Spack Build Issues

2021-03-22

spack build of mfem on develop (ubuntu 18.04, python 2)

root@e405e7c5c09d:/build_test_non_cuda# spack debug report
* **Spack:** 0.9-17078-ef43ae1575
* **Python:** 2.7.17
* **Platform:** linux-ubuntu18.04-zen2
* **Concretizer:** original

###################################################################################################################################################################################### 100.0%
==> Error: UnicodeEncodeError: 'ascii' codec can't encode character u'\ufeff' in position 0: ordinal not in range(128)

/spack/var/spack/repos/builtin/packages/mfem/package.py:733, in patch:
        731    def patch(self):
        732        # Remove the byte order mark since it messes with some compilers
  >>    733        filter_file(u'\uFEFF', '', 'fem/gslib.hpp')
        734        filter_file(u'\uFEFF', '', 'fem/gslib.cpp')
        735        filter_file(u'\uFEFF', '', 'linalg/hiop.hpp')

cuda tangles, such as:

bin/spack spec raja+cuda
Input spec
--------------------------------
raja+cuda
Concretized
--------------------------------
==> Error: There are no valid versions for cuda that match ':'

if libxml2 is not an external package, the hwloc build fails. Solution: add libxml2 as external package in ci containers

2020-01

with clang on sierra, python builds w/o ctypes support: This causes py-setuptools to fail.

==> '/p/gpfs1/cyrush/2018.11.ascent.xlc/ascent/uberenv_libs/spack/opt/spack/linux-rhel7-ppc64le/clang-coral/python-2.7.15-nc4tjupjudvrdyck4mj53i33p3q4tk5u/bin/python2.7' '-s' 'setup.py' '--no-user-cfg' 'build'
Traceback (most recent call last):
  File "setup.py", line 11, in <module>
    import setuptools
  File "/tmp/cyrush/spack-stage/spack-stage-3MVWpq/setuptools-40.2.0/setuptools/__init__.py", line 16, in <module>
    from setuptools.dist import Distribution, Feature
  File "/tmp/cyrush/spack-stage/spack-stage-3MVWpq/setuptools-40.2.0/setuptools/dist.py", line 25, in <module>
    from setuptools import windows_support
  File "/tmp/cyrush/spack-stage/spack-stage-3MVWpq/setuptools-40.2.0/setuptools/windows_support.py", line 2, in <module>
    import ctypes
  File "/p/gpfs1/cyrush/2018.11.ascent.xlc/ascent/uberenv_libs/spack/opt/spack/linux-rhel7-ppc64le/clang-coral/python-2.7.15-nc4tjupjudvrdyck4mj53i33p3q4tk5u/lib/python2.7/ctypes/__init__.py", line 7, in <module>
    from _ctypes import Union, Structure, Array
ImportError: No module named _ctypes

with clang on sierra, fortran compiler wrappers aren't working, causing CMake's FindMPI to fail.

     35    -- Unable to determine MPI from MPI driver /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-clang-upstream-2018.12.03/bin/mpif90
  >> 36    CMake Error at /usr/WS1/cyrush/2019.01.conduit.build/conduit/scripts/uberenv_libs_test_lassen_clang/spack/opt/spack/linux-rhel7-ppc64le/clang-coral/cmake-3.9.6-mfftj4x3yhtwt57zc6dtfecvcflybkqy/sha
           re/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
     37      Could NOT find MPI_Fortran (missing: MPI_Fortran_LIBRARIES

On intel on cori, python+shared ends up with a python polluted by the system python:

import sys;from distutils.sysconfig import get_python_inc;sys.stdout.write(get_python_inc())
/usr/include/python2.7

2019/3/6

cori using gcc 5.3.0, fortran compiler does not work:

     24      cray-mpich, which is required by cray-libsci/18.07.1, is not available for the GNU compiler.
     25    -- Check for working Fortran compiler: /opt/cray/pe/craype/2.5.15/bin/ftn
     26    -- Check for working Fortran compiler: /opt/cray/pe/craype/2.5.15/bin/ftn  -- broken
  >> 27    CMake Error at /global/u1/c/cyrush/work/2019.03.ascent/ascent/uberenv_libs/spack/opt/spack/cray-cnl9-haswell/gcc-5.3.0/cmake-3.9.6-jgkufnm5ieooe3h22mbobtrr7r3byow5/share/cmake-3.9/Modu
           les/CMakeTestFortranCompiler.cmake:44 (message):
     28      The Fortran compiler "/opt/cray/pe/craype/2.5.15/bin/ftn" is not able to
     29      compile a simple test program.
     30    
     31      It fails with the following output:
     32    
     33       Change Dir: /global/u1/c/cyrush/work/2019.03.ascent/ascent/uberenv_libs/spack/var/spack/stage/conduit-master-3khzp27fj7zo5nsnwof6wpyilcyvqklu/conduit/spack-build/CMakeFiles/CMakeTmp

     ...

     53    
     54        cray-mpich, which is required by cray-libsci/18.07.1, is not available for the GNU compiler.