admin/containers/scripted_gmx_docker_builds.py

   1 #!/usr/bin/env python
   2 #
   3 # This file is part of the GROMACS molecular simulation package.
   4 #
   5 # Copyright (c) 2020,2021, 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
   8 # top-level source directory and at http://www.gromacs.org.
   9 #
  10 # GROMACS is free software; you can redistribute it and/or
  11 # modify it under the terms of the GNU Lesser General Public License
  12 # as published by the Free Software Foundation; either version 2.1
  13 # of the License, or (at your option) any later version.
  14 #
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  17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18 # Lesser General Public License for more details.
  19 #
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  21 # License along with GROMACS; if not, see
  22 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24 #
  25 # If you want to redistribute modifications to GROMACS, please
  26 # consider that scientific software is very special. Version
  27 # control is crucial - bugs must be traceable. We will be happy to
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  29 # derived work must not be called official GROMACS. Details are found
  30 # in the README & COPYING files - if they are missing, get the
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  34 # the research papers on the package. Check out http://www.gromacs.org.
  35
  36 """Building block based Dockerfile generation for CI testing images.
  37
  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.
  45
  46 Based on the example script provided by the NVidia HPCCM repository.
  47
  48 Reference:
  49     `NVidia HPC Container Maker <https://github.com/NVIDIA/hpc-container-maker>`__
  50
  51 Authors:
  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>
  56
  57 Usage::
  58
  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 -
  62
  63 See Also:
  64     :file:`buildall.sh`
  65
  66 """
  67
  68 import argparse
  69 import collections
  70 import typing
  71 from distutils.version import StrictVersion
  72
  73 import hpccm
  74 import hpccm.config
  75 from hpccm.building_blocks.base import bb_base
  76
  77 try:
  78     import utility
  79 except ImportError:
  80     raise RuntimeError(
  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.')
  83
  84 # Basic packages for all final images.
  85 _common_packages = ['build-essential',
  86                     'ca-certificates',
  87                     'ccache',
  88                     'git',
  89                     'gnupg',
  90                     'gpg-agent',
  91                     'libfftw3-dev',
  92                     'libhwloc-dev',
  93                     'liblapack-dev',
  94                     'libx11-dev',
  95                     'moreutils',
  96                     'ninja-build',
  97                     'rsync',
  98                     'valgrind',
  99                     'vim',
 100                     'wget',
 101                     'xsltproc']
 102
 103 _opencl_extra_packages = [
 104     'nvidia-opencl-dev',
 105     # The following require apt_ppas=['ppa:intel-opencl/intel-opencl']
 106     'intel-opencl-icd',
 107     'ocl-icd-libopencl1',
 108     'ocl-icd-opencl-dev',
 109     'opencl-headers',
 110 ]
 111
 112 _rocm_extra_packages = [
 113         # The following require
 114         #             apt_keys=['http://repo.radeon.com/rocm/rocm.gpg.key'],
 115         #             apt_repositories=['deb [arch=amd64] http://repo.radeon.com/rocm/apt/4.0.1/ xenial main']
 116         'libelf1',
 117         'rocm-opencl',
 118         'rocm-dev',
 119         'clinfo'
 120 ]
 121
 122
 123 # Extra packages needed to build Intel Compute Runtime
 124 _intel_compute_runtime_extra_packages = ['pkg-config',
 125                                          'libxml2',
 126                                          'libxml2-dev',
 127                                          'libigc',
 128                                          'libigc-dev',
 129                                          'libigdgmm11',
 130                                          'libigdgmm-dev',
 131                                          'libze-loader',
 132                                          'libze-loader-dev',
 133                                          'ocl-icd-libopencl1',
 134                                          'ocl-icd-opencl-dev',
 135                                          'opencl-headers']
 136
 137 # Extra packages needed to build Python installations from source.
