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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>
54 $ python3 scripted_gmx_docker_builds.py --help
55 $ python3 scripted_gmx_docker_builds.py --format docker > Dockerfile && docker build .
56 $ python3 scripted_gmx_docker_builds.py | docker build -
63 from distutils.version import StrictVersion
67 from hpccm.building_blocks.base import bb_base
73 'This module assumes availability of supporting modules in the same directory. Add the directory to '
74 'PYTHONPATH or invoke Python from within the module directory so module location can be resolved.')
76 # Basic packages for all final images.
77 _common_packages = ['build-essential',
94 # Extra packages needed to build Python installations from source.
95 _python_extra_packages = ['build-essential',
114 # Extra packages needed for images for building documentation.
115 _docs_extra_packages = ['autoconf',
130 'texlive-latex-base',
131 'texlive-latex-extra',
132 'texlive-fonts-recommended',
133 'texlive-fonts-extra']
135 # Supported Python versions for maintained branches.
136 _python_versions = ['3.6.10', '3.7.7', '3.8.2']
138 # Parse command line arguments
139 parser = argparse.ArgumentParser(description='GROMACS CI image creation script', parents=[utility.parser])
141 parser.add_argument('--format', type=str, default='docker',
142 choices=['docker', 'singularity'],
143 help='Container specification format (default: docker)')
144 parser.add_argument('--venvs', nargs='*', type=str, default=_python_versions,
145 help='List of Python versions ("major.minor.patch") for which to install venvs. '
146 'Default: {}'.format(' '.join(_python_versions)))
149 def base_image_tag(args) -> str:
150 # Check if we use CUDA images or plain linux images
151 if args.cuda is not None:
152 cuda_version_tag = 'nvidia/cuda:' + args.cuda + '-devel'
153 if args.centos is not None:
154 cuda_version_tag += '-centos' + args.centos
155 elif args.ubuntu is not None:
156 cuda_version_tag += '-ubuntu' + args.ubuntu
158 raise RuntimeError('Logic error: no Linux distribution selected.')
160 base_image_tag = cuda_version_tag
162 if args.centos is not None:
163 base_image_tag = 'centos:centos' + args.centos
164 elif args.ubuntu is not None:
165 base_image_tag = 'ubuntu:' + args.ubuntu
167 raise RuntimeError('Logic error: no Linux distribution selected.')
168 return base_image_tag
171 def get_llvm_packages(args) -> typing.Iterable[str]:
172 # If we use the package version of LLVM, we need to install extra packages for it.
173 if (args.llvm is not None) and (args.tsan is None):
174 return ['libomp-dev',
175 'clang-format-' + str(args.llvm),
176 'clang-tidy-' + str(args.llvm)]
181 def get_compiler(args, tsan_stage: hpccm.Stage = None) -> bb_base:
183 if args.icc is not None:
184 raise RuntimeError('Intel compiler toolchain recipe not implemented yet')
186 if args.llvm is not None:
187 # Build our own version instead to get TSAN + OMP
188 if args.tsan is not None:
189 if tsan_stage is not None:
190 compiler = tsan_stage.runtime(_from='tsan')
192 raise RuntimeError('No TSAN stage!')
193 # Build the default compiler if we don't need special support
195 compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
197 elif (args.gcc is not None):
198 compiler = hpccm.building_blocks.gnu(extra_repository=True,
202 raise RuntimeError('Logic error: no compiler toolchain selected.')
206 def get_mpi(args, compiler):
207 # If needed, add MPI to the image
208 if args.mpi is not None:
209 if args.mpi == 'openmpi':
211 if args.cuda is not None:
214 if hasattr(compiler, 'toolchain'):
215 return hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
217 raise RuntimeError('compiler is not an HPCCM compiler building block!')
219 elif args.mpi == 'impi':
220 raise RuntimeError('Intel MPI recipe not implemented yet.')
222 raise RuntimeError('Requested unknown MPI implementation.')
227 def get_opencl(args):
228 # Add OpenCL environment if needed
229 if (args.opencl is not None):
230 if args.opencl == 'nvidia':
231 if (args.cuda is None):
232 raise RuntimeError('Need Nvidia environment for Nvidia OpenCL image')
234 return hpccm.building_blocks.packages(ospackages=['nvidia-opencl-dev'])
236 elif args.opencl == 'intel':
237 return hpccm.building_blocks.packages(
238 apt_ppas=['ppa:intel-opencl/intel-opencl'],
239 ospackages=['opencl-headers', 'ocl-icd-libopencl1',
240 'ocl-icd-opencl-dev', 'intel-opencl-icd'])
242 elif args.opencl == 'amd':
243 # libelf1 is a necessary dependency for something in the ROCm stack,
244 # which they should set up, but seem to have omitted.
245 return hpccm.building_blocks.packages(
246 apt_keys=['http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key'],
247 apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main'],
248 ospackages=['ocl-icd-libopencl1', 'ocl-icd-opencl-dev', 'opencl-headers', 'libelf1', 'rocm-opencl'])
254 if (args.clfft is not None):
255 return hpccm.building_blocks.generic_cmake(
256 repository='https://github.com/clMathLibraries/clFFT.git',
257 prefix='/usr/local', recursive=True, branch=args.clfft, directory='clFFT/src')
262 def add_tsan_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
263 """Isolate the expensive TSAN preparation stage.
