Hi Govind
Govind Songara wrote:
> Hi Gus,
> OpenMPI was not built with tm support.
> The submission/execution hosts does not have any of the
> PBS environment variable set
> PBS_O_WORKDIR, $PBS_NODEFILE.
> How i can make set it
> regards
> Govind
>
I missed the final part of your message,
about the Torque environment.
This is now more of a Torque question,
and you may want to ask it in the Torque mailing list:
http://www.supercluster.org/mailman/listinfo/torqueusers
The Torque system administration guide may also help:
http://www.clusterresources.com/products/torque/docs/
Anyway, you may not have configured Torque.
However, how did you figure out that the PBS_O_WORKDIR
and PBS_NODEFILE are not set?
Try to put "ls $PBS_O_WORKDIR" and "cat $PBS_NODEFILE" in your
Torque/PBS script. You can even comment out the mpirun command,
just to test the Torque environment.
I think Torque sets them for each job, PBS_NODEFILE depends on
how many nodes and processors you requested,
and PBS_O_WORKDIR is just your work directory,
from where you launched the job with qsub.
Assuming your Torque is in /var/spool/torque (it may be different
in your system), on the head node, does the file
/var/spool/torque/server_priv/nodes list all your nodes,
with the correct number of processors?
It should look somewhat like this
("np" is the total number of 'cores' on each node):
node01 np=2
node02 np=2
...
I hope this helps.
Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------
On 9 June 2010 18:45, Gus Correa <g...@ldeo.columbia.edu
<mailto:g...@ldeo.columbia.edu>> wrote:
Hi Govind
Besides what Ralph said, make sure your OpenMPI was
built with Torque ("tm") support.
Suggestion:
Do:
ompi_info --all | grep tm
It should show lines like these:
MCA ras: tm (MCA v2.0, API v2.0, Component v1.4.2)
MCA plm: tm (MCA v2.0, API v2.0, Component v1.4.2)
...
***
If your OpenMPI doesn't have torque support,
you may need to add the nodes list to your mpirun command.
Suggestion:
/usr/lib64/openmpi/1.4-gcc/bin/mpirun -hostfile $PBS_NODEFILE -np 4
./hello
***
Also, assuming your OpenMPI has torque support:
Did you request 4 nodes from torque?
If you don't request the nodes and processors,
torque will give you the default values
(which may be one processor and one node).
Suggestion:
A script like this (adjusted to your site), tcsh style here,
say, called run_my_pbs_job.tcsh:
*********
#! /bin/tcsh
#PBS -l nodes=4:ppn=1
#PBS -q default@your.torque.server
#PBS -N myjob
cd $PBS_O_WORKDIR
/usr/lib64/openmpi/1.4-gcc/bin/mpirun -np 4 ./hello
*********
Then do:
qsub run_my_pbs_job.tcsh
**
You can get more information about the PBS syntax using "man qsub".
**
I hope this helps,
Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------
Ralph Castain wrote:
On Jun 9, 2010, at 10:00 AM, Govind Songara wrote:
Thanks Ralph after giving full path of hello it runs.
But it run only on one rank
Hello World! from process 0 out of 1 on node56.beowulf.cluster
Just to check things out, I would do:
mpirun --display-allocation --display-map -np 4 ....
That should show you the allocation and where OMPI is putting
the procs.
there also a error
>cat my-script.sh.e43
stty: standard input: Invalid argument
Not really sure here - must be an error in the script itself.
On 9 June 2010 16:46, Ralph Castain <r...@open-mpi.org
<mailto:r...@open-mpi.org> <mailto:r...@open-mpi.org
<mailto:r...@open-mpi.org>>> wrote:
You need to include the path to "hello" unless it sits in
your
PATH environment!
On Jun 9, 2010, at 9:37 AM, Govind wrote:
#!/bin/sh
/usr/lib64/openmpi/1.4-gcc/bin/mpirun hello
On 9 June 2010 16:21, David Zhang
<solarbik...@gmail.com <mailto:solarbik...@gmail.com>
<mailto:solarbik...@gmail.com
<mailto:solarbik...@gmail.com>>> wrote:
what does your my-script.sh looks like?
On Wed, Jun 9, 2010 at 8:17 AM, Govind
<govind.r...@gmail.com <mailto:govind.r...@gmail.com>
<mailto:govind.r...@gmail.com
<mailto:govind.r...@gmail.com>>> wrote:
Hi,
I have installed following openMPI packge on
worker node
from repo
openmpi-libs-1.4-4.el5.x86_64
openmpi-1.4-4.el5.x86_64
mpitests-openmpi-3.0-2.el5.x86_64
mpi-selector-1.0.2-1.el5.noarch
torque-client-2.3.6-2cri.el5.x86_64
torque-2.3.6-2cri.el5.x86_64
torque-mom-2.3.6-2cri.el5.x86_64
Having some problem on running MPI jobs with
torque
qsub -q long -l nodes=4 my-script.sh
42.pbs1 <http://42.pbs1.pp.rhul.ac.uk/>
cat my-script.sh.e41
stty: standard input: Invalid argument
--------------------------------------------------------------------------
mpirun was unable to launch the specified
application as
it could not find an executable:
Executable: hello
Node: node56.beowulf.cluster
while attempting to start process rank 0.
==================================
I could run the binary directly on the node
without any
problem.
mpiexec -n 4 hello
Hello World! from process 2 out of 4 on
node56.beowulf.cluster
Hello World! from process 0 out of 4 on
node56.beowulf.cluster
Hello World! from process 3 out of 4 on
node56.beowulf.cluster
Hello World! from process 1 out of 4 on
node56.beowulf.cluster
Could you please advise, if I missing
anything here.
Regards
Govind
_______________________________________________
users mailing list
us...@open-mpi.org
<mailto:us...@open-mpi.org> <mailto:us...@open-mpi.org
<mailto:us...@open-mpi.org>>
http://www.open-mpi.org/mailman/listinfo.cgi/users
-- David Zhang
University of California, San Diego
_______________________________________________
users mailing list
us...@open-mpi.org <mailto:us...@open-mpi.org>
<mailto:us...@open-mpi.org <mailto:us...@open-mpi.org>>
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org <mailto:us...@open-mpi.org>
<mailto:us...@open-mpi.org <mailto:us...@open-mpi.org>>
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org <mailto:us...@open-mpi.org>
<mailto:us...@open-mpi.org <mailto:us...@open-mpi.org>>
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org <mailto:us...@open-mpi.org>
<mailto:us...@open-mpi.org <mailto:us...@open-mpi.org>>
http://www.open-mpi.org/mailman/listinfo.cgi/users
------------------------------------------------------------------------
_______________________________________________
users mailing list
us...@open-mpi.org <mailto:us...@open-mpi.org>
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org <mailto:us...@open-mpi.org>
http://www.open-mpi.org/mailman/listinfo.cgi/users
------------------------------------------------------------------------
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