 138 _python_extra_packages = ['build-essential',
 139                           'ca-certificates',
 140                           'ccache',
 141                           'curl',
 142                           'git',
 143                           'libbz2-dev',
 144                           'libffi-dev',
 145                           'liblzma-dev',
 146                           'libncurses5-dev',
 147                           'libncursesw5-dev',
 148                           'libreadline-dev',
 149                           'libsqlite3-dev',
 150                           'libssl-dev',
 151                           'llvm',
 152                           'python-openssl',
 153                           'vim',
 154                           'wget',
 155                           'zlib1g-dev']
 156
 157 # Extra packages needed for images for building documentation.
 158 _docs_extra_packages = ['autoconf',
 159                         'automake',
 160                         'autopoint',
 161                         'autotools-dev',
 162                         'bison',
 163                         'flex',
 164                         'ghostscript',
 165                         'graphviz',
 166                         'help2man',
 167                         'imagemagick',
 168                         'libtool',
 169                         'mscgen',
 170                         'm4',
 171                         'openssh-client',
 172                         'texinfo',
 173                         'texlive-latex-base',
 174                         'texlive-latex-extra',
 175                         'texlive-fonts-recommended',
 176                         'texlive-fonts-extra']
 177
 178 # Parse command line arguments
 179 parser = argparse.ArgumentParser(description='GROMACS CI image creation script',
 180                                  parents=[utility.parser])
 181
 182 parser.add_argument('--format', type=str, default='docker',
 183                     choices=['docker', 'singularity'],
 184                     help='Container specification format (default: docker)')
 185
 186
 187 def base_image_tag(args) -> str:
 188     # Check if we use CUDA images or plain linux images
 189     if args.cuda is not None:
 190         cuda_version_tag = 'nvidia/cuda:' + args.cuda + '-devel'
 191         if args.centos is not None:
 192             cuda_version_tag += '-centos' + args.centos
 193         elif args.ubuntu is not None:
 194             cuda_version_tag += '-ubuntu' + args.ubuntu
 195         else:
 196             raise RuntimeError('Logic error: no Linux distribution selected.')
 197
 198         base_image_tag = cuda_version_tag
 199     else:
 200         if args.centos is not None:
 201             base_image_tag = 'centos:centos' + args.centos
 202         elif args.ubuntu is not None:
 203             base_image_tag = 'ubuntu:' + args.ubuntu
 204         else:
 205             raise RuntimeError('Logic error: no Linux distribution selected.')
 206     return base_image_tag
 207
 208
 209 def get_llvm_packages(args) -> typing.Iterable[str]:
 210     # If we use the package version of LLVM, we need to install extra packages for it.
 211     if (args.llvm is not None) and (args.tsan is None):
 212         packages = [f'libomp-{args.llvm}-dev',
 213                     f'libomp5-{args.llvm}',
 214                     'clang-format-' + str(args.llvm),
 215                     'clang-tidy-' + str(args.llvm)]
 216         if args.hipsycl is not None:
 217             packages += [f'llvm-{args.llvm}-dev',
 218                          f'libclang-{args.llvm}-dev',
 219                          f'lld-{args.llvm}']
 220         return packages
 221     else:
 222         return []
 223
 224 def get_opencl_packages(args) -> typing.Iterable[str]:
 225     if (args.doxygen is None) and (args.oneapi is None):
 226         return _opencl_extra_packages
 227     else:
 228         return []
 229
 230 def get_rocm_packages(args) -> typing.Iterable[str]:
 231     if (args.rocm is None):
 232         return []
 233     else:
 234         return _rocm_extra_packages
 235
 236 def get_compiler(args, compiler_build_stage: hpccm.Stage = None) -> bb_base:
 237     # Compiler
 238     if args.llvm is not None:
 239         # Build our own version instead to get TSAN + OMP
 240         if args.tsan is not None:
 241             if compiler_build_stage is not None:
 242                 compiler = compiler_build_stage.runtime(_from='tsan')
 243             else:
 244                 raise RuntimeError('No TSAN compiler build stage!')
 245         # Build the default compiler if we don't need special support
 246         else:
 247             compiler = hpccm.building_blocks.llvm(extra_repository=True, version=args.llvm)
 248
 249     elif args.oneapi is not None:
 250         if compiler_build_stage is not None:
 251             compiler = compiler_build_stage.runtime(_from='oneapi')
 252             # Prepare the toolchain (needed only for builds done within the Dockerfile, e.g.