265 This is a very expensive stage, but has few and disjoint dependencies, and
266 its output is easily compartmentalized (/usr/local) so we can isolate this
267 build stage to maximize build cache hits and reduce rebuild time, bookkeeping,
268 and final image size.
270 if not isinstance(output_stages, collections.abc.MutableMapping):
271 raise RuntimeError('Need output_stages container.')
272 tsan_stage = hpccm.Stage()
273 tsan_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='tsan')
275 tsan_stage += hpccm.building_blocks.packages(ospackages=['git', 'ca-certificates', 'build-essential', 'cmake'])
276 # CMake will get duplicated later, but this is an expensive image, and it isn't worth optimizing
277 # out that duplication...
278 tsan_stage += hpccm.building_blocks.python(python3=True, python2=False, devel=False)
280 compiler_branch = 'release_' + str(input_args.llvm) + '0'
281 tsan_stage += hpccm.building_blocks.generic_cmake(
282 repository='https://git.llvm.org/git/llvm.git',
283 prefix='/usr/local', recursive=True, branch=compiler_branch,
284 cmake_opts=['-D CMAKE_BUILD_TYPE=Release', '-D LLVM_ENABLE_PROJECTS="clang;openmp;clang-tools-extra"',
285 '-D LIBOMP_TSAN_SUPPORT=on'],
286 preconfigure=['export branch=' + compiler_branch,
287 '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/libcxx.git)',
288 '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/libcxxabi.git)',
289 '(cd projects; git clone --depth=1 --branch $branch https://git.llvm.org/git/compiler-rt.git)',
290 '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/openmp.git)',
291 '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/clang.git)',
292 '(cd ..; git clone --depth=1 --branch $branch https://git.llvm.org/git/clang-tools-extra.git)'],
293 postinstall=['ln -s /usr/local/bin/clang++ /usr/local/bin/clang++-' + str(input_args.llvm),
294 'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-' + str(input_args.llvm),
295 'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-' + str(input_args.llvm),
296 'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
297 output_stages['tsan'] = tsan_stage
300 def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
301 """Get shell commands to set up the venv for the requested Python version."""
302 major = version.version[0]
303 minor = version.version[1]
305 pyenv = '$HOME/.pyenv/bin/pyenv'
307 py_ver = '{}.{}'.format(major, minor)
308 venv_path = '$HOME/venv/py{}'.format(py_ver)
309 commands = ['$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {path}'.format(
315 commands.append('{path}/bin/python -m pip install --upgrade pip setuptools'.format(
318 # Install dependencies for building and testing gmxapi Python package.
319 # WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
320 # TODO: Get requirements.txt from an input argument.
321 commands.append("""{path}/bin/python -m pip install --upgrade \
330 'scikit-build>=0.10'""".format(path=venv_path))
335 def add_python_stages(building_blocks: typing.Mapping[str, bb_base],
337 output_stages: typing.MutableMapping[str, hpccm.Stage]):
338 """Add the stage(s) necessary for the requested venvs.
340 One intermediate build stage is created for each venv (see --venv option).
342 Each stage partially populates Python installations and venvs in the home
343 directory. The home directory is collected by the 'pyenv' stage for use by
344 the main build stage.
346 if len(input_args.venvs) < 1:
347 raise RuntimeError('No venvs to build...')
348 if output_stages is None or not isinstance(output_stages, collections.abc.Mapping):
349 raise RuntimeError('Need a container for output stages.')
351 # Main Python stage that collects the environments from individual stages.
352 # We collect the stages individually, rather than chaining them, because the
353 # copy is a bit slow and wastes local Docker image space for each filesystem
355 pyenv_stage = hpccm.Stage()
356 pyenv_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='pyenv')
357 pyenv_stage += building_blocks['compiler']
358 pyenv_stage += building_blocks['mpi']
359 pyenv_stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
361 for version in [StrictVersion(py_ver) for py_ver in sorted(input_args.venvs)]:
362 stage_name = 'py' + str(version)
363 stage = hpccm.Stage()
364 stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as=stage_name)
365 stage += building_blocks['compiler']
366 stage += building_blocks['mpi']
367 stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
369 # TODO: Use a non-root user for testing and Python virtual environments.
370 stage += hpccm.primitives.shell(commands=[
371 'curl https://pyenv.run | bash',
372 """echo 'export PYENV_ROOT="$HOME/.pyenv"' >> $HOME/.bashrc""",
373 """echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> $HOME/.bashrc""",
374 """echo 'eval "$(pyenv init -)"' >> $HOME/.bashrc""",
375 """echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bashrc"""])
376 pyenv = '$HOME/.pyenv/bin/pyenv'
377 commands = ['PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}'.format(
379 version=str(version))]
380 stage += hpccm.primitives.shell(commands=commands)
382 commands = prepare_venv(version)
383 stage += hpccm.primitives.shell(commands=commands)
385 # TODO: Update user home directory.
