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Table of Contents

PY-SCIPY crashes during installation

Spack has a ready-made recipe for installing the scipy module for Python, which is called py-scipy. During IMAS eco-system installation, while providing necessary python packages the one of which is the py-scipy, the installation of the py-scipy has crashed. The error message is ambiguous and is shown below:

Code Block
pip._internal.exceptions.InstallationError: Could not build wheels for scipy, which is required to install pyproject.toml-based projects

How to reproduce issue

  1. Log in to Marconi cluster

  2. Load intel/pe-xe-2020–binary module

    Code Block
    module load intel/pe-xe-2020--binary


  3. Load intelmpi/2020--binary module 

    Code Block
    module load intelmpi/2020--binary


  4. Clone spack repository

    Code Block
    git clone https://github.com/spack/spack.git


  5. To ensure the same environment set the packages.yaml file as below. This only adds packages marked as external:

    Expand

    the packages.yaml is located here: 

    Code Block
    vim ./spack/etc/spack/defaults/packages.yaml

    And it should have following body:

    Code Block
    # -------------------------------------------------------------------------
# This file controls default concretization preferences for Spack.
#
# Settings here are versioned with Spack and are intended to provide
# sensible defaults out of the box. Spack maintainers should edit this
# file to keep it current.
#
# Users can override these settings by editing the following files.
#
# Per-spack-instance settings (overrides defaults):
#   $SPACK_ROOT/etc/spack/packages.yaml
#
# Per-user settings (overrides default and site settings):
#   ~/.spack/packages.yaml
# -------------------------------------------------------------------------
packages:
  cmake:
   externals:
   - spec: cmake@3.23.0
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/cmake/3.23.0/gcc/7.3.0
  automake:
   externals:
   - spec: automake@1.16.5
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/automake/1.16.5/gcc/7.3.0
  autoconf:
   externals:
   - spec: autoconf@2.69
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/autoconf/2.69/gcc/7.3.0
  diffutils:
   externals:
   - spec: diffutils@3.8
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/diffutils/3.8/gcc/7.3.0
  perl:
   externals:
   - spec: perl@5.34.1
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/perl/5.34.1/gcc/7.3.0
  tar:
   externals:
   - spec: tar@1.34
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/tar/1.34/gcc/7.3.0
  gettext:
   externals:
   - spec: gettext@0.21
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/gettext/0.21/gcc/7.3.0
  libunwind:
   externals:
   - spec: libunwind@1.6.2
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/libunwind/1.6.2/gcc/7.3.0
  m4:
   externals:
   - spec: m4@1.4.19
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/m4/1.4.19/gcc/7.3.0
  bison:
   externals:
   - spec: bison@3.8.2
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/bison/3.8.2/gcc/7.3.0
  all:
    compiler: [gcc, intel, pgi, clang, xl, nag, fj, aocc]
    providers:
      awk: [gawk]
      blas: [openblas, amdblis]
      D: [ldc]
      daal: [intel-daal]
      elf: [elfutils]
      fftw-api: [fftw, amdfftw]
      flame: [libflame, amdlibflame]
      fuse: [libfuse]
      gl: [glx, osmesa]
      glu: [mesa-glu, openglu]
      golang: [go, gcc]
      go-external-or-gccgo-bootstrap: [go-bootstrap, gcc]
      iconv: [libiconv]
      ipp: [intel-ipp]
      java: [openjdk, jdk, ibm-java]
      jpeg: [libjpeg-turbo, libjpeg]
      lapack: [openblas, amdlibflame]
      libglx: [mesa+glx, mesa18+glx]
      libllvm: [llvm]
      libosmesa: [mesa+osmesa, mesa18+osmesa]
      lua-lang: [lua, lua-luajit-openresty, lua-luajit]
      luajit: [lua-luajit-openresty, lua-luajit]
      mariadb-client: [mariadb-c-client, mariadb]
      mkl: [intel-mkl]
      mpe: [mpe2]
      mpi: [openmpi, mpich]
      mysql-client: [mysql, mariadb-c-client]
      opencl: [pocl]
      onedal: [intel-oneapi-dal]
      pbs: [openpbs, torque]
      pil: [py-pillow]
      pkgconfig: [pkgconf, pkg-config]
      rpc: [libtirpc]
      scalapack: [netlib-scalapack, amdscalapack]
      sycl: [hipsycl]
      szip: [libaec, libszip]
      tbb: [intel-tbb]
      unwind: [libunwind]
      uuid: [util-linux-uuid, libuuid]
      xxd: [xxd-standalone, vim]
      yacc: [bison, byacc]
      ziglang: [zig]
    permissions:
      read: world
      write: user



  6. Source SPACK to your environment:

    Code Block
    source spack/share/spack/setup-env.sh


  7. Install Python: 

    Code Block
    spack install python@3.9.10 +tkinter %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  8. Install py-matplotlib: 

    Code Block
    spack install --fail-fast py-matplotlib backend=tkagg %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  9. Install py-cython: 

    Code Block
    spack install --fail-fast py-cython %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  10. Install py-pyyaml: 

    Code Block
    spack install --fail-fast py-pyyaml %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  11. Install py-scipy: 

    Code Block
    spack install --fail-fast py-scipy %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"

    During this installation you should get an error: 

    Code Block
    pip._internal.exceptions.InstallationError: Could not build wheels for scipy, which is required to install pyproject.toml-based projects


 Solution

After many attempts and tests, a solution was found. The py-scipy package must be the first Python package to be installed before any other.

  1. Log in to Marconi cluster

  2. Load intel/pe-xe-2020–binary module

    Code Block
    module load intel/pe-xe-2020--binary


  3. Load intelmpi/2020--binary module 

    Code Block
    module load intelmpi/2020--binary


  4. Clone spack repository

    Code Block
    git clone https://github.com/spack/spack.git


  5. To ensure the same environment set the packages.yaml file as below. This only adds packages marked as external:

    Expand

    the packages.yaml is located here: 

    Code Block
    vim ./spack/etc/spack/defaults/packages.yaml

    And it should have following body:

    Code Block
    # -------------------------------------------------------------------------
# This file controls default concretization preferences for Spack.
#
# Settings here are versioned with Spack and are intended to provide
# sensible defaults out of the box. Spack maintainers should edit this
# file to keep it current.
#
# Users can override these settings by editing the following files.
#
# Per-spack-instance settings (overrides defaults):
#   $SPACK_ROOT/etc/spack/packages.yaml
#
# Per-user settings (overrides default and site settings):
#   ~/.spack/packages.yaml
# -------------------------------------------------------------------------
packages:
  cmake:
   externals:
   - spec: cmake@3.23.0
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/cmake/3.23.0/gcc/7.3.0
  automake:
   externals:
   - spec: automake@1.16.5
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/automake/1.16.5/gcc/7.3.0
  autoconf:
   externals:
   - spec: autoconf@2.69
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/autoconf/2.69/gcc/7.3.0
  diffutils:
   externals:
   - spec: diffutils@3.8
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/diffutils/3.8/gcc/7.3.0
  perl:
   externals:
   - spec: perl@5.34.1
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/perl/5.34.1/gcc/7.3.0
  tar:
   externals:
   - spec: tar@1.34
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/tar/1.34/gcc/7.3.0
  gettext:
   externals:
   - spec: gettext@0.21
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/gettext/0.21/gcc/7.3.0
  libunwind:
   externals:
   - spec: libunwind@1.6.2
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/libunwind/1.6.2/gcc/7.3.0
  m4:
   externals:
   - spec: m4@1.4.19
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/m4/1.4.19/gcc/7.3.0
  bison:
   externals:
   - spec: bison@3.8.2
     prefix: /marconi/home/userexternal/msmukows/spackdir/libs/bison/3.8.2/gcc/7.3.0
  all:
    compiler: [gcc, intel, pgi, clang, xl, nag, fj, aocc]
    providers:
      awk: [gawk]
      blas: [openblas, amdblis]
      D: [ldc]
      daal: [intel-daal]
      elf: [elfutils]
      fftw-api: [fftw, amdfftw]
      flame: [libflame, amdlibflame]
      fuse: [libfuse]
      gl: [glx, osmesa]
      glu: [mesa-glu, openglu]
      golang: [go, gcc]
      go-external-or-gccgo-bootstrap: [go-bootstrap, gcc]
      iconv: [libiconv]
      ipp: [intel-ipp]
      java: [openjdk, jdk, ibm-java]
      jpeg: [libjpeg-turbo, libjpeg]
      lapack: [openblas, amdlibflame]
      libglx: [mesa+glx, mesa18+glx]
      libllvm: [llvm]
      libosmesa: [mesa+osmesa, mesa18+osmesa]
      lua-lang: [lua, lua-luajit-openresty, lua-luajit]
      luajit: [lua-luajit-openresty, lua-luajit]
      mariadb-client: [mariadb-c-client, mariadb]
      mkl: [intel-mkl]
      mpe: [mpe2]
      mpi: [openmpi, mpich]
      mysql-client: [mysql, mariadb-c-client]
      opencl: [pocl]
      onedal: [intel-oneapi-dal]
      pbs: [openpbs, torque]
      pil: [py-pillow]
      pkgconfig: [pkgconf, pkg-config]
      rpc: [libtirpc]
      scalapack: [netlib-scalapack, amdscalapack]
      sycl: [hipsycl]
      szip: [libaec, libszip]
      tbb: [intel-tbb]
      unwind: [libunwind]
      uuid: [util-linux-uuid, libuuid]
      xxd: [xxd-standalone, vim]
      yacc: [bison, byacc]
      ziglang: [zig]
    permissions:
      read: world
      write: user



  6. Source SPACK to your environment:

    Code Block
    source spack/share/spack/setup-env.sh


  7. Install Python: 

    Code Block
    spack install python@3.9.10 +tkinter %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  8. Install py-scipy: 

    Code Block
    spack install --fail-fast py-scipy %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  9. Install py-matplotlib: 

    Code Block
    spack install --fail-fast py-matplotlib backend=tkagg %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  10. Install py-cython: 

    Code Block
    spack install --fail-fast py-cython %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


  11. Install py-pyyaml: 

    Code Block
    spack install --fail-fast py-pyyaml %intel@19.1.3.304 cflags="-fPIC" cxxflags="-fPIC" cppflags="-fPIC"


 BLITZ and missing -pthread flag

After installing all dependencies, the very next step is to install IMAS itself. During this installation the cpp interface component is complaining about blitz not being compiled in thread-safe  manner and suggests that maybe the -pthread flag was missing during Blitz compilation/installation. The bad news is that the whole eco-system was compiled using at least those two flags: '-fPIC -pthread', therefore the error is confusing.