 253             # OpenMPI builds, which don't currently work for other reasons)
 254             oneapi_toolchain = hpccm.toolchain(CC=f'/opt/intel/oneapi/compiler/{args.oneapi}/linux/bin/intel64/icx',
 255                                                CXX=f'/opt/intel/oneapi/compiler/{args.oneapi}/linux/bin/intel64/icpx')
 256             setattr(compiler, 'toolchain', oneapi_toolchain)
 257
 258         else:
 259             raise RuntimeError('No oneAPI compiler build stage!')
 260
 261     elif args.gcc is not None:
 262         compiler = hpccm.building_blocks.gnu(extra_repository=True,
 263                                              version=args.gcc,
 264                                              fortran=False)
 265     else:
 266         raise RuntimeError('Logic error: no compiler toolchain selected.')
 267     return compiler
 268
 269
 270 def get_mpi(args, compiler):
 271     # If needed, add MPI to the image
 272     if args.mpi is not None:
 273         if args.mpi == 'openmpi':
 274             use_cuda = False
 275             if args.cuda is not None:
 276                 use_cuda = True
 277
 278             if hasattr(compiler, 'toolchain'):
 279                 if args.oneapi is not None:
 280                     raise RuntimeError('oneAPI building OpenMPI is not supported')
 281                 return hpccm.building_blocks.openmpi(toolchain=compiler.toolchain, cuda=use_cuda, infiniband=False)
 282             else:
 283                 raise RuntimeError('compiler is not an HPCCM compiler building block!')
 284
 285         elif args.mpi == 'impi':
 286             # TODO Intel MPI from the oneAPI repo is not working reliably,
 287             # reasons are unclear. When solved, add packagages called:
 288             # 'intel-oneapi-mpi', 'intel-oneapi-mpi-devel'
 289             # during the compiler stage.
 290             # TODO also consider hpccm's intel_mpi package if that doesn't need
 291             # a license to run.
 292             raise RuntimeError('Intel MPI recipe not implemented yet.')
 293         else:
 294             raise RuntimeError('Requested unknown MPI implementation.')
 295     else:
 296         return None
 297
 298
 299 def get_clfft(args):
 300     if (args.clfft is not None):
 301         return hpccm.building_blocks.generic_cmake(
 302             repository='https://github.com/clMathLibraries/clFFT.git',
 303             prefix='/usr/local', recursive=True, branch=args.clfft, directory='clFFT/src')
 304     else:
 305         return None
 306
 307 def get_hipsycl(args):
 308     if args.hipsycl is None:
 309         return None
 310     if args.llvm is None:
 311         raise RuntimeError('Can not build hipSYCL without llvm')
 312
 313     if args.rocm is None:
 314         raise RuntimeError('hipSYCL requires the rocm packages')
 315
 316     cmake_opts = [f'-DLLVM_DIR=/usr/lib/llvm-{args.llvm}/cmake',
 317                   f'-DCLANG_EXECUTABLE_PATH=/usr/bin/clang++-{args.llvm}',
 318                   '-DCMAKE_PREFIX_PATH=/opt/rocm/lib/cmake',
 319                   '-DWITH_ROCM_BACKEND=ON']
 320     if args.cuda is not None:
 321         cmake_opts += [f'-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda',
 322                        '-DWITH_CUDA_BACKEND=ON']
 323
 324     postinstall = [
 325             # https://github.com/illuhad/hipSYCL/issues/361#issuecomment-718943645
 326             'for f in /opt/rocm/amdgcn/bitcode/*.bc; do ln -s "$f" "/opt/rocm/lib/$(basename $f .bc).amdgcn.bc"; done'
 327             ]
 328     if args.cuda is not None:
 329         postinstall += [
 330             # https://github.com/illuhad/hipSYCL/issues/410#issuecomment-743301929
 331             f'sed s/_OPENMP/__OPENMP_NVPTX__/ -i /usr/lib/llvm-{args.llvm}/lib/clang/*/include/__clang_cuda_complex_builtins.h',
 332             # Not needed unless we're building with CUDA 11.x, but no harm in doing always
 333             f'ln -s /usr/local/cuda/compat/* /usr/local/cuda/lib64/'
 334             ]
 335
 336     return hpccm.building_blocks.generic_cmake(
