Can you please attach your configure log. It looks like both MXM and the Vader BTL (used for OSC) are complaining because they can't find your KNEM installation.
Josh On Tue, Jan 17, 2017 at 7:16 AM, Juan A. Cordero Varelaq < bioinformatica-i...@us.es> wrote: > Hi, I am running on my SCG cluster the following script (using qsub): > > #!/bin/bash > #$-cwd > #$ -S /bin/bash > #$ -V > #$ -q normal > #$ -pe mpi 40 > #$ -P Lab219 > #$ -o output > #$ -e error > module load PhyML/3.3 > mpirun --mca pml yalla -np 40 phyml-mpi -i proteic -b 10 -d aa > > where phyml-mpi is the parallel version for OMPI of the program PhyML. > --mca pml yalla option is called to used MXM (I have mellanox OFED). > > > It gives me lots of errors related to KNEM (see error and output files > from qsub in the attachments). However, I specified the KNEM directory when > installing OMPI. I can't really understand such errors, and would > appreciate any hint on this issue. I have run open-mpi on an own script > (just a loop running inside something as: command --help) and got no error. > > > Thanks in advance > > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users >
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