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21 # License along with GROMACS; if not, see
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34 # the research papers on the package. Check out http://www.gromacs.org.
36 """Building block based Dockerfile generation for CI testing images.
38 Generates a set of docker images used for running GROMACS CI on Gitlab.
39 The images are prepared according to a selection of build configuration targets
40 that hope to cover a broad enough scope of different possible systems,
41 allowing us to check compiler types and versions, as well as libraries used
42 for accelerators and parallel communication systems. Each combinations is
43 described as an entry in the build_configs dictionary, with the script
44 analysing the logic and adding build stages as needed.
46 Based on the example script provided by the NVidia HPCCM repository.
49 `NVidia HPC Container Maker <https://github.com/NVIDIA/hpc-container-maker>`__
52 * Paul Bauer <paul.bauer.q@gmail.com>
53 * Eric Irrgang <ericirrgang@gmail.com>
54 * Joe Jordan <e.jjordan12@gmail.com>
55 * Mark Abraham <mark.j.abraham@gmail.com>
59 $ python3 scripted_gmx_docker_builds.py --help
60 $ python3 scripted_gmx_docker_builds.py --format docker > Dockerfile && docker build .
61 $ python3 scripted_gmx_docker_builds.py | docker build -
71 from distutils.version import StrictVersion
75 from hpccm.building_blocks.base import bb_base
81 'This module assumes availability of supporting modules in the same directory. Add the directory to '
82 'PYTHONPATH or invoke Python from within the module directory so module location can be resolved.')
84 # Basic packages for all final images.
85 _common_packages = ['build-essential',
103 _opencl_extra_packages = [
105 # The following require apt_ppas=['ppa:intel-opencl/intel-opencl']
107 'ocl-icd-libopencl1',
108 'ocl-icd-opencl-dev',
110 # The following require
111 # apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
112 # apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
119 # Extra packages needed to build Python installations from source.
120 _python_extra_packages = ['build-essential',
139 # Extra packages needed for images for building documentation.
140 _docs_extra_packages = ['autoconf',
156 'texlive-latex-base',
157 'texlive-latex-extra',
158 'texlive-fonts-recommended',
159 'texlive-fonts-extra']
161 # Parse command line arguments
162 parser = argparse.ArgumentParser(description='GROMACS CI image creation script',
163 parents=[utility.parser])
165 parser.add_argument('--format', type=str, default='docker',
166 choices=['docker', 'singularity'],
167 help='Container specification format (default: docker)')
170 def base_image_tag(args) -> str:
171 # Check if we use CUDA images or plain linux images
172 if args.cuda is not None:
173 cuda_version_tag = 'nvidia/cuda:' + args.cuda + '-devel'
174 if args.centos is not None:
175 cuda_version_tag += '-centos' + args.centos
176 elif args.ubuntu is not None:
177 cuda_version_tag += '-ubuntu' + args.ubuntu
179 raise RuntimeError('Logic error: no Linux distribution selected.')
181 base_image_tag = cuda_version_tag
183 if args.centos is not None:
184 base_image_tag = 'centos:centos' + args.centos
185 elif args.ubuntu is not None:
186 base_image_tag = 'ubuntu:' + args.ubuntu
188 raise RuntimeError('Logic error: no Linux distribution selected.')
189 return base_image_tag
192 def get_llvm_packages(args) -> typing.Iterable[str]:
193 # If we use the package version of LLVM, we need to install extra packages for it.
194 if (args.llvm is not None) and (args.tsan is None):
195 return ['libomp-dev',
197 'clang-format-' + str(args.llvm),
198 'clang-tidy-' + str(args.llvm)]
202 def get_opencl_packages(args) -> typing.Iterable[str]:
203 if (args.doxygen is None) and (args.oneapi is None):
204 return _opencl_extra_packages
208 def get_compiler(args, compiler_build_stage: hpccm.Stage = None) -> bb_base:
210 if args.llvm is not None:
211 # Build our own version instead to get TSAN + OMP
212 if args.tsan is not None:
213 if compiler_build_stage is not None:
214 compiler = compiler_build_stage.runtime(_from='tsan')
216 raise RuntimeError('No TSAN compiler build stage!')