 337         repository='https://github.com/illuhad/hipSYCL.git',
 338         directory='/var/tmp/hipSYCL',
 339         prefix='/usr/local', recursive=True, commit=args.hipsycl,
 340         cmake_opts=['-DCMAKE_BUILD_TYPE=Release', *cmake_opts],
 341         postinstall=postinstall)
 342
 343 def get_intel_compute_runtime(args):
 344     # The only reason we need to build Compute Runtime ourselves is because Intel packages have no DG1 support
 345     # Otherwise, we could have just installed DEB packages from GitHub or Intel PPA
 346     if args.intel_compute_runtime is None:
 347         return None
 348
 349     cmake_opts = ['-DCMAKE_BUILD_TYPE=Release',
 350                   '-DSKIP_UNIT_TESTS=TRUE',
 351                   '-DSUPPORT_GEN8=0', '-DSUPPORT_GEN9=1', '-DSUPPORT_GEN11=1', '-DSUPPORT_GEN12LP=1', '-DSUPPORT_DG1=1',
 352                   '-DBUILD_WITH_L0=1']
 353
 354     return hpccm.building_blocks.generic_cmake(
 355         repository='https://github.com/intel/compute-runtime.git',
 356         directory='compute-runtime',
 357         prefix='/usr/local', recursive=True, branch=args.intel_compute_runtime,
 358         cmake_opts=cmake_opts,
 359         postinstall=['ldconfig'])
 360
 361 def add_tsan_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
 362     """Isolate the expensive TSAN preparation stage.
 363
 364     This is a very expensive stage, but has few and disjoint dependencies, and
 365     its output is easily compartmentalized (/usr/local) so we can isolate this
 366     build stage to maximize build cache hits and reduce rebuild time, bookkeeping,
 367     and final image size.
 368     """
 369     if not isinstance(output_stages, collections.abc.MutableMapping):
 370         raise RuntimeError('Need output_stages container.')
 371     tsan_stage = hpccm.Stage()
 372     tsan_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='tsan')
 373
 374     tsan_stage += hpccm.building_blocks.packages(ospackages=['git', 'ca-certificates', 'build-essential', 'cmake'])
 375     # CMake will get duplicated later, but this is an expensive image, and it isn't worth optimizing
 376     # out that duplication...
 377     tsan_stage += hpccm.building_blocks.python(python3=True, python2=False, devel=False)
 378
 379     compiler_branch = 'release/' + str(input_args.llvm) + '.x'
 380     tsan_stage += hpccm.building_blocks.generic_cmake(
 381         repository='https://github.com/llvm/llvm-project.git',
 382         directory='/var/tmp/llvm-project/llvm/',
 383         prefix='/usr/local', recursive=True, branch=compiler_branch,
 384         cmake_opts=['-D CMAKE_BUILD_TYPE=Release', '-D LLVM_ENABLE_PROJECTS="clang;openmp;clang-tools-extra;compiler-rt;lld"',
 385                     '-D LIBOMP_TSAN_SUPPORT=on'],
 386         postinstall=['ln -s /usr/local/bin/clang++ /usr/local/bin/clang++-' + str(input_args.llvm),
 387                      'ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-' + str(input_args.llvm),
 388                      'ln -s /usr/local/bin/clang-tidy /usr/local/bin/clang-tidy-' + str(input_args.llvm),
 389                      'ln -s /usr/local/share/clang/run-clang-tidy.py /usr/local/bin/run-clang-tidy-' + str(input_args.llvm) + '.py',
 390                      'ln -s /usr/local/bin/run-clang-tidy-' + str(input_args.llvm) + '.py /usr/local/bin/run-clang-tidy-' + str(input_args.llvm),
 391                      'ln -s /usr/local/libexec/c++-analyzer /usr/local/bin/c++-analyzer-' + str(input_args.llvm)])
 392     output_stages['compiler_build'] = tsan_stage
 393
 394 def oneapi_runtime(_from='0'):
 395     oneapi_runtime_stage = hpccm.Stage()
 396     oneapi_runtime_stage += hpccm.primitives.copy(_from='oneapi-build',
 397                                                   files={"/opt/intel": "/opt/intel",
 398                                                          "/etc/bash.bashrc": "/etc/bash.bashrc"})
 399     return oneapi_runtime_stage
 400
 401 def add_oneapi_compiler_build_stage(input_args, output_stages: typing.Mapping[str, hpccm.Stage]):
 402     """Isolate the oneAPI preparation stage.
