Open MPI logo

Open MPI User's Mailing List Archives

  |   Home   |   Support   |   FAQ   |   all Open MPI User's mailing list

Subject: Re: [OMPI users] run openMPI jobs with SGE,
From: Huynh Thuc Cuoc (htcuoc_at_[hidden])
Date: 2010-04-09 08:58:20


Dear friend,
1.
I prefer to use sge qsub cmd, for examples:

[huong_at_ioitg2 MyPhylo]$ qsub -pe orte 3 myphylo.qsub
Your job 35 ("myphylo.qsub") has been submitted
[huong_at_ioitg2 MyPhylo]$ qstat
job-ID prior name user state submit/start at
queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
     35 0.55500 myphylo.qs huong r 04/09/2010 19:28:59
all.q_at_[hidden] 3
[huong_at_ioitg2 MyPhylo]$ qstat
[huong_at_ioitg2 MyPhylo]$

This job is running on node2 of my cluster.
My softs as following:
headnode: 4 CPUs. $GRAM, CentOS 5.4 + sge 6.2u4 (qmaster and also execd
host) + openmpi 1.4.1
nodes 4CPUs, 1GRAM, CentOS 5.4 + sgeexecd + openmpi1.4.1
PE=orte and set to 4 slots.
The app myphylo.qsub has the long cmd in the shell:
/opt/openmpi/bin/mpirun -np 10 $HOME/MyPhylo/bin/par-phylo-builder --data .
. . .
Try to set PE as orte, use default PE = make instead.

2. I test your cmd on my sytem as:
a.
[huong_at_ioitg2 MyPhylo]$ qrsh -verbose -pe make mpirun -np 6 hostname
error: Numerical value invalid!
The initial portion of string "mpirun" contains no decimal number
[huong_at_ioitg2 MyPhylo]$ qrsh -verbose -pe orte 2 mpirun -np 6 hostname
Your job 36 ("mpirun") has been submitted
waiting for interactive job to be scheduled ...
Your interactive job 36 has been successfully scheduled.
Establishing builtin session to host ioitg2.ioit-grid.ac.vn ...
bash: mpirun: command not found
[huong_at_ioitg2 MyPhylo]$

ERROR ! So I try:
[huong_at_ioitg2 MyPhylo]$ qrsh -verbose -pe orte 2 /opt/openmpi/bin/mpirun -np
6 hostname
Your job 38 ("mpirun") has been submitted
waiting for interactive job to be scheduled ...
Your interactive job 38 has been successfully scheduled.
Establishing builtin session to host ioitg2.ioit-grid.ac.vn ...
ioitg2.ioit-grid.ac.vn
ioitg2.ioit-grid.ac.vn
ioitg2.ioit-grid.ac.vn
ioitg2.ioit-grid.ac.vn
ioitg2.ioit-grid.ac.vn
ioitg2.ioit-grid.ac.vn
[huong_at_ioitg2 MyPhylo]$

This OK.
What is: the PATH points to where mpirun is located.

TRY.

Good chance
HT Cuoc

On Fri, Apr 9, 2010 at 11:02 AM, Cristobal Navarro <axischire_at_[hidden]>wrote:

> Hello,
>
> after some days of work and testing, i managed to install SGE on two
> machines, also installed openMPI 1.4.1 for each one.
>
> SGE is working, i can submit jobs and it schedules the jobs to the
> available cores total of 6,
>
> my problem is that im trying to run an openMPI job and i cant.
>
> this is an example of what i am trying.
>

>
> $qrsh -verbose -pe pempi mpirun -np 6 hostname
> Your job 105 ("mpirun") has been submitted
> waiting for interactive job to be scheduled ...
>
> Your "qrsh" request could not be scheduled, try again later.
>
> im not sure what this can be,
> in the ompi_info i have gridengine support.
>
> where do you recommend to look ??
> thanks in advance
>
> Cristobal
>
>
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>