Hi,
I have run the same command but disabling KNEM (with -mca
btl_sm_use_knem 0), and it gives me, still, the same errors. Futhermore,
I've noticed when I run, for instance, ompi_info, I get one of the same
errors as when running mpirun:
Warning: Conflicting CPU frequencies detected, using: 2001.000000
Does anyone know what may be happening?
Cheers
On 18/01/17 15:16, Juan A. Cordero Varelaq wrote:
Hi,
when I try sudo modprobe knem, I get:
FATAL: Error inserting knem
(/lib/modules/3.13.0-37-generic/updates/dkms/knem.ko): Invalid module
format
Cheers,
Juan
On 18/01/17 15:08, Gilles Gouaillardet wrote:
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 <mailto: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
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