3 # This file is part of the GROMACS molecular simulation package.
5 # Copyright (c) 2020, by the GROMACS development team, led by
6 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
7 # and including many others, as listed in the AUTHORS file in the
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10 # GROMACS is free software; you can redistribute it and/or
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13 # of the License, or (at your option) any later version.
15 # GROMACS is distributed in the hope that it will be useful,
16 # but WITHOUT ANY WARRANTY; without even the implied warranty of
17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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21 # License along with GROMACS; if not, see
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37 Generates a set of docker images used for running GROMACS CI on Gitlab.
38 The images are prepared according to a selection of build configuration targets
39 that hope to cover a broad enough scope of different possible systems,
40 allowing us to check compiler types and versions, as well as libraries used
41 for accelerators and parallel communication systems. Each combinations is
42 described as an entry in the build_configs dictionary, with the script
43 analysing the logic and adding build stages as needed.
45 Based on the example script provided by the NVidia HPCCM repository.
48 * Paul Bauer <paul.bauer.q@gmail.com>
49 * Eric Irrgang <ericirrgang@gmail.com>
50 * Joe Jordan <e.jjordan12@gmail.com>
51 * Mark Abraham <mark.j.abraham@gmail.com>
55 $ python3 scripted_gmx_docker_builds.py --help
56 $ python3 scripted_gmx_docker_builds.py --format docker > Dockerfile && docker build .
57 $ python3 scripted_gmx_docker_builds.py | docker build -
64 from distutils.version import StrictVersion
68 from hpccm.building_blocks.base import bb_base
74 'This module assumes availability of supporting modules in the same directory. Add the directory to '
75 'PYTHONPATH or invoke Python from within the module directory so module location can be resolved.')
77 # Basic packages for all final images.
78 _common_packages = ['build-essential',
95 # Extra packages needed to build Python installations from source.
96 _python_extra_packages = ['build-essential',
115 # Extra packages needed for images for building documentation.
116 _docs_extra_packages = ['autoconf',
131 'texlive-latex-base',
132 'texlive-latex-extra',
133 'texlive-fonts-recommended',
134 'texlive-fonts-extra']
136 # Supported Python versions for maintained branches.
137 _python_versions = ['3.6.10', '3.7.7', '3.8.2']
139 # Parse command line arguments
140 parser = argparse.ArgumentParser(description='GROMACS CI image creation script', parents=[utility.parser])
142 parser.add_argument('--format', type=str, default='docker',
143 choices=['docker', 'singularity'],
144 help='Container specification format (default: docker)')
145 parser.add_argument('--venvs', nargs='*', type=str, default=_python_versions,
146 help='List of Python versions ("major.minor.patch") for which to install venvs. '
147 'Default: {}'.format(' '.join(_python_versions)))
150 def base_image_tag(args) -> str:
151 # Check if we use CUDA images or plain linux images
152 if args.cuda is not None:
153 cuda_version_tag = 'nvidia/cuda:' + args.cuda + '-devel'
154 if args.centos is not None:
155 cuda_version_tag += '-centos' + args.centos
156 elif args.ubuntu is not None:
157 cuda_version_tag += '-ubuntu' + args.ubuntu
159 raise RuntimeError('Logic error: no Linux distribution selected.')
161 base_image_tag = cuda_version_tag
163 if args.centos is not None:
164 base_image_tag = 'centos:centos' + args.centos
165 elif args.ubuntu is not None:
166 base_image_tag = 'ubuntu:' + args.ubuntu
168 raise RuntimeError('Logic error: no Linux distribution selected.')
169 return base_image_tag
172 def get_llvm_packages(args) -> typing.Iterable[str]:
173 # If we use the package version of LLVM, we need to install extra packages for it.
174 if (args.llvm is not None) and (args.tsan is None):
175 return ['libomp-dev',
176 'clang-format-' + str(args.llvm),
177 'clang-tidy-' + str(args.llvm)]
182 def get_compiler(args, compiler_build_stage: hpccm.Stage = None) -> bb_base:
184 if args.icc is not None:
185 raise RuntimeError('Intel compiler toolchain recipe not implemented yet')
187 if args.llvm is not None:
188 # Build our own version instead to get TSAN + OMP
189 if args.tsan is not None:
190 if compiler_build_stage is not None:
191 compiler = compiler_build_stage.runtime(_from='tsan')
193 raise RuntimeError('No TSAN compiler build stage!')
