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 <mailto: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
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