386 pyenv_stage += hpccm.primitives.copy(_from=stage_name, _mkdir=True, src=['/root/'],
389 # Add the intermediate build stage to the sequence
390 output_stages[stage_name] = stage
392 # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
393 # # `version` should be a system installation or pyenv environment (or pyenv-virtualenv)
394 # # with the dependencies for all of the Python aspects of CMake-driven builds.
395 # commands = '{pyenv} global {version}'.format(
398 # pyenv_stage += hpccm.primitives.shell(commands=commands)
400 # Add the aggregating build stage to the sequence. This allows the main stage to copy
401 # the files in a single stage, potentially reducing the overall output image size.
402 output_stages['pyenv'] = pyenv_stage
405 def add_doxygen_stages(input_args,
406 output_stages: typing.MutableMapping[str, hpccm.Stage]):
407 """Add appropriate stages according to doxygen input arguments."""
408 if input_args.doxygen is None:
410 if input_args.doxygen == '1.8.5':
411 doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
412 output_stages['main'] += hpccm.building_blocks.generic_autotools(
413 repository='https://github.com/westes/flex.git',
414 commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
415 prefix='/tmp/install-of-flex',
416 configure_opts=['--disable-shared'],
417 preconfigure=['./autogen.sh'])
418 output_stages['main'] += hpccm.building_blocks.generic_autotools(
419 repository='https://github.com/doxygen/doxygen.git',
420 commit=doxygen_commit,
423 '--flex /tmp/install-of-flex/bin/flex',
426 'sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
427 output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['sphinx==1.6.1'])
429 raise RuntimeError('Unhandled doxygen version: {}'.format(input_args.doxygen))
432 def build_stages(args) -> typing.Iterable[hpccm.Stage]:
433 """Define and sequence the stages for the recipe corresponding to *args*."""
435 # A Dockerfile or Singularity recipe can have multiple build stages.
436 # The main build stage can copy files from previous stages, though only
437 # the last stage is included in the tagged output image. This means that
438 # large or expensive sets of build instructions can be isolated in
439 # local/temporary images, but all of the stages need to be output by this
440 # script, and need to occur in the correct order, so we create a sequence
441 # object early in this function.
442 stages = collections.OrderedDict()
444 # If we need the TSAN compilers, the early build is more involved.
445 if args.llvm is not None and args.tsan is not None:
446 add_tsan_stage(input_args=args, output_stages=stages)
448 # Building blocks are chunks of container-builder instructions that can be
449 # copied to any build stage with the addition operator.
450 building_blocks = collections.OrderedDict()
452 # These are the most expensive and most reusable layers, so we put them first.
453 building_blocks['compiler'] = get_compiler(args, tsan_stage=stages.get('tsan'))
454 building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
456 # Install additional packages early in the build to optimize Docker build layer cache.
457 os_packages = _common_packages + get_llvm_packages(args)
458 if args.doxygen is not None:
459 os_packages += _docs_extra_packages
460 building_blocks['ospackages'] = hpccm.building_blocks.packages(ospackages=os_packages)
462 building_blocks['cmake'] = hpccm.building_blocks.cmake(eula=True, version=args.cmake)
463 building_blocks['opencl'] = get_opencl(args)
464 building_blocks['clfft'] = get_clfft(args)
466 # Add Python environments to MPI images, only, so we don't have to worry
467 # about whether to install mpi4py.
468 if args.mpi is not None and len(args.venvs) > 0:
469 add_python_stages(building_blocks=building_blocks, input_args=args, output_stages=stages)
471 # Create the stage from which the targeted image will be tagged.
472 stages['main'] = hpccm.Stage()
474 stages['main'] += hpccm.primitives.baseimage(image=base_image_tag(args))
475 for bb in building_blocks.values():
479 # We always add Python3 and Pip
480 stages['main'] += hpccm.building_blocks.python(python3=True, python2=False, devel=True)
481 stages['main'] += hpccm.building_blocks.pip(upgrade=True, pip='pip3',
482 packages=['pytest', 'networkx', 'numpy'])
484 # Add documentation requirements (doxygen and sphinx + misc).
485 if args.doxygen is not None:
486 add_doxygen_stages(args, stages)
488 if 'pyenv' in stages and stages['pyenv'] is not None:
489 stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/.pyenv/'],
491 stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/venv/'],
493 # TODO: Update user home directory.
494 # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
495 # stages['main'] += hpccm.primitives.copy(_from='pyenv', src=['/root/.bashrc'],
498 # Make sure that `python` resolves to something.
499 stages['main'] += hpccm.primitives.shell(commands=['test -x /usr/bin/python || '
500 'update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && '
501 '/usr/bin/python --version'])
503 # Note that the list of stages should be sorted in dependency order.
504 for build_stage in stages.values():
505 if build_stage is not None:
509 if __name__ == '__main__':
510 args = parser.parse_args()
512 # Set container specification output format
513 hpccm.config.set_container_format(args.format)
515 container_recipe = build_stages(args)
517 # Output container specification
518 for stage in container_recipe: