Dear users,
I am totally stuck using openmpi. I have two versions on my machine:
1.8.1 and 2.0.0, and none of them work. When use the mpirun *1.8.1
version*, I get the following error:
librdmacm: Fatal: unable to open RDMA device
librdmacm: Fatal: unable to open RDMA device
librdmacm: Fatal:
problems. You need to install them in totally
different locations. Then you need to _prefix_ your PATH and
LD_LIBRARY_PATH with the location of the version you want to use.
HTH
Ralph
On Aug 19, 2016, at 12:53 AM, Juan A. Cordero Varelaq
mailto:bioinformatica-i...@us.es>> wrote:
Dear use
strings /.../lib/libmpi.so
and check they do not reference the wrong version
(that can happen if a library was built and then moved)
Cheers,
Gilles
On Monday, August 22, 2016, Juan A. Cordero Varelaq
mailto:bioinformatica-i...@us.es>> wrote:
Dear Ralph,
The existence of t
still face issues with version mismatch, you can
mpirun --tag-output ldd a.out
in your script, and double check all nodes are using the correct libs
Cheers,
Gilles
On Monday, August 22, 2016, Juan A. Cordero Varelaq
mailto:bioinformatica-i...@us.es>> wrote:
Hi Gilles,
adding *
--mca btl ^usnic ...
/* i am pretty sure mpirun ... would do the trick too */
if you get the same error message you posted earlier, then there is an
issue with your infiniband fabric, and your sysadmin will hopefully
solve that.
Cheers,
Gilles
On 8/23/2016 5:02 PM, Juan A. Cordero Varelaq
Hi,
I have an directory in /opt/openshmem which contains software from
mellanox. Should I specify during OMPI installation (at the configure
step) where that directory is located? If yes, how? I have been looking
for a "--with-oshmem=" but haven't found anything, as for instance
other Mellano
independent libraries
Cheers,
Gilles
On Wednesday, January 11, 2017, Juan A. Cordero Varelaq
mailto:bioinformatica-i...@us.es>> wrote:
Hi,
I have an directory in /opt/openshmem which contains software from
mellanox. Should I specify during OMPI installation (at the
con
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 ver
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
mailto:bioinformatica-i...@us.es>> wrote:
Sure, I attach the config.log from the openmpi installation.
On
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
mailto:bioinformatica-i...@us.es>> wrote:
Hi,
knem and MOFED drive
using: 2001.00
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
Hi,
I am seriously struggling with running OpenMPI on my SGE HPC under
Ubuntu 12.04:
* Every time I run a command from OpenMPI, let's say ompi_info, I get
the following as the first line of the output:
o Warning: Conflicting CPU frequencies detected, using: 2001.00.
* I get the a
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