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Installation issue: gdal #12586

@omsai

Description

@omsai

@adamjstewart if I understand the error correctly, it appears that if any of gdal's dependencies have MPI enabled, MPI must be loaded for libgdal to link correctly. Specifically, I propose we add an mpi variant to gdal and maybe couple it to enable/disable all the mpi aware dependencies of gdal. Does that make sense? If so I can create a pull request with the change.

Steps to reproduce the issue

$ spack env status
==> Using spack.yaml in current directory: /shared/stormcenter/Shen/src/MEX-2.3.0
$ spack install  # see spack.yaml below
...
  >> 3041    /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
             al.so: undefined reference to `ompi_mpi_cxx_op_intercept'
  >> 3042    /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
             al.so: undefined reference to `MPI::Datatype::Free()'
  >> 3043    /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
             al.so: undefined reference to `MPI::Comm::Comm()'
  >> 3044    /tmp/xis14008/spack-stage/spack-stage-5eNDNt/spack-src/.libs/libgd
             al.so: undefined reference to `MPI::Win::Free()'
  >> 3045    collect2: error: ld returned 1 exit status
  >> 3046    make[1]: *** [gdalinfo] Error 1
     3047    make[1]: *** Waiting for unfinished jobs....
     3048    make[1]: Leaving directory `/tmp/xis14008/spack-stage/spack-stage-
             5eNDNt/spack-src/apps'
  >> 3049    make: *** [apps-target] Error 2

See build log for details:
  /shared/stormcenter/Shen/src/spack/var/spack/stage/gdal-3.0.1-4mvstpuneibqvhr45imvl3waobwa5hx6/spack-build-out.txt

Attached the full log file [2.3 MB]: spack-build-out.txt

Platform and user environment

Please report your OS here:

$ uname -a 
Linux cn01 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Nov 23 16:03:01 EST 2016 x86_64 x86_64 x86_64 GNU/Linux
$ lsb_release -d
Description:    Red Hat Enterprise Linux Server release 6.7 (Santiago)
# ~/.spack/linux/compilers.yaml
compilers:
- compiler:
    environment: {}
    extra_rpaths: []
    flags: {}
    modules: []
    operating_system: rhel6
    paths:
      cc: /usr/bin/gcc
      cxx: /usr/bin/g++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    spec: [email protected]
    target: x86_64
- compiler:
    environment: {}
    extra_rpaths: []
    flags: {}
    modules: []
    operating_system: rhel6
    paths:
      cc: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/gcc
      cxx: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/g++
      f77: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/gfortran
      fc: /shared/stormcenter/Shen/src/spack/opt/spack/linux-rhel6-x86_64/gcc-4.4.7/gcc-6.3.0-m5d7f4djpmzkxwvwe2ggpqj2bl44enm6/bin/gfortran
    spec: [email protected]
    target: x86_64
# spack.yaml

# This is a Spack Environment file.
#
# It describes a set of packages to be installed, along with
# configuration settings.
spack:
  # add package specs to the `specs` list
  specs:
  - gdal +hdf4 +hdf5 +jasper +netcdf +crypto +grib +curl ^hdf5 +hl ^openmpi +pmi fabrics=auto
    %[email protected]
  view: false
  mirrors: {}
  repos: []
  upstreams: {}
  modules:
    enable: []
  definitions: []
  packages:
    cmake:
      buildable: false
      paths:
        [email protected]: /apps2/cmake/3.10.2
      version: []
      providers: {}
      modules: {}
      compiler: []
    gmake:
      buildable: false
      paths:
        [email protected]: /usr
      version: []
      providers: {}
      modules: {}
      compiler: []
  config: {}

Additional information

$ spack concretize -f
==> Concretized gdal+crypto+curl+grib+hdf4+hdf5+jasper+netcdf ^hdf5+hl ^openmpi%[email protected] fabrics=auto +pmi
 -   4mvstpu  [email protected]%[email protected]~armadillo~cfitsio+crypto~cryptopp+curl~expat~geos~gif+grib+hdf4+hdf5+jasper~java+jpeg~kea~libiconv+liblzma+libtool+libz~mdb+netcdf~odbc~opencl~openjpeg~pcre~perl~pg~png~poppler+proj~python~qhull~sosi~sqlite3~xerces~xml2~zstd arch=linux-rhel6-x86_64
[+]  4vx5fvr      ^[email protected]%[email protected]~darwinssl~gssapi~libssh~libssh2~nghttp2 arch=linux-rhel6-x86_64
[+]  b6r6fnb          ^[email protected]%[email protected]+systemcerts arch=linux-rhel6-x86_64
[+]  w4idrsb              ^[email protected]%[email protected]+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-rhel6-x86_64
[+]  qn2pvbe                  ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  gt74ike                      ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  rqwrhpn                          ^[email protected]%[email protected]~symlinks~termlib arch=linux-rhel6-x86_64
[+]  cmluutb                              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  rjqs3cq              ^[email protected]%[email protected]+optimize+pic+shared arch=linux-rhel6-x86_64
[+]  yyiyegm      ^[email protected]%[email protected]~guile+nls patches=ca60bd9c1a1b35bc0dc58b6a4a19d5c2651f7a94a4b22b2c5ea001a1ca7a8a7f arch=linux-rhel6-x86_64
[+]  lyr63eg      ^[email protected]%[email protected]~szip arch=linux-rhel6-x86_64
[+]  hseynw6          ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  iej2wmo              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  opcp74a              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  twor3y6                  ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-rhel6-x86_64
[+]  x33qfwi                      ^[email protected]%[email protected]+shared arch=linux-rhel6-x86_64
[+]  mw4lps6                      ^[email protected]%[email protected]~python arch=linux-rhel6-x86_64
[+]  aso4k7z                          ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  o2xme3g                          ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  hhxm2xj                      ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  h3gzxvn              ^[email protected]%[email protected] patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-rhel6-x86_64
[+]  kuyi76p                  ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  jay4qjn          ^[email protected]%[email protected]+lex patches=09c22e5c6fef327d3e48eb23f0d610dcd3a35ab9207f12e0f875701c677978d3 arch=linux-rhel6-x86_64
[+]  3crh7lk              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  6j77nxv              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  of3s2pk              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  pu7o7ls          ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  enxs2ae              ^[email protected]%[email protected]~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-rhel6-x86_64
[+]  5f2wqfv              ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  u2ffeby      ^[email protected]%[email protected]~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-rhel6-x86_64
[+]  oxprqis          ^[email protected]%[email protected]~cuda+cxx_exceptions fabrics=auto ~java~legacylaunchers~memchecker+pmi schedulers=none ~sqlite3~thread_multiple+vt arch=linux-rhel6-x86_64
[+]  njk5j57              ^[email protected]%[email protected]~cairo~cuda~gl+libxml2~nvml+pci+shared arch=linux-rhel6-x86_64
[+]  bkmqzbd                  ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  5u6bbgi                      ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  nxxlgnc                  ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  e2ecn35      ^[email protected]%[email protected] build_type=Release +jpeg~opengl patches=95a654159688eaffdf035a467914c5953068ad0fd62d18229de5779a17ec380b,db104400a2e72f610b8fa4d061a32282254819c70b024ef1cf99fef64aca67e3 +shared arch=linux-rhel6-x86_64
[+]  qsmbnxo      ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  l5srte6      ^[email protected]%[email protected]+jpeg patches=9485efc0a62a02207d34ac0c4d22e421c975b6ce85397c5e557c0105a232aaa3,ac81bd50db5950b42e48de78845ad91c60bc107ccaa1acd78836e03fdf4a2313,e0d45d3c34bf92df2d1d140957f110dc84759420e68a97e1e3d6ab90c81777d8 +proj+zlib arch=linux-rhel6-x86_64
[+]  poxlp53          ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  25tmaus          ^[email protected]%[email protected] arch=linux-rhel6-x86_64
[+]  qpmcb6k              ^[email protected]%[email protected]+fts~functions arch=linux-rhel6-x86_64
[+]  gxgix6l      ^[email protected]%[email protected]~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf patches=10a1c3f7fa05e2c82457482e272bbe04d66d0047b237ad0a73e87d63d848b16c +pic+shared arch=linux-rhel6-x86_64

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