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SeisSol / PUMGen

Mesh generation for SeisSol
BSD 3-Clause "New" or "Revised" License
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Compiling PUMGen with spack in Shaheen II #56

Open Tariq97 opened 1 year ago

Tariq97 commented 1 year ago

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:

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

Thomas-Ulrich commented 1 year ago

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 commented 1 year ago

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