217 # Build the default compiler if we don't need special support
219 compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
221 elif args.oneapi is not None:
222 if compiler_build_stage is not None:
223 compiler = compiler_build_stage.runtime(_from='oneapi')
224 # Prepare the toolchain (needed only for builds done within the Dockerfile, e.g.
225 # OpenMPI builds, which don't currently work for other reasons)
226 oneapi_toolchain = hpccm.toolchain(CC='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icx',
227 CXX='/opt/intel/oneapi/compiler/latest/linux/bin/intel64/icpx')
228 setattr(compiler, 'toolchain', oneapi_toolchain)
231 raise RuntimeError('No oneAPI compiler build stage!')
233 elif args.gcc is not None:
234 compiler = hpccm.building_blocks.gnu(extra_repository=True,
238 raise RuntimeError('Logic error: no compiler toolchain selected.')
242 def get_mpi(args, compiler):
243 # If needed, add MPI to the image
244 if args.mpi is not None:
245 if args.mpi == 'openmpi':
247 if args.cuda is not None:
250 if hasattr(compiler, 'toolchain'):
251 if args.oneapi is not None:
252 raise RuntimeError('oneAPI building OpenMPI is not supported')
253 return hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
255 raise RuntimeError('compiler is not an HPCCM compiler building block!')
257 elif args.mpi == 'impi':
258 # TODO Intel MPI from the oneAPI repo is not working reliably,
259 # reasons are unclear. When solved, add packagages called:
260 # 'intel-oneapi-mpi', 'intel-oneapi-mpi-devel'
261 # during the compiler stage.
262 # TODO also consider hpccm's intel_mpi package if that doesn't need
264 raise RuntimeError('Intel MPI recipe not implemented yet.')
266 raise RuntimeError('Requested unknown MPI implementation.')
272 if (args.clfft is not None):
273 return hpccm.building_blocks.generic_cmake(
274 repository='https://github.com/clMathLibraries/clFFT.git',
275 prefix='/usr/local', recursive=True, branch=args.clfft, directory='clFFT/src')
280 def add_tsan_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
281 """Isolate the expensive TSAN preparation stage.
283 This is a very expensive stage, but has few and disjoint dependencies, and
284 its output is easily compartmentalized (/usr/local) so we can isolate this
285 build stage to maximize build cache hits and reduce rebuild time, bookkeeping,
286 and final image size.
288 if not isinstance(output_stages, collections.abc.MutableMapping):
289 raise RuntimeError('Need output_stages container.')
290 tsan_stage = hpccm.Stage()
291 tsan_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='tsan')
293 tsan_stage += hpccm.building_blocks.packages(ospackages=['git', 'ca-certificates', 'build-essential', 'cmake'])
294 # CMake will get duplicated later, but this is an expensive image, and it isn't worth optimizing
295 # out that duplication...
