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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. Below you can find an error message from reproduction attempt: 

Code Block
make -C ./src/3.36.0/ual/4.10.1/examples/cpp all || exit 1
make[2]: Entering directory `/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/examples/cpp'
icpc `pkg-config blitz --cflags` -I/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/cppinterface/src -I/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/lowlevel -g -O0 -fPIC -shared-intel -c test_pulse_create.cpp
In file included from /marconi_work/FUSIO_HLST/switmdir/libs-intel/blitz/1.0.1/intel/19.1.3.304/hftjglypfr4ovoej6dkxwuedupjqez3m/include/blitz/array-impl.h(46),
                 from /marconi_work/FUSIO_HLST/switmdir/libs-intel/blitz/1.0.1/intel/19.1.3.304/hftjglypfr4ovoej6dkxwuedupjqez3m/include/blitz/array.h(37),
                 from /marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/cppinterface/src/UALDef.h(30),
                 from /marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/cppinterface/src/UALClasses.h(7),
                 from test_pulse_create.cpp(1):
/marconi_work/FUSIO_HLST/switmdir/libs-intel/blitz/1.0.1/intel/19.1.3.304/hftjglypfr4ovoej6dkxwuedupjqez3m/include/blitz/blitz.h(152): error: #error directive: Blitz is configured with --enable-threadsafe, but no compiler thread support is found. Did you forget, e.g., "--pthread"?
     #error Blitz is configured with --enable-threadsafe, but no compiler thread support is found. Did you forget, e.g., "--pthread"?
      ^

compilation aborted for test_pulse_create.cpp (code 2)
make[2]: *** [test_pulse_create.o] Error 2
make[2]: Leaving directory `/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/examples/cpp'
make[1]: *** [examples/cpp] Error 1
make[1]: Leaving directory `/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer'
make: *** [all] Error 2

As you can see for some reason IMAS is complaining on Blitz being compiled with --enable-threadsafe flag but at the same time no thread support for compiler is found: 

Code Block
/marconi_work/FUSIO_HLST/switmdir/libs-intel/blitz/1.0.1/intel/19.1.3.304/hftjglypfr4ovoej6dkxwuedupjqez3m/include/blitz/blitz.h(152): error: #error directive: Blitz is configured with --enable-threadsafe, but no compiler thread support is found. Did you forget, e.g., "--pthread"?
     #error Blitz is configured with --enable-threadsafe, but no compiler thread support is found. Did you forget, e.g., "--pthread"?

 How to reproduce issue

To avoid installing whole IMAS-Spack eco-system from scratch a minimal working example was prepared. This just takes the part of the IMAS code and tries to compile it the very same way as the IMAS installer does it.

  1. Log in to Marconi cluster

  2. Prepare $MODULEPATH thus the imasenv module can be found and loaded: 

    Code Block
    module use /marconi/home/userexternal/msmukows/public/modules


  3. Load imasenv/3.36.0/intel/2020-test module

    Code Block
    module load imasenv/3.36.0/intel/2020-test


  4. Navigate to the directory with example code:

    Code Block
    cd /marconi_work/FUSIO_HLST/testdir/tests/blitz_pthread_issue_intel_2020


  5. There should be a file named: "test_pulse_create.cpp":


    Code Block
    .
└── test_pulse_create.cpp


  6. Now execute compilation command:

    Code Block
    icpc `pkg-config blitz --cflags` -I/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/cppinterface/src -I/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/lowlevel -g -O0 -fPIC -shared-intel -c test_pulse_create.cpp

    You should see the very same error message as above - Blitz -pthread error

 Solution

After a long search a solution has been found, however it is not very elegant. Requires editing pkg-config for Blitz, which by default is prepared by SPACK. 

The change is subtle and affects only CFLAGS which should look like this:

Code Block
Cflags: -I${includedir} -pthread

Below is a before and after comparison:

Vanilla Blitz's pkg-config - provided by SPACKChanged pkg-config for Blitz


Code Block
# generated by configure / remove this line to disable regeneration
prefix=/marconi_work/FUSIO_HLST/switmdir/libs-intel/blitz/1.0.1/intel/19.1.3.304/hftjglypfr4ovoej6dkxwuedupjqez3m
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include

Name: blitz
Description: blitz Library
Version: 0.10
Requires:
Libs: -L${libdir} -lblitz
Cflags: -I${includedir}



Code Block
# generated by configure / remove this line to disable regeneration
prefix=/marconi_work/FUSIO_HLST/switmdir/libs-intel/blitz/1.0.1/intel/19.1.3.304/hftjglypfr4ovoej6dkxwuedupjqez3m
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include

Name: blitz
Description: blitz Library
Version: 0.10
Requires:
Libs: -L${libdir} -lblitz
Cflags: -I${includedir} -pthread


The above solution acts the same way as adding the -pthread flag explicitly to the compilation command in point 6 at 2.1 How to reproduce issue, something like below: 

Code Block
icpc `pkg-config blitz --cflags` -I/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/cppinterface/src -I/marconi_work/FUSIO_HLST/msmukows/IMAS_INSTALLER/intel_installer/src/3.36.0/ual/4.10.1/lowlevel -g -O0 -fPIC -shared-intel -c -pthread test_pulse_create.cpp