194 # Build the default compiler if we don't need special support
196 compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
198 elif args.oneapi is not None:
199 if compiler_build_stage is not None:
200 compiler = compiler_build_stage.runtime(_from='oneapi')
201 # Prepare the toolchain (needed only for builds done within the Dockerfile, e.g.
202 # OpenMPI builds, which don't currently work for other reasons)
203 oneapi_toolchain = hpccm.toolchain(CC='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icc',
204 CXX='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icpc')
205 setattr(compiler, 'toolchain', oneapi_toolchain)
208 raise RuntimeError('No oneAPI compiler build stage!')
210 elif args.gcc is not None:
211 compiler = hpccm.building_blocks.gnu(extra_repository=True,
215 raise RuntimeError('Logic error: no compiler toolchain selected.')
219 def get_mpi(args, compiler):
220 # If needed, add MPI to the image
221 if args.mpi is not None:
222 if args.mpi == 'openmpi':
224 if args.cuda is not None:
227 if hasattr(compiler, 'toolchain'):
228 if args.oneapi is not None:
229 raise RuntimeError('oneAPI building OpenMPI is not supported')
230 return hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
232 raise RuntimeError('compiler is not an HPCCM compiler building block!')
234 elif args.mpi == 'impi':
235 # TODO Intel MPI from the oneAPI repo is not working reliably,
236 # reasons are unclear. When solved, add packagages called:
237 # 'intel-oneapi-mpi', 'intel-oneapi-mpi-devel'
238 # during the compiler stage.
239 # TODO also consider hpccm's intel_mpi package if that doesn't need
241 raise RuntimeError('Intel MPI recipe not implemented yet.')
243 raise RuntimeError('Requested unknown MPI implementation.')
248 def get_opencl(args):
249 # Add OpenCL environment if needed
250 if (args.opencl is not None):
251 if args.opencl == 'nvidia':
252 if (args.cuda is None):
253 raise RuntimeError('Need Nvidia environment for Nvidia OpenCL image')
255 return hpccm.building_blocks.packages(ospackages=['nvidia-opencl-dev'])
257 elif args.opencl == 'intel':
258 # Note, when using oneapi, there is bundled OpenCL support, so this
259 # installation is not needed.
260 return hpccm.building_blocks.packages(
261 apt_ppas=['ppa:intel-opencl/intel-opencl'],
262 ospackages=['opencl-headers', 'ocl-icd-libopencl1',
263 'ocl-icd-opencl-dev', 'intel-opencl-icd'])
265 elif args.opencl == 'amd':
266 # libelf1 is a necessary dependency for something in the ROCm stack,
267 # which they should set up, but seem to have omitted.
268 return hpccm.building_blocks.packages(
269 apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
270 apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main'],
271 ospackages=['ocl-icd-libopencl1', 'ocl-icd-opencl-dev', 'opencl-headers', 'libelf1', 'rocm-opencl', 'rocm-dev', 'clinfo'])
277 if (args.clfft is not None):
278 return hpccm.building_blocks.generic_cmake(
279 repository='https://github.com/clMathLibraries/clFFT.git',
280 prefix='/usr/local', recursive=True, branch=args.clfft, directory='clFFT/src')
285 def add_tsan_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
286 """Isolate the expensive TSAN preparation stage.
288 This is a very expensive stage, but has few and disjoint dependencies, and
289 its output is easily compartmentalized (/usr/local) so we can isolate this
290 build stage to maximize build cache hits and reduce rebuild time, bookkeeping,
291 and final image size.
293 if not isinstance(output_stages, collections.abc.MutableMapping):
294 raise RuntimeError('Need output_stages container.')
295 tsan_stage = hpccm.Stage()
296 tsan_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='tsan')
298 tsan_stage += hpccm.building_blocks.packages(ospackages=['git', 'ca-certificates', 'build-essential', 'cmake'])
299 # CMake will get duplicated later, but this is an expensive image, and it isn't worth optimizing
300 # out that duplication...
