MOOSE on copenhagen university HPC #28805
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AndreasHjortsoe
asked this question in
Q&A Getting Started
Replies: 2 comments 6 replies
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Hello Can you please attach the logs for building petsc (if you think there were issues), libmesh (there is a configure.log) that should help and moose? |
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I'm actually local up at DTU. Are you using Niflheim? If so, I can probably help out. |
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Issue or question about MOOSE
Issue description
I am trying to install MOOSE on a HPC cluster in copenhagen.
I initialize with:
When i run "./update_and_rebuild_petsc.sh":
When i run "./update_and_rebuild_libmesh.sh":
i got errors, showing that there was no available MPI_Comm, indicating that there are issues with libmesh finding my MPI.
Now i can run "./update_and_rebuild_wasp.sh", and make without errors.
Running tests
After running make, i tried ./run_tests, which yeilded 51/51 failed tests. Can anyone help with troubleshooting please?
Output from running ./run_tests -i always_bad: i am unsure why it takes so long to run. Yesterday it ran much faster, but today it is slow. Yesterday i got CODE 1 error for both, instead of the TIMEOUT error.
Diagnostics output - i see nothing out of the ordinary here, but there might be
####################################################################################################
Influential Environment Variables
CC=mpicc
CONDA_CHANNEL=https://conda.software.inl.gov/public
CURL_CA_BUNDLE=
CXX=mpicxx
F77=mpif77
F90=mpif90
FC=mpif90
FI_PROVIDER=tcp
HDF5_DIR=/usr
LD_LIBRARY_PATH=/usr/lib64/mpich/lib
MODULESHOME=/usr/share/lmod/lmod
MOOSE_JOBS=6
PATH=/usr/lib64/mpich/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/groups/hep/hjortso/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
####################################################################################################
Compiler(s) (CC CXX FC F77 F90):
which $CC; /usr/lib64/mpich/bin/mpicc
$CC --version; gcc (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)
$CC -show; gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -I/usr/include/mpich-x86_64 -L/usr/lib64/mpich/lib -Wl,-rpath -Wl,/usr/lib64/mpich/lib -Wl,--enable-new-dtags -lmpi
which $CXX; /usr/lib64/mpich/bin/mpicxx
$CXX --version; g++ (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)
$CXX -show; g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -I/usr/include/mpich-x86_64 -L/usr/lib64/mpich/lib -lmpicxx -Wl,-rpath -Wl,/usr/lib64/mpich/lib -Wl,--enable-new-dtags -lmpi
which $FC; /usr/lib64/mpich/bin/mpif90
$FC --version; GNU Fortran (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)
$FC -show; gfortran -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -I/usr/include/mpich-x86_64 -I/usr/lib64/gfortran/modules/mpich -L/usr/lib64/mpich/lib -lmpifort -Wl,-rpath -Wl,/usr/lib64/mpich/lib -Wl,--enable-new-dtags -lmpi
which $F77; /usr/lib64/mpich/bin/mpif77
$F77 --version; GNU Fortran (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)
$F77 -show; gfortran -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -fallow-argument-mismatch -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -I/usr/include/mpich-x86_64 -I/usr/lib64/gfortran/modules/mpich -L/usr/lib64/mpich/lib -lmpifort -Wl,-rpath -Wl,/usr/lib64/mpich/lib -Wl,--enable-new-dtags -lmpi
which $F90; /usr/lib64/mpich/bin/mpif90
$F90 --version; GNU Fortran (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)
$F90 -show; gfortran -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -I/usr/include/mpich-x86_64 -I/usr/lib64/gfortran/modules/mpich -L/usr/lib64/mpich/lib -lmpifort -Wl,-rpath -Wl,/usr/lib64/mpich/lib -Wl,--enable-new-dtags -lmpi
OK
####################################################################################################
Python Sanity Checks
/usr/bin/env python3 --version; (reporting as: Python 3.9.18) matches
which python3 python;
/usr/bin/python3 --version; == Python 3.9.18
/usr/bin/python --version; == Python 3.9.18
OK
####################################################################################################
Python Modules (TestHarness, run-ability)
OK
checks PASSED
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