 403
 404     This stage is isolated so that its installed components are minimized in the
 405     final image (chiefly /opt/intel) and its environment setup script can be
 406     sourced. This also helps with rebuild time and final image size.
 407     """
 408     if not isinstance(output_stages, collections.abc.MutableMapping):
 409         raise RuntimeError('Need output_stages container.')
 410     oneapi_stage = hpccm.Stage()
 411     oneapi_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='oneapi-build')
 412
 413     version = str(input_args.oneapi)
 414
 415     # Add required components for the next stage (both for hpccm and Intel's setvars.sh script)
 416     oneapi_stage += hpccm.building_blocks.packages(ospackages=['wget', 'gnupg2', 'ca-certificates', 'lsb-release'])
 417     oneapi_stage += hpccm.building_blocks.packages(
 418         apt_keys=['https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB'],
 419         apt_repositories=['deb https://apt.repos.intel.com/oneapi all main'],
 420         # Add minimal packages (not the whole HPC toolkit!)
 421         ospackages=[f'intel-oneapi-dpcpp-cpp-{version}',
 422             f'intel-oneapi-openmp-{version}',
 423             f'intel-oneapi-mkl-{version}',
 424             f'intel-oneapi-mkl-devel-{version}']
 425     )
 426     # Ensure that all bash shells on the final container will have access to oneAPI
 427     oneapi_stage += hpccm.primitives.shell(
 428             commands=['echo "source /opt/intel/oneapi/setvars.sh" >> /etc/bash.bashrc',
 429                       'unlink /opt/intel/oneapi/compiler/latest',
 430                      f'ln -sf /opt/intel/oneapi/compiler/{version} /opt/intel/oneapi/compiler/latest']
 431             )
 432     setattr(oneapi_stage, 'runtime', oneapi_runtime)
 433
 434     output_stages['compiler_build'] = oneapi_stage
 435
 436 def prepare_venv(version: StrictVersion) -> typing.Sequence[str]:
 437     """Get shell commands to set up the venv for the requested Python version."""
 438     major = version.version[0]
 439     minor = version.version[1]  # type: int
 440
 441     pyenv = '$HOME/.pyenv/bin/pyenv'
 442
 443     py_ver = f'{major}.{minor}'
 444     venv_path = f'$HOME/venv/py{py_ver}'
 445     commands = [f'$({pyenv} prefix `{pyenv} whence python{py_ver}`)/bin/python -m venv {venv_path}']
 446
 447     commands.append(f'{venv_path}/bin/python -m pip install --upgrade pip setuptools')
 448     # Install dependencies for building and testing gmxapi Python package.
 449     # WARNING: Please keep this list synchronized with python_packaging/requirements-test.txt
 450     # TODO: Get requirements.txt from an input argument.
 451     commands.append(f"""{venv_path}/bin/python -m pip install --upgrade \
 452             'cmake>=3.16.3' \
 453             'flake8>=3.7.7' \
 454             'gcovr>=4.2' \
 455             'mpi4py>=3.0.3' \
 456             'networkx>=2.0' \
 457             'numpy>=1' \
 458             'pip>=10.1' \
 459             'Pygments>=2.2.0' \
 460             'pytest>=3.9' \
 461             'setuptools>=42' \
 462             'scikit-build>=0.10' \
 463             'Sphinx>=1.6.3' \
 464             'sphinxcontrib-plantuml>=0.14'""")
 465
 466     # TODO: Remove 'importlib_resources' dependency when Python >=3.7 is required.
 467     if minor == 6:
 468         commands.append(f"""{venv_path}/bin/python -m pip install --upgrade \
 469                 'importlib_resources'""")
 470
 471     return commands
 472
 473
 474 def add_python_stages(building_blocks: typing.Mapping[str, bb_base],
 475                       input_args,
 476                       output_stages: typing.MutableMapping[str, hpccm.Stage]):
 477     """Add the stage(s) necessary for the requested venvs.
 478
 479     One intermediate build stage is created for each venv (see --venv option).
 480
 481     Each stage partially populates Python installations and venvs in the home
 482     directory. The home directory is collected by the 'pyenv' stage for use by
 483     the main build stage.
 484     """
 485     if len(input_args.venvs) < 1:
 486         raise RuntimeError('No venvs to build...')
 487     if output_stages is None or not isinstance(output_stages, collections.abc.Mapping):
 488         raise RuntimeError('Need a container for output stages.')
 489
 490     # Main Python stage that collects the environments from individual stages.
 491     # We collect the stages individually, rather than chaining them, because the
 492     # copy is a bit slow and wastes local Docker image space for each filesystem
 493     # layer.
 494     pyenv_stage = hpccm.Stage()
 495     pyenv_stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as='pyenv')
 496     pyenv_stage += building_blocks['compiler']
 497     pyenv_stage += building_blocks['mpi']
 498     pyenv_stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
 499
 500     for version in [StrictVersion(py_ver) for py_ver in sorted(input_args.venvs)]:
 501         stage_name = 'py' + str(version)
 502         stage = hpccm.Stage()
 503         stage += hpccm.primitives.baseimage(image=base_image_tag(input_args), _as=stage_name)
 504         stage += building_blocks['compiler']
 505         stage += building_blocks['mpi']
 506         stage += hpccm.building_blocks.packages(ospackages=_python_extra_packages)
 507
 508         # TODO: Use a non-root user for testing and Python virtual environments.
 509         stage += hpccm.primitives.shell(commands=[
 510             'curl https://pyenv.run | bash',
 511             """echo 'export PYENV_ROOT="$HOME/.pyenv"' >> $HOME/.bashrc""",
 512             """echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> $HOME/.bashrc""",
 513             """echo 'eval "$(pyenv init -)"' >> $HOME/.bashrc""",
 514             """echo 'eval "$(pyenv virtualenv-init -)"' >> $HOME/.bashrc"""])
 515         pyenv = '$HOME/.pyenv/bin/pyenv'
 516         commands = [f'PYTHON_CONFIGURE_OPTS="--enable-shared" {pyenv} install -s {version}']
 517         stage += hpccm.primitives.shell(commands=commands)
 518
 519         commands = prepare_venv(version)
 520         stage += hpccm.primitives.shell(commands=commands)
 521
 522         # TODO: Update user home directory.
 523         pyenv_stage += hpccm.primitives.copy(_from=stage_name, _mkdir=True, src=['/root/'],
 524                                              dest='/root')
 525
 526         # Add the intermediate build stage to the sequence
 527         output_stages[stage_name] = stage
 528
 529     # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
 530     # # `version` should be a system installation or pyenv environment (or pyenv-virtualenv)
 531     # # with the dependencies for all of the Python aspects of CMake-driven builds.
 532     # commands = '{pyenv} global {version}'.format(
 533     #             pyenv=pyenv,
 534     #             version=...)
 535     # pyenv_stage += hpccm.primitives.shell(commands=commands)
 536
 537     # Add the aggregating build stage to the sequence. This allows the main stage to copy
 538     # the files in a single stage, potentially reducing the overall output image size.
 539     output_stages['pyenv'] = pyenv_stage
 540
 541
 542 def add_documentation_dependencies(input_args,
 543                                    output_stages: typing.MutableMapping[str, hpccm.Stage]):
 544     """Add appropriate layers according to doxygen input arguments."""