301 tsan_stage += hpccm.building_blocks.python(python3=True, python2=False, devel=False)
303 compiler_branch = 'release_' + str(input_args.llvm) + '0'
304 tsan_stage += hpccm.building_blocks.generic_cmake(
305 repository='https://git.llvm.org/git/llvm.git',
306 prefix='/usr/local', recursive=True, branch=compiler_branch,
307 cmake_opts=['-D CMAKE_BUILD_TYPE=Release', '-D LLVM_ENABLE_PROJECTS="clang;openmp;clang-tools-extra"',
308 '-D LIBOMP_TSAN_SUPPORT=on'],
309 preconfigure=['export branch=' + compiler_branch,
310 '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/libcxx.git)',
311 '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/libcxxabi.git)',
312 '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/compiler-rt.git)',
313 '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/openmp.git)',
314 '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/clang.git)',
315 '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/clang-tools-extra.git)'],
316 postinstall=['ln -s /usr/local/bin/clang++ /usr/local/bin/clang++-' + str(input_args.llvm),
317 'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-' + str(input_args.llvm),
318 'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-' + str(input_args.llvm),
319 'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
320 output_stages['compiler_build'] = tsan_stage
322 def oneapi_runtime(_from='0'):
323 oneapi_runtime_stage = hpccm.Stage()
324 oneapi_runtime_stage += hpccm.primitives.copy(_from='oneapi-build',
325 files={"/opt/intel": "/opt/intel",
326 "/etc/bash.bashrc": "/etc/bash.bashrc"})
327 return oneapi_runtime_stage
329 def add_oneapi_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
330 """Isolate the oneAPI preparation stage.
332 This stage is isolated so that its installed components are minimized in the
333 final image (chiefly /opt/intel) and its environment setup script can be
334 sourced. This also helps with rebuild time and final image size.
336 Note that the ICC compiler inside oneAPI on linux also needs
337 gcc to build other components and provide libstdc++.
339 if not isinstance(output_stages, collections.abc.MutableMapping):
340 raise RuntimeError('Need output_stages container.')
341 oneapi_stage = hpccm.Stage()
342 oneapi_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='oneapi-build')
344 # Add required components for the next stage (both for hpccm and Intel's setvars.sh script)
345 oneapi_stage += hpccm.building_blocks.packages(ospackages=['wget', 'gnupg2', 'ca-certificates', 'lsb-release'])
346 oneapi_stage += hpccm.building_blocks.packages(
347 apt_keys=['https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB'],
348 apt_repositories=['deb https://apt.repos.intel.com/oneapi all main'],
349 # Add minimal packages (not the whole HPC toolkit!)
350 ospackages=['intel-oneapi-dpcpp-compiler', 'intel-oneapi-icc', 'intel-oneapi-mkl', 'intel-oneapi-mkl-devel']
352 # Ensure that all bash shells on the final container will have access to oneAPI
353 oneapi_stage += hpccm.primitives.shell(
354 commands=['echo "source /opt/intel/oneapi/setvars.sh" >> /etc/bash.bashrc']
356 setattr(oneapi_stage, 'runtime', oneapi_runtime)
358 output_stages['compiler_build'] = oneapi_stage
360 def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
361 """Get shell commands to set up the venv for the requested Python version."""
362 major = version.version[0]
363 minor = version.version[1] # type: int
365 pyenv = '$HOME/.pyenv/bin/pyenv'
367 py_ver = '{}.{}'.format(major, minor)
368 venv_path = '$HOME/venv/py{}'.format(py_ver)
369 commands = ['$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {path}'.format(
375 commands.append('{path}/bin/python -m pip install --upgrade pip setuptools'.format(
378 # Install dependencies for building and testing gmxapi Python package.
379 # WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
380 # TODO: Get requirements.txt from an input argument.
381 commands.append("""{path}/bin/python -m pip install --upgrade \
390 'scikit-build>=0.10'""".format(path=venv_path))
392 # TODO: Remove 'importlib_resources' dependency when Python >=3.7 is required.
394 commands.append("""{path}/bin/python -m pip install --upgrade \
395 'importlib_resources'""".format(path=venv_path))
400 def add_python_stages(building_blocks: typing.Mapping[str, bb_base],
402 output_stages: typing.MutableMapping[str, hpccm.Stage]):
403 """Add the stage(s) necessary for the requested venvs.
405 One intermediate build stage is created for each venv (see --venv option).
407 Each stage partially populates Python installations and venvs in the home
408 directory. The home directory is collected by the 'pyenv' stage for use by
409 the main build stage.
411 if len(input_args.venvs) < 1:
412 raise RuntimeError('No venvs to build...')
413 if output_stages is None or not isinstance(output_stages, collections.abc.Mapping):
414 raise RuntimeError('Need a container for output stages.')
416 # Main Python stage that collects the environments from individual stages.
417 # We collect the stages individually, rather than chaining them, because the
418 # copy is a bit slow and wastes local Docker image space for each filesystem
420 pyenv_stage = hpccm.Stage()
421 pyenv_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='pyenv')
422 pyenv_stage += building_blocks['compiler']
423 pyenv_stage += building_blocks['mpi']
424 pyenv_stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
426 for version in [StrictVersion(py_ver) for py_ver in sorted(input_args.venvs)]:
427 stage_name = 'py' + str(version)
428 stage = hpccm.Stage()
429 stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as=stage_name)
430 stage += building_blocks['compiler']
431 stage += building_blocks['mpi']
432 stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
434 # TODO: Use a non-root user for testing and Python virtual environments.
435 stage += hpccm.primitives.shell(commands=[
436 'curl https://pyenv.run | bash',
437 """echo 'export PYENV_ROOT="$HOME/.pyenv"' >> $HOME/.bashrc""",
438 """echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> $HOME/.bashrc""",
439 """echo 'eval "$(pyenv init -)"' >> $HOME/.bashrc""",
440 """echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bashrc"""])
441 pyenv = '$HOME/.pyenv/bin/pyenv'
442 commands = ['PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}'.format(
444 version=str(version))]
445 stage += hpccm.primitives.shell(commands=commands)
447 commands = prepare_venv(version)
448 stage += hpccm.primitives.shell(commands=commands)
450 # TODO: Update user home directory.
451 pyenv_stage += hpccm.primitives.copy(_from=stage_name, _mkdir=True, src=['/root/'],
454 # Add the intermediate build stage to the sequence
455 output_stages[stage_name] = stage
457 # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
458 # # `version` should be a system installation or pyenv environment (or pyenv-virtualenv)
459 # # with the dependencies for all of the Python aspects of CMake-driven builds.
460 # commands = '{pyenv} global {version}'.format(
463 # pyenv_stage += hpccm.primitives.shell(commands=commands)
465 # Add the aggregating build stage to the sequence. This allows the main stage to copy
466 # the files in a single stage, potentially reducing the overall output image size.
467 output_stages['pyenv'] = pyenv_stage
470 def add_documentation_dependencies(input_args,
471 output_stages: typing.MutableMapping[str, hpccm.Stage]):
472 """Add appropriate layers according to doxygen input arguments."""
473 if input_args.doxygen is None:
475 output_stages['main'] += hpccm.primitives.shell(
476 commands=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
477 output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1'])
478 if input_args.doxygen == '1.8.5':
479 doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
480 output_stages['main'] += hpccm.building_blocks.generic_autotools(
481 repository='https://github.com/westes/flex.git',
482 commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
483 prefix='/tmp/install-of-flex',
484 configure_opts=['--disable-shared'],
485 preconfigure=['./autogen.sh'])
486 output_stages['main'] += hpccm.building_blocks.generic_autotools(
487 repository='https://github.com/doxygen/doxygen.git',
488 commit=doxygen_commit,
491 '--flex /tmp/install-of-flex/bin/flex',
494 version = input_args.doxygen
495 archive_name = 'doxygen-{}.linux.bin.tar.gz'.format(version)
496 archive_url = 'https://sourceforge.net/projects/doxygen/files/rel-{}/{}'.format(
500 binary_path = 'doxygen-{}/bin/doxygen'.format(version)
502 'mkdir doxygen && cd doxygen',
503 'wget {}'.format(archive_url),
504 'tar xf {} {}'.format(archive_name, binary_path),
505 'cp {} /usr/local/bin/'.format(binary_path),
506 'cd .. && rm -rf doxygen'
508 output_stages['main'] += hpccm.primitives.shell(commands=commands)
511 def build_stages(args) -> typing.Iterable[hpccm.Stage]:
512 """Define and sequence the stages for the recipe corresponding to *args*."""
