpccm.building_blocks.packages(
+ ospackages=os_packages,
+ apt_ppas=['ppa:intel-opencl/intel-opencl'],
+ apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
+ apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
+ )
- building_blocks['cmake'] = hpccm.building_blocks.cmake(eula=True, version=args.cmake)
- building_blocks['opencl'] = get_opencl(args)
building_blocks['clfft'] = get_clfft(args)
# Add Python environments to MPI images, only, so we don't have to worry
packages=['pytest', 'networkx', 'numpy'])
# Add documentation requirements (doxygen and sphinx + misc).
- if (args.doxygen is not None):
- if (args.doxygen == '1.8.5'):
- doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
- else:
- doxygen_commit = 'a6d4f4df45febe588c38de37641513fd576b998f'
- stages['main'] += hpccm.building_blocks.generic_autotools(
- repository='https://github.com/westes/flex.git',
- commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
- prefix='/tmp/install-of-flex',
- configure_opts=['--disable-shared'],
- preconfigure=['./autogen.sh'])
- stages['main'] += hpccm.building_blocks.generic_autotools(
- repository='https://github.com/doxygen/doxygen.git',
- commit=doxygen_commit,
- prefix='',
- configure_opts=[
- '--flex /tmp/install-of-flex/bin/flex',
- '--static'],
- postinstall=[
- 'sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
- stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1'])
+ if args.doxygen is not None:
+ add_documentation_dependencies(args, stages)
if 'pyenv' in stages and stages['pyenv'] is not None:
stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/.pyenv/'],
# stages['main'] += hpccm.primitives.copy(_from='pyenv', src=['/root/.bashrc'],
# dest='/root/')
+ # Make sure that `python` resolves to something.
+ stages['main'] += hpccm.primitives.shell(commands=['test -x /usr/bin/python || '
+ 'update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && '
+ '/usr/bin/python --version'])
+
# Note that the list of stages should be sorted in dependency order.
for build_stage in stages.values():
if build_stage is not None:
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff