spack.yaml

spack:
  repos:
  - /opt/scitas-cryoem-spack-packages

  mirrors:
    cache:
      fetch:
        url: file:///buildcache
        access_pair:
          - null
          - null
        access_token: null
        profile: null
        endpoint_url: null
      push:
        url: file:///buildcache
        access_pair:
          - null
          - null
        access_token: null
        profile: null
        endpoint_url: null

  packages:
    all:
      target: [x86_64_v3]
      providers:
        mpi: [openmpi]
        jpeg: [libjpeg]
    gcc:
      externals:
      - spec: gcc@9.4.0 languages=c,c++,fortran
        prefix: /usr
        extra_attributes:
          compilers:
            c: /usr/bin/x86_64-linux-gnu-gcc-9
            cxx: /usr/bin/x86_64-linux-gnu-g++-9
            fortran: /usr/bin/x86_64-linux-gnu-gfortran-9
    boost:
      variants: [+atomic+chrono~clanglibcpp~container~context~contract~coroutine+date_time~debug+exception~fiber+filesystem+graph~graph_parallel~icu+iostreams~json+locale+log+math~mpi+multithreaded~nowide+numpy~pic+program_options+python+random+regex+serialization+shared+signals~singlethreaded~stacktrace+system~taggedlayout+test+thread+timer~type_erasure~versionedlayout+wave]
    cairo:
      variants: [+X+fc+ft+png+pdf+gobject]
    cuda:
      version: [11.4.3]
      variants: [+allow-unsupported-compilers]
    openmpi:
      variants: [+cuda +thread_multiple +singularity schedulers=slurm +pmix fabrics=ucx]
      version: [4.1.3]
    ucx:
      variants: [+cuda cuda_arch=70 +gdrcopy]
    relion:
      version: [4.0-beta]
    rdma-core:
      version: [34.0]
    mesa:
      variants: [~llvm]
    py-tensorflow:
      variants: [+cuda cuda_arch=70 +mpi]
    protobuf:
      version: [3.11.1]
    slurm:
      version: [20-02-7-1]
    wxwidgets:
      version: [3.0.2]
    python:
      variants: [+bz2+ctypes+dbm~debug+ensurepip+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl+tkinter~ucs4+uuid+zlib]
    py-setuptools:
      version: [51.0.0]
    py-six:
      version: [1.15.0]
    py-numpy:
      version: [1.19.5]
    nccl:
      variants: [+cuda cuda_arch=70]
    hwloc:
      variants: [+cuda cuda_arch=70]

  definitions:
  - mpi_codes:
    - relion +cuda cuda_arch=70 +double-gpu ~gui
    - relion@3.1.3 +cuda cuda_arch=70 +double-gpu ~gui
    - fftw +mpi
    - eman2 +cuda +mpi

    # do to mpi dependent dependency
    - cistem
    - ctffind
    - unblur
    - py-pymol
  specs:
    # required pacakges
    - gctf@1.18
    - py-cryolobm
    - py-pyem
    - matrix:
      - [$mpi_codes]
      - [^openmpi]
#  concretization: together
  view:
    default:
      root: /opt/view
      exclude: ['^cuda@:11.2', 'cuda@:11.2', 'relion@3.1.3']
      link_type: symlink
  compilers:
  - compiler:
      spec: gcc@9.4.0
      paths:
        cc: /usr/bin/gcc-9
        cxx: /usr/bin/g++-9
        f77: /usr/bin/gfortran-9
        fc: /usr/bin/gfortran-9
      flags: {}
      operating_system: ubuntu20.04
      target: x86_64
      modules: []
      environment: {}
      extra_rpaths: []