296 tsan_stage += hpccm.building_blocks.python(python3=True, python2=False, devel=False)
298 compiler_branch = 'release/' + str(input_args.llvm) + '.x'
299 tsan_stage += hpccm.building_blocks.generic_cmake(
300 repository='https://github.com/llvm/llvm-project.git',
301 directory='/var/tmp/llvm-project/llvm/',
302 prefix='/usr/local', recursive=True, branch=compiler_branch,
303 cmake_opts=['-D CMAKE_BUILD_TYPE=Release', '-D LLVM_ENABLE_PROJECTS="clang;openmp;clang-tools-extra;compiler-rt;lld"',
304 '-D LIBOMP_TSAN_SUPPORT=on'],
305 postinstall=['ln -s /usr/local/bin/clang++ /usr/local/bin/clang++-' + str(input_args.llvm),
306 'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-' + str(input_args.llvm),
307 'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-' + str(input_args.llvm),
308 'ln -s /usr/local/share/clang/run-clang-tidy.py /usr/local/bin/run-clang-tidy-' + str(input_args.llvm) + '.py',
309 'ln -s /usr/local/bin/run-clang-tidy-' + str(input_args.llvm) + '.py /usr/local/bin/run-clang-tidy-' + str(input_args.llvm),
310 'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
311 output_stages['compiler_build'] = tsan_stage
313 def oneapi_runtime(_from='0'):
314 oneapi_runtime_stage = hpccm.Stage()
315 oneapi_runtime_stage += hpccm.primitives.copy(_from='oneapi-build',
316 files={"/opt/intel": "/opt/intel",
317 "/etc/bash.bashrc": "/etc/bash.bashrc"})
318 return oneapi_runtime_stage
320 def add_oneapi_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
321 """Isolate the oneAPI preparation stage.
323 This stage is isolated so that its installed components are minimized in the
324 final image (chiefly /opt/intel) and its environment setup script can be
325 sourced. This also helps with rebuild time and final image size.
327 if not isinstance(output_stages, collections.abc.MutableMapping):
328 raise RuntimeError('Need output_stages container.')
329 oneapi_stage = hpccm.Stage()
330 oneapi_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='oneapi-build')
332 version = str(input_args.oneapi)
334 # Add required components for the next stage (both for hpccm and Intel's setvars.sh script)
335 oneapi_stage += hpccm.building_blocks.packages(ospackages=['wget', 'gnupg2', 'ca-certificates', 'lsb-release'])
336 oneapi_stage += hpccm.building_blocks.packages(
337 apt_keys=['https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB'],
338 apt_repositories=['deb https://apt.repos.intel.com/oneapi all main'],
339 # Add minimal packages (not the whole HPC toolkit!)
340 ospackages=['intel-oneapi-dpcpp-{}'.format(version),
341 'intel-oneapi-openmp-{}'.format(version),
342 'intel-oneapi-mkl-{}'.format(version),
343 'intel-oneapi-mkl-devel-{}'.format(version)]
345 # Ensure that all bash shells on the final container will have access to oneAPI
346 oneapi_stage += hpccm.primitives.shell(
347 commands=['echo "source /opt/intel/oneapi/setvars.sh" >> /etc/bash.bashrc']
349 setattr(oneapi_stage, 'runtime', oneapi_runtime)
351 output_stages['compiler_build'] = oneapi_stage
353 def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
354 """Get shell commands to set up the venv for the requested Python version."""
355 major = version.version[0]
356 minor = version.version[1] # type: int
358 pyenv = '$HOME/.pyenv/bin/pyenv'
360 py_ver = '{}.{}'.format(major, minor)
361 venv_path = '$HOME/venv/py{}'.format(py_ver)
362 commands = ['$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {path}'.format(
368 commands.append('{path}/bin/python -m pip install --upgrade pip setuptools'.format(
371 # Install dependencies for building and testing gmxapi Python package.
372 # WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
373 # TODO: Get requirements.txt from an input argument.
374 commands.append("""{path}/bin/python -m pip install --upgrade \
383 'scikit-build>=0.10'""".format(path=venv_path))
385 # TODO: Remove 'importlib_resources' dependency when Python >=3.7 is required.
387 commands.append("""{path}/bin/python -m pip install --upgrade \
388 'importlib_resources'""".format(path=venv_path))
393 def add_python_stages(building_blocks: typing.Mapping[str, bb_base],
395 output_stages: typing.MutableMapping[str, hpccm.Stage]):
396 """Add the stage(s) necessary for the requested venvs.
398 One intermediate build stage is created for each venv (see --venv option).
400 Each stage partially populates Python installations and venvs in the home
401 directory. The home directory is collected by the 'pyenv' stage for use by
402 the main build stage.
404 if len(input_args.venvs) < 1:
405 raise RuntimeError('No venvs to build...')
406 if output_stages is None or not isinstance(output_stages, collections.abc.Mapping):
407 raise RuntimeError('Need a container for output stages.')
409 # Main Python stage that collects the environments from individual stages.
410 # We collect the stages individually, rather than chaining them, because the
411 # copy is a bit slow and wastes local Docker image space for each filesystem
413 pyenv_stage = hpccm.Stage()
414 pyenv_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='pyenv')
415 pyenv_stage += building_blocks['compiler']
416 pyenv_stage += building_blocks['mpi']
417 pyenv_stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
419 for version in [StrictVersion(py_ver) for py_ver in sorted(input_args.venvs)]:
420 stage_name = 'py' + str(version)
421 stage = hpccm.Stage()
422 stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as=stage_name)
423 stage += building_blocks['compiler']
424 stage += building_blocks['mpi']
425 stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
427 # TODO: Use a non-root user for testing and Python virtual environments.
428 stage += hpccm.primitives.shell(commands=[
429 'curl https://pyenv.run | bash',
430 """echo 'export PYENV_ROOT="$HOME/.pyenv"' >> $HOME/.bashrc""",
431 """echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> $HOME/.bashrc""",
432 """echo 'eval "$(pyenv init -)"' >> $HOME/.bashrc""",
433 """echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bashrc"""])
434 pyenv = '$HOME/.pyenv/bin/pyenv'
435 commands = ['PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}'.format(
437 version=str(version))]
438 stage += hpccm.primitives.shell(commands=commands)
440 commands = prepare_venv(version)
441 stage += hpccm.primitives.shell(commands=commands)
443 # TODO: Update user home directory.
444 pyenv_stage += hpccm.primitives.copy(_from=stage_name, _mkdir=True, src=['/root/'],
447 # Add the intermediate build stage to the sequence
448 output_stages[stage_name] = stage
450 # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
451 # # `version` should be a system installation or pyenv environment (or pyenv-virtualenv)
452 # # with the dependencies for all of the Python aspects of CMake-driven builds.
453 # commands = '{pyenv} global {version}'.format(
456 # pyenv_stage += hpccm.primitives.shell(commands=commands)
458 # Add the aggregating build stage to the sequence. This allows the main stage to copy
459 # the files in a single stage, potentially reducing the overall output image size.
460 output_stages['pyenv'] = pyenv_stage
463 def add_documentation_dependencies(input_args,
464 output_stages: typing.MutableMapping[str, hpccm.Stage]):
465 """Add appropriate layers according to doxygen input arguments."""
466 if input_args.doxygen is None:
468 output_stages['main'] += hpccm.primitives.shell(
469 commands=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
470 output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1', 'gcovr'])
471 if input_args.doxygen == '1.8.5':
472 doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
473 output_stages['main'] += hpccm.building_blocks.generic_autotools(
474 repository='https://github.com/westes/flex.git',
475 commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
476 prefix='/tmp/install-of-flex',
477 configure_opts=['--disable-shared'],
478 preconfigure=['./autogen.sh'])
479 output_stages['main'] += hpccm.building_blocks.generic_autotools(
480 repository='https://github.com/doxygen/doxygen.git',
481 commit=doxygen_commit,
484 '--flex /tmp/install-of-flex/bin/flex',
487 version = input_args.doxygen
488 archive_name = 'doxygen-{}.linux.bin.tar.gz'.format(version)
489 archive_url = 'https://sourceforge.net/projects/doxygen/files/rel-{}/{}'.format(
493 binary_path = 'doxygen-{}/bin/doxygen'.format(version)
495 'mkdir doxygen && cd doxygen',
496 'wget {}'.format(archive_url),
497 'tar xf {} {}'.format(archive_name, binary_path),
498 'cp {} /usr/local/bin/'.format(binary_path),
499 'cd .. && rm -rf doxygen'
501 output_stages['main'] += hpccm.primitives.shell(commands=commands)
504 def build_stages(args) -> typing.Iterable[hpccm.Stage]:
505 """Define and sequence the stages for the recipe corresponding to *args*."""