 545     if input_args.doxygen is None:
 546         return
 547     # Always clone the same version of linkchecker (latest release at June 1, 2021)
 548     output_stages['main'] += hpccm.building_blocks.pip(pip='pip3', packages=['git+https://github.com/linkchecker/linkchecker.git@v10.0.1'])
 549     output_stages['main'] += hpccm.primitives.shell(
 550         commands=['sed -i \'/\"XPS\"/d;/\"PDF\"/d;/\"PS\"/d;/\"EPS\"/d;/disable ghostscript format types/d\' /etc/ImageMagick-6/policy.xml'])
 551     if input_args.doxygen == '1.8.5':
 552         doxygen_commit = 'ed4ed873ab0e7f15116e2052119a6729d4589f7a'
 553         output_stages['main'] += hpccm.building_blocks.generic_autotools(
 554             repository='https://github.com/westes/flex.git',
 555             commit='f7788a9a0ecccdc953ed12043ccb59ca25714018',
 556             prefix='/tmp/install-of-flex',
 557             configure_opts=['--disable-shared'],
 558             preconfigure=['./autogen.sh'])
 559         output_stages['main'] += hpccm.building_blocks.generic_autotools(
 560             repository='https://github.com/doxygen/doxygen.git',
 561             commit=doxygen_commit,
 562             prefix='',
 563             configure_opts=[
 564                 '--flex /tmp/install-of-flex/bin/flex',
 565                 '--static'])
 566     else:
 567         version = input_args.doxygen
 568         archive_name = f'doxygen-{version}.linux.bin.tar.gz'
 569         archive_url = f'https://sourceforge.net/projects/doxygen/files/rel-{version}/{archive_name}'
 570         binary_path = f'doxygen-{version}/bin/doxygen'
 571         commands = [
 572             'mkdir doxygen && cd doxygen',
 573             f'wget {archive_url}',
 574             f'tar xf {archive_name} {binary_path}',
 575             f'cp {binary_path} /usr/local/bin/',
 576             'cd .. && rm -rf doxygen'
 577         ]
 578         output_stages['main'] += hpccm.primitives.shell(commands=commands)
 579
 580
 581 def build_stages(args) -> typing.Iterable[hpccm.Stage]:
 582     """Define and sequence the stages for the recipe corresponding to *args*."""
 583
 584     # A Dockerfile or Singularity recipe can have multiple build stages.
 585     # The main build stage can copy files from previous stages, though only
 586     # the last stage is included in the tagged output image. This means that
 587     # large or expensive sets of build instructions can be isolated in
 588     # local/temporary images, but all of the stages need to be output by this
 589     # script, and need to occur in the correct order, so we create a sequence
 590     # object early in this function.
 591     stages = collections.OrderedDict()
 592
 593     # If we need TSAN or oneAPI support the early build is more complex,
 594     # so that our compiler images don't have all the cruft needed to get those things
 595     # installed.
 596     if args.llvm is not None and args.tsan is not None:
 597         add_tsan_compiler_build_stage(input_args=args, output_stages=stages)
 598     if args.oneapi is not None:
 599         add_oneapi_compiler_build_stage(input_args=args, output_stages=stages)
 600
 601     # Building blocks are chunks of container-builder instructions that can be
 602     # copied to any build stage with the addition operator.
 603     building_blocks = collections.OrderedDict()
 604     building_blocks['base_packages'] = hpccm.building_blocks.packages(
 605         ospackages=_common_packages)
 606
 607     # These are the most expensive and most reusable layers, so we put them first.
 608     building_blocks['compiler'] = get_compiler(args, compiler_build_stage=stages.get('compiler_build'))
 609     building_blocks['mpi'] = get_mpi(args, building_blocks['compiler'])
 610     for i, cmake in enumerate(args.cmake):
 611         building_blocks['cmake' + str(i)] = hpccm.building_blocks.cmake(
 612             eula=True,
 613             prefix=f'/usr/local/cmake-{cmake}',
 614             version=cmake)
 615
 616     # Install additional packages early in the build to optimize Docker build layer cache.
