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pyiron / pyiron_atomistics

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.
https://pyiron-atomistics.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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LAMMPS job crash immediately "couldn't read file /mpcdf/soft/SLE_15/packages/x86_64/Modules/5.0.1/libexec/modulecmd.tcl" #1553

Closed lfzhu-phys closed 3 weeks ago

lfzhu-phys commented 1 month ago

I just tried to submit a few lammps jobs. They crash immediately with following error. Does anyone else also encounter these problem?

couldn't read file "/mpcdf/soft/SLE_15/packages/x86_64/Modules/5.0.1/libexec/modulecmd.tcl": no such file or directory couldn't read file "/mpcdf/soft/SLE_15/packages/x86_64/Modules/5.0.1/libexec/modulecmd.tcl": no such file or directory couldn't read file "/mpcdf/soft/SLE_15/packages/x86_64/Modules/5.0.1/libexec/modulecmd.tcl": no such file or directory [cmti093:37763] OPAL ERROR: Unreachable in file pmix3x_client.c at line 111

The application appears to have been direct launched using "srun", but OMPI was not built with SLURM's PMI support and therefore cannot execute. There are several options for building PMI support under SLURM, depending upon the SLURM version you are using:

version 16.05 or later: you can use SLURM's PMIx support. This requires that you configure and build SLURM --with-pmix.

Versions earlier than 16.05: you must use either SLURM's PMI-1 or PMI-2 support. SLURM builds PMI-1 by default, or you can manually install PMI-2. You must then build Open MPI using --with-pmi pointing to the SLURM PMI library location.

niklassiemer commented 1 month ago

What version of lammps did you use? Can you usually load the modules stated therein?

lfzhu-phys commented 1 month ago

@niklassiemer Thanks a lot for looking into it. I just tested one job it works again. Did you do anything on the cluster? If not, the only difference is that yesterday I submitted the job in home, but used the same notebook. I wonder that would affect anything. If you have any clue about it, please let me know. Thanks.

niklassiemer commented 1 month ago

No, I did not change anything and I am not aware of any difference in functionality between /u and /cmmc/ptmp. Nonetheless, thanks a lot for the issue, thats the only way I can know of potential problems even if they might dissappear :) (just to be sure, your new calculations did also run on cmti and not on cmmg?)

pmrv commented 3 weeks ago

I observed this back then as well, but I believe it to be related to an upgrade of the cluster itself. It went away after restarting shells for me.