Juan, So you need to load the knem module sudo modprobe knem and then you can check it is correctly loaded with lsmod
Loading the module should automagically create /dev/knem, but maybe not with the permissions you expect Cheers, Gilles On Wednesday, January 18, 2017, Juan A. Cordero Varelaq < bioinformatica-i...@us.es> wrote: > Hi, > > knem and MOFED drivers are installed in /opt: > > - /opt/knem-1.1.90mlnx2 > - /opt/mellanox/fca > - /opt/mellanox/mxm > - /opt/mellanox/openshmem > > However /dev/knem does not exist. > > Cheers, > > Juan > On 18/01/17 11:36, Gilles Gouaillardet wrote: > > 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 > <javascript:_e(%7B%7D,'cvml','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> 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 >>> >> >> >> >> _______________________________________________ >> users mailing >> listus...@lists.open-mpi.orghttps://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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