Juan, You also need to make sure knem and MOFED drivers are loaded on all the compute nodes. You also need to double check the permissions of /dev/knem
Cheers, Gilles On Wednesday, January 18, 2017, Juan A. Cordero Varelaq < bioinformatica-i...@us.es> wrote: > Sure, I attach the config.log from the openmpi installation. > > On 17/01/17 17:55, Joshua Ladd wrote: > > 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 > <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','users@lists.open-mpi.org');> >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> > > > > _______________________________________________ > users mailing listus...@lists.open-mpi.org > <javascript:_e(%7B%7D,'cvml','users@lists.open-mpi.org');>https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > >
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