514 # A Dockerfile or Singularity recipe can have multiple build stages.
515 # The main build stage can copy files from previous stages, though only
516 # the last stage is included in the tagged output image. This means that
517 # large or expensive sets of build instructions can be isolated in
518 # local/temporary images, but all of the stages need to be output by this
519 # script, and need to occur in the correct order, so we create a sequence
520 # object early in this function.
521 stages = collections.OrderedDict()
523 # If we need TSAN or oneAPI support the early build is more complex,
524 # so that our compiler images don't have all the cruft needed to get those things
526 if args.llvm is not None and args.tsan is not None:
527 add_tsan_compiler_build_stage(input_args=args, output_stages=stages)
528 if args.oneapi is not None:
529 add_oneapi_compiler_build_stage(input_args=args, output_stages=stages)
531 # Building blocks are chunks of container-builder instructions that can be
532 # copied to any build stage with the addition operator.
533 building_blocks = collections.OrderedDict()
535 # These are the most expensive and most reusable layers, so we put them first.
536 building_blocks['compiler'] = get_compiler(args, compiler_build_stage=stages.get('compiler_build'))
537 building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
539 # Install additional packages early in the build to optimize Docker build layer cache.
540 os_packages = _common_packages + get_llvm_packages(args)
541 if args.doxygen is not None:
542 os_packages += _docs_extra_packages
543 if args.oneapi is not None:
544 os_packages += ['lsb-release']
545 building_blocks['ospackages'] = hpccm.building_blocks.packages(ospackages=os_packages)
547 building_blocks['cmake'] = hpccm.building_blocks.cmake(eula=True, version=args.cmake)
548 building_blocks['opencl'] = get_opencl(args)
549 building_blocks['clfft'] = get_clfft(args)
551 # Add Python environments to MPI images, only, so we don't have to worry
552 # about whether to install mpi4py.
553 if args.mpi is not None and len(args.venvs) > 0:
554 add_python_stages(building_blocks=building_blocks, input_args=args, output_stages=stages)
556 # Create the stage from which the targeted image will be tagged.
557 stages['main'] = hpccm.Stage()
559 stages['main'] += hpccm.primitives.baseimage(image=base_image_tag(args))
560 for bb in building_blocks.values():
564 # We always add Python3 and Pip
565 stages['main'] += hpccm.building_blocks.python(python3=True, python2=False, devel=True)
566 stages['main'] += hpccm.building_blocks.pip(upgrade=True, pip='pip3',
567 packages=['pytest', 'networkx', 'numpy'])
569 # Add documentation requirements (doxygen and sphinx + misc).
570 if args.doxygen is not None:
571 add_documentation_dependencies(args, stages)
573 if 'pyenv' in stages and stages['pyenv'] is not None:
574 stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/.pyenv/'],
576 stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/venv/'],
578 # TODO: Update user home directory.
579 # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
580 # stages['main'] += hpccm.primitives.copy(_from='pyenv', src=['/root/.bashrc'],
583 # Make sure that `python` resolves to something.
584 stages['main'] += hpccm.primitives.shell(commands=['test -x /usr/bin/python || '
585 'update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && '
586 '/usr/bin/python --version'])
588 # Note that the list of stages should be sorted in dependency order.
589 for build_stage in stages.values():
590 if build_stage is not None:
594 if __name__ == '__main__':
595 args = parser.parse_args()
597 # Set container specification output format
598 hpccm.config.set_container_format(args.format)
600 container_recipe = build_stages(args)
602 # Output container specification
603 for stage in container_recipe: