Simfactory on Bridges2

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Issue #2597 new
Maria created an issue

Please help me set up simfactory in Bridges2, a PSC supercomputer. Works with SLURM. Here is the user guide: https://www.psc.edu/resources/bridges-2/user-guide-2/

My $PROJECT directory is /ocean/projects/tra210033p/babiuc and I think this is also where the simulations directory should reside. It does not have a “scratch“ directory.

The command:

./simfactory/bin/sim setup-silent

creates a br012.ib.bridges2.psc.edu.ini file, which I renamed to bridges2.ini.

I edited this file and created by hand bridges2.cgf, bridges2.sub and bridges2.run, which are attached.


Comments (3)

  1. Erik Schnetter

    The file bridges2.ini is wrong. It is missing the section header [bridges2] in the beginning. Look at other ini files for examples.

  2. Maria reporter

    Oh, I'm sorry, I did not pay attention to that, and in fact the file I sent to you indeed did not have that header. The original file had the header [br012.ib.bridges2.psc.edu]. I changed it to [bridges2] and started to compile!

    ...only to stop at this error: MPI_DIR is set to a directory that does not exist (MPI_DIR = /opt/modulefiles/production/openmpi/4.0.5-gcc10.2.0.lua); continuing anyway No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR = /opt/modulefiles/production/openmpi/4.0.5-gcc10.2.0.lua) ERROR: MPI could not be configured: neither automatic nor manual configuration succeeded

    CST error 1: -> Configuration script for thorn MPI returned exit code 5 Error message: 'MPI could not be configured: neither automatic nor manual configuration succeeded'

    The link seems correct, but it points to a file, not a directory. It seems that the file has the links to the library path. How shall I proceed?

    Maria

  3. Maria reporter

    Update: I changed the directories for MPI, HDF5, FFTW and OPENBLAS and the configuration built up to the end, when it gave this error:

    /ocean/projects/tra210033p/babiuc/Cactus/configs/etk/lib/libthorn_IOHDF5.a(Write.c.o): In function IOHDF5_Write': /ocean/projects/tra210033p/babiuc/Cactus/arrangements/CactusPUGHIO/IOHDF5/src/Write.c:131: undefined reference toH5Pset_fapl_mpio'
    /ocean/projects/tra210033p/babiuc/Cactus/configs/etk/lib/libthorn_IOHDF5Util.a(DumpVar.c.o): In function WriteDataCollective': /ocean/projects/tra210033p/babiuc/Cactus/arrangements/CactusPUGHIO/IOHDF5Util/src/DumpVar.c:779: undefined reference toH5Pset_dxpl_mpio'
    collect2: error: ld returned 1 exit status
    make[1]: *** [/ocean/projects/tra210033p/babiuc/Cactus/lib/make/make.configuration:150: /ocean/projects/tra210033p/babiuc/Cactus/exe/cactus_etk] Error 1
    make: *** [Makefile:265: etk] Error 2

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