[petsc-users] Symbol lookup errors after change of module system on cluster

[Matthias Hesselmann]

Dear users,

since the operating system of the cluster I am running my application on with PETSC (Version 3.19) has been changed from CentOS 7 to Rocky Linux 8 and also the module system has been changed to Lmod, I get the following error message when running my application:

Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
mpiexec noticed that process rank 0 with PID 0 on node login18-x-2 exited on signal 15 (Terminated).
make: *** [Makefile:96: cathode-run] Error 143

When running the application with LD_DEBUG=files, it says that certain symbols cannot be looked up by PETSC, e.g.:

/cvmfs/software.hpc.rwth.de/Linux/RH8/x86_64/intel/skylake_avx512/software/UCX/1.12.1-GCCcore-11.3.0/lib/ucx/libuct_cma.so.0: error: symbol lookup error: undefined symbol: ucs_module_global_init (fatal)
[...]
/rwthfs/rz/cluster/home/mh787286/petsc/arch-linux-c-debug/lib/libpetsc.so.3.19: error: symbol lookup error: undefined symbol: MPID_Abort (fatal)
/rwthfs/rz/cluster/home/mh787286/petsc/arch-linux-c-debug/lib/libpetsc.so.3.19: error: symbol lookup error: undefined symbol: ps_tool_initialize (fatal)

I attached the output in the "LD_DEBUG_make_cathode-run" file. When I look up the dependencies of libpetsc.so.3.19 with the ldd  command, I can find the locations of the dependent libraries listed in the LD_LIBRARY_PATH (see configure.log). Thus, PETSC should be able to link to these libraries.

I load the modules GCC/11.3.0 and OpenMPI/4.1.4. Furthermore, please also find the make file attached as "Makefile" as well as the configure.log and make.log.

Is there anything I need to change in the make file to adapt it to the new module system, or are there any issues with missing links/ libraries after the update?

Kind regards,
Matthias


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