507 # A Dockerfile or Singularity recipe can have multiple build stages.
508 # The main build stage can copy files from previous stages, though only
509 # the last stage is included in the tagged output image. This means that
510 # large or expensive sets of build instructions can be isolated in
511 # local/temporary images, but all of the stages need to be output by this
512 # script, and need to occur in the correct order, so we create a sequence
513 # object early in this function.
514 stages = collections.OrderedDict()
516 # If we need TSAN or oneAPI support the early build is more complex,
517 # so that our compiler images don't have all the cruft needed to get those things
519 if args.llvm is not None and args.tsan is not None:
520 add_tsan_compiler_build_stage(input_args=args, output_stages=stages)
521 if args.oneapi is not None:
522 add_oneapi_compiler_build_stage(input_args=args, output_stages=stages)
524 # Building blocks are chunks of container-builder instructions that can be
525 # copied to any build stage with the addition operator.
526 building_blocks = collections.OrderedDict()
527 building_blocks['base_packages'] = hpccm.building_blocks.packages(
528 ospackages=_common_packages)
530 # These are the most expensive and most reusable layers, so we put them first.
531 building_blocks['compiler'] = get_compiler(args, compiler_build_stage=stages.get('compiler_build'))
532 building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
533 for i, cmake in enumerate(args.cmake):
534 building_blocks['cmake' + str(i)] = hpccm.building_blocks.cmake(
536 prefix='/usr/local/cmake-{}'.format(cmake),
539 # Install additional packages early in the build to optimize Docker build layer cache.
540 os_packages = list(get_llvm_packages(args)) + get_opencl_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['extra_packages'] = hpccm.building_blocks.packages(
546 ospackages=os_packages,
547 apt_ppas=['ppa:intel-opencl/intel-opencl'],
548 apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
549 apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main']
552 building_blocks['clfft'] = get_clfft(args)
554 # Add Python environments to MPI images, only, so we don't have to worry
555 # about whether to install mpi4py.
556 if args.mpi is not None and len(args.venvs) > 0:
557 add_python_stages(building_blocks=building_blocks, input_args=args, output_stages=stages)
559 # Create the stage from which the targeted image will be tagged.
560 stages['main'] = hpccm.Stage()
562 stages['main'] += hpccm.primitives.baseimage(image=base_image_tag(args))
563 for bb in building_blocks.values():
567 # We always add Python3 and Pip
568 stages['main'] += hpccm.building_blocks.python(python3=True, python2=False, devel=True)
569 stages['main'] += hpccm.building_blocks.pip(upgrade=True, pip='pip3',
570 packages=['pytest', 'networkx', 'numpy'])
572 # Add documentation requirements (doxygen and sphinx + misc).
573 if args.doxygen is not None:
574 add_documentation_dependencies(args, stages)
576 if 'pyenv' in stages and stages['pyenv'] is not None:
577 stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/.pyenv/'],
579 stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/venv/'],
581 # TODO: Update user home directory.
582 # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
583 # stages['main'] += hpccm.primitives.copy(_from='pyenv', src=['/root/.bashrc'],
586 # Make sure that `python` resolves to something.
587 stages['main'] += hpccm.primitives.shell(commands=['test -x /usr/bin/python || '
588 'update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && '
589 '/usr/bin/python --version'])
591 # Note that the list of stages should be sorted in dependency order.
592 for build_stage in stages.values():
593 if build_stage is not None:
597 if __name__ == '__main__':
598 args = parser.parse_args()
600 # Set container specification output format
601 hpccm.config.set_container_format(args.format)
603 container_recipe = build_stages(args)
605 # Output container specification
606 for stage in container_recipe: