Compiling PUMGen with spack in Shaheen II

[Tariq97]

Describe the issue.

I tried compiling PUMGen with spack with simmetrix on Shaheen II and results in the following error.
The process followed is from here https://github.com/SeisSol/PUMGen/wiki/How-to-compile-PUMGen
It works fine without simmetrix support.

Warning: Missing a source id for pumgen@develop
==> cmake@3.22.1 : has external module in ['cmake/3.22.1']
[+] /sw/xc40cle7up03/cmake/3.22.1/sles15gcc7.5.0 (external cmake-3.22.1-qjzmxoytejx2kwaimenr4ujer6vt4pvk)
==> mpich@7.7.20 : has external module in ['cray-mpich/7.7.20']
[+] /opt/cray/pe/mpt/7.7.20/gni/mpich-gnu/8.2 (external mpich-7.7.20-bp2ketiytzqupkh6d2fxcrmq4yjmvrmy)
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pkgconf-1.8.0-dmhzeibcqxi6yg4exzxag33jfqujas4u
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zlib-1.2.12-2iy6zo4llskya72xxnv4r52nko77n5yr
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/libsigsegv-2.13-7nszos2mb27ryu723ecv6qywsmleytbn
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/berkeley-db-18.1.40-f6yqlyfh7wjo5z6w4qqjmmtd7cczhjcz
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/libiconv-1.16-7kytbtbz2kbbhrqgk4op6n3p4pc65ydi
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/unzip-6.0-5rypjotvucn7ybwg4rg2i53nsx53audx
[+] /project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/ (external MeshSimAdvanced-17.0-230211-rqnbybfe2gixxb24a7iljmbxv2pks3ck)
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/metis-5.1.0-bg7sv5uhluisethpqx4ucwmdhdyc6374
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/yaml-cpp-0.6.2-pfuf254e5xskpx633r5yfrv7vdzzdsdq
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/ncurses-6.2-ogfyosttxxa2nnd5bhe2gz6eqbypyclw
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/hdf5-1.12.2-aeb4we5wlzg6eihfbs7qnccorsjjf5yp
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/m4-1.4.19-elt3djcwlagzqn7hh7fy5sxwu66yiclc
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/diffutils-3.8-vzww3xpckh42iwf7pj6ajo5xrb4srit2
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/parmetis-4.0.3-gnfpqd6nkjjg4am2rxzlb2iolrun2ufc
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/readline-8.1-ny5b7atuia442wolp6bsjk3fj4hhl73w
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/libtool-2.4.7-kh54yxuwrtgpgzgh47qnwvctwkqtxuwp
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/netcdf-c-4.7.4-jh5i74zk7ddgb56axyivuwzpxyzxxw2g
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/bzip2-1.0.8-ebhtdwpuvbsgxmmtugns5aydyzi67bp7
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/gdbm-1.19-2imglgcvgz5avog5nkzfs7r6vh4sjbjc
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/perl-5.34.1-oy5gobc3rknssbkfgqk7qcoglsznf2sj
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/autoconf-2.69-s5tnyypge46n3dzdug3ld6loq6ifuvg3
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/openssl-1.1.1o-3epcw2my3ryqvnqraxjfzsgz2zv5hebn
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/automake-1.16.5-hmdsbthd6hupeae5oyw5x7o3yo3wtmp6
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/curl-7.83.0-y6rehiyz46rug2hznic6kg54n2qndpk7
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/numactl-2.0.14-sadzwhwiktstycpaauiznlenepqs2f7s
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zoltan-3.83-pdznfhwg7f4vopqjyhblwetjmovwmz3r
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/lua-5.3.2-jbld6b5jyg7rrteuaobsxayf7bipg4yd
[+] /lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/asagi-1.0.1-4y25gc35plzxmiguxh44zhcunjatmezj
==> Installing pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw
==> No binary for pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw found: installing from source
==> Using cached archive: /lustre2/project/k1589/aquibt/myLibs/spack/var/spack/cache/_source-cache/git//SCOREC/core.git/a295720d7b4828282484f2b78bac1f6504512de4.tar.gz
==> Warning: Fetching from mirror without a checksum!
  This package is normally checked out from a version control system, but it has been archived on a spack mirror.  This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure!
==> No patches needed for pumi
==> pumi: Executing phase: 'cmake'
==> Error: ProcessError: Command exited with status 1:
    'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DBUILD_TESTING:BOOL=OFF' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON' '-DCMAKE_INSTALL_RPATH:STRING=/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/lib64;/opt/cray/pe/mpt/7.7.20/gni/mpich-gnu/8.2/lib;/project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zoltan-3.83-pdznfhwg7f4vopqjyhblwetjmovwmz3r/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/metis-5.1.0-bg7sv5uhluisethpqx4ucwmdhdyc6374/lib;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/parmetis-4.0.3-gnfpqd6nkjjg4am2rxzlb2iolrun2ufc/lib;/opt/gcc/11.2.0/snos' '-DCMAKE_PREFIX_PATH:STRING=/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/zoltan-3.83-pdznfhwg7f4vopqjyhblwetjmovwmz3r;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/parmetis-4.0.3-gnfpqd6nkjjg4am2rxzlb2iolrun2ufc;/lustre2/project/k1589/aquibt/myLibs/spack/opt/spack/cray-cnl7-broadwell/gcc-11.2.0/metis-5.1.0-bg7sv5uhluisethpqx4ucwmdhdyc6374;/project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/;/opt/cray/pe/mpt/7.7.20/gni/mpich-gnu/8.2;/sw/xc40cle7up03/cmake/3.22.1/sles15gcc7.5.0' '-DSCOREC_CXX_WARNINGS=OFF' '-DENABLE_ZOLTAN:BOOL=ON' '-DCMAKE_C_COMPILER=/lustre2/project/k1589/aquibt/myLibs/spack/lib/spack/env/gcc/gcc' '-DCMAKE_CXX_COMPILER=/lustre2/project/k1589/aquibt/myLibs/spack/lib/spack/env/gcc/g++' '-DBUILD_SHARED_LIBS:BOOL=OFF' '-DCMAKE_Fortran_COMPILER=/lustre2/project/k1589/aquibt/myLibs/spack/lib/spack/env/gcc/gfortran' '-DPUMI_FORTRAN_INTERFACE:BOOL=OFF' '-DMDS_ID_TYPE=long' '-DSKIP_SIMMETRIX_VERSION_CHECK=ON' '-DIS_TESTING:BOOL=OFF' '-DMESHES=/tmp/aquibt/spack-stage/spack-stage-pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/spack-src/pumi-meshes' '-DENABLE_SIMMETRIX=ON' '-DSIM_DISCRETE=ON' '-DSIM_MPI=mpich7' '/tmp/aquibt/spack-stage/spack-stage-pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/spack-src'

1 error found in build log:
     37    -- ENABLE_SIMMETRIX: ON
     38    -- ENABLE_OMEGA_H: OFF
     39    -- ENABLE_FPP: OFF
     40    -- Skipping Simmetrix SimModSuite version check. This may result in undefined behavior
     41    -- Building with SimModSuite 17.0.230211
     42    -- SIM_ARCHOS x64_rhel7_gcc48
  >> 43    CMake Error at cmake/FindSimModSuite.cmake:33 (message):
     44      simmetrix library SimPartitionWrapper-mpich7 not found in
     45    Call Stack (most recent call first):
     46      cmake/FindSimModSuite.cmake:167 (simLibCheck)
     47      CMakeLists.txt:114 (find_package)
     48    
     49    

See build log for details:
  /tmp/aquibt/spack-stage/spack-stage-pumi-2.2.7-dc77sgihmwnw4pz2au6hu7yssmepekbw/spack-build-out.txt

To reproduce

1. Simmodeler (17.0-230211) installed from http://www.simmetrix.com/index.php/support/support-downloads/download-release?prod=M&release=17.0-230211

2. All zip files are combined using

for filename in *.tgz
do
  tar zxf $filename
done

3. Loaded modules on Shaheeen II

  1) modules/3.2.11.4                                 16) pmi/5.0.17
  2) craype-network-aries                             17) dmapp/7.1.1-7.0.3.1_3.49__g93a7e9f.ari
  3) cray-mpich/7.7.18                                18) gni-headers/5.0.12.0-7.0.3.1_3.32__gd0d73fe.ari
  4) slurm/slurm                                      19) xpmem/2.2.27-7.0.3.1_3.31__gada73ac.ari
  5) dws/3.0.36-7.0.3.1_3.55__g6985c90.ari            20) job/2.2.4-7.0.3.1_3.40__g36b56f4.ari
  6) eproxy/2.0.24-7.0.3.1_3.25__g8e04b33.ari         21) dvs/2.12_2.2.224-7.0.3.1_3.50__gc77db2af
  7) craype-haswell                                   22) alps/6.6.67-7.0.3.1_3.48__gb91cd181.ari
  8) xalt/1.1.2                                       23) rca/2.2.20-7.0.3.1_3.53__g8e3fb5b.ari
  9) darshan/3.3.1                                    24) atp/3.14.5
 10) ksl/ksl                                          25) perftools-base/21.09.0
 11) gcc/11.2.0                                       26) PrgEnv-gnu/6.0.10
 12) craype/2.7.10                                    27) python/3.10.1-cdl
 13) cray-libsci/20.09.1                              28) cmake/3.26.4
 14) udreg/2.3.2-7.0.3.1_3.50__g5f0d670.ari           29) seissol-env-develop-gcc-11.2.0-q7rdeu3
 15) ugni/6.0.14.0-7.0.3.1_6.31__g8101a58.ari

4. Edited /.spack/packages.yaml file

packages:
  simmetrix-simmodsuite:
    externals:
    - spec: simmetrix-simmodsuite@17.0-230211
      prefix: /project/k1589/aquibt/myLibs/meshing_software/simmodeler/17.0-230211/

I do not see any simmetrix-simmodsuite@17.0230211 file in simmodeler directory.

[Thomas-Ulrich]

Hi,
The problem is at this line:
https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/pumi/package.py#L100
spack tries to find the libSimPartitionWrapper adapted to your mpi:
But it seems you are using cray-mpich version 7, and there is no such a file as libSimPartitionWrapper-mpich7.a

(base) ulrich@heisenbug:~$ ls /import/heisenbug-dump/ulrich/myLibs/SimLib/17.0-220511/lib/x64_rhel8_gcc83/
acisKrnl  libSimAbstract.a  libSimAdvMeshing.a  libSimField.a    libSimMeshing.a    libSimModel.a         libSimPartitionedMesh.a      libSimPartitionWrapper.a         libSimPartitionWrapper-openmpi3.a
psKrnl    libSimAcis2021.a  libSimDiscrete.a    libSimLicense.a  libSimMeshTools.a  libSimParasolid330.a  libSimPartitionedMesh-mpi.a  libSimPartitionWrapper-mpich3.a  libSimPartitionWrapper-openmpi4.a

you can try to manually change the line and see if that works:
mpi_id = spec["mpi"].name + '3'

[Tariq97]

Hi,

Thank you for your reply and sorry for my late response.
The change you mentioned doesn't solve the issue. The same error as above is found.

Thanks,
Tariq