 617     os_packages = list(get_llvm_packages(args)) + get_opencl_packages(args) + get_rocm_packages(args)
 618     if args.doxygen is not None:
 619         os_packages += _docs_extra_packages
 620     if args.oneapi is not None:
 621         os_packages += ['lsb-release']
 622     if args.hipsycl is not None:
 623         os_packages += ['libboost-fiber-dev']
 624     if args.intel_compute_runtime is not None:
 625         os_packages += _intel_compute_runtime_extra_packages
 626     building_blocks['extra_packages'] = []
 627     if args.rocm is not None:
 628         building_blocks['extra_packages'] += hpccm.building_blocks.packages(
 629             apt_keys=['http://repo.radeon.com/rocm/rocm.gpg.key'],
 630             apt_repositories=[f'deb [arch=amd64] http://repo.radeon.com/rocm/apt/{args.rocm}/ xenial main']
 631         )
 632     building_blocks['extra_packages'] += hpccm.building_blocks.packages(
 633         ospackages=os_packages,
 634         apt_ppas=['ppa:intel-opencl/intel-opencl'])
 635
 636     if args.cuda is not None and args.llvm is not None:
 637         # Hack to tell clang what version of CUDA we're using
 638         # based on https://github.com/llvm/llvm-project/blob/1fdec59bffc11ae37eb51a1b9869f0696bfd5312/clang/lib/Driver/ToolChains/Cuda.cpp#L43
 639         cuda_version_split = args.cuda.split('.')
 640         # LLVM requires having the version in x.y.z format, while args.cuda be be either x.y or x.y.z
 641         cuda_version_str = '{}.{}.{}'.format(
 642             cuda_version_split[0],
 643             cuda_version_split[1],
 644             cuda_version_split[2] if len(cuda_version_split) > 2 else 0
 645         )
 646         building_blocks['cuda-clang-workaround'] = hpccm.primitives.shell(commands=[
 647             f'echo "CUDA Version {cuda_version_str}" > /usr/local/cuda/version.txt'
 648             ])
 649
 650     building_blocks['clfft'] = get_clfft(args)
 651
 652     building_blocks['hipSYCL'] = get_hipsycl(args)
 653
 654     building_blocks['intel-compute-runtime'] = get_intel_compute_runtime(args)
 655
 656     # Add Python environments to MPI images, only, so we don't have to worry
 657     # about whether to install mpi4py.
 658     if args.mpi is not None and len(args.venvs) > 0:
 659         add_python_stages(building_blocks=building_blocks, input_args=args, output_stages=stages)
 660
 661     # Create the stage from which the targeted image will be tagged.
 662     stages['main'] = hpccm.Stage()
 663
 664     stages['main'] += hpccm.primitives.baseimage(image=base_image_tag(args))
 665     for bb in building_blocks.values():
 666         if bb is not None:
 667             stages['main'] += bb
 668
 669     # We always add Python3 and Pip
 670     stages['main'] += hpccm.building_blocks.python(python3=True, python2=False)
 671
 672     # Add documentation requirements (doxygen and sphinx + misc).
 673     if args.doxygen is not None:
 674         add_documentation_dependencies(args, stages)
 675
 676     if 'pyenv' in stages and stages['pyenv'] is not None:
 677         stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/.pyenv/'],
 678                                                 dest='/root/.pyenv')
 679         stages['main'] += hpccm.primitives.copy(_from='pyenv', _mkdir=True, src=['/root/venv/'],
 680                                                 dest='/root/venv')
 681         # TODO: Update user home directory.
 682         # TODO: If we activate pyenv for login shells, the `global` "version" should be full-featured.
 683         # stages['main'] += hpccm.primitives.copy(_from='pyenv', src=['/root/.bashrc'],
 684         #                                         dest='/root/')
 685
 686     # Make sure that `python` resolves to something.
 687     stages['main'] += hpccm.primitives.shell(commands=['test -x /usr/bin/python || '
 688                                                        'update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && '
 689                                                        '/usr/bin/python --version'])
 690
 691     # Note that the list of stages should be sorted in dependency order.
 692     for build_stage in stages.values():
 693         if build_stage is not None:
 694             yield build_stage
 695
 696
 697 if __name__ == '__main__':
 698     args = parser.parse_args()
 699
 700     # Set container specification output format
 701     hpccm.config.set_container_format(args.format)
 702
 703     container_recipe = build_stages(args)
 704
 705     # Output container specification
 706     for stage in container_recipe:
 707         print(stage)