Dear friend,<br>1.<br>I prefer to use sge qsub cmd, for examples:<br><br>[huong@ioitg2 MyPhylo]$ qsub -pe orte 3 myphylo.qsub<br>Your job 35 (&quot;myphylo.qsub&quot;) has been submitted<br>[huong@ioitg2 MyPhylo]$ qstat<br>
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID <br>-----------------------------------------------------------------------------------------------------------------<br>
     35 0.55500 myphylo.qs huong        r     04/09/2010 19:28:59 <a href="mailto:all.q@node2.ioit-grid.ac.vn">all.q@node2.ioit-grid.ac.vn</a>        3        <br>[huong@ioitg2 MyPhylo]$ qstat<br>[huong@ioitg2 MyPhylo]$ <br>
<br>This job is running on node2 of my cluster.<br>My softs as following:<br>headnode: 4 CPUs. $GRAM, CentOS 5.4 + sge 6.2u4 (qmaster and also execd host) + openmpi 1.4.1<br>nodes 4CPUs, 1GRAM, CentOS 5.4 + sgeexecd + openmpi1.4.1<br>
PE=orte and set to 4 slots.<br>The app myphylo.qsub has the long cmd in the shell:<br>/opt/openmpi/bin/mpirun -np 10 $HOME/MyPhylo/bin/par-phylo-builder --data . . . .<br>Try to set PE as orte, use default PE = make instead.<br>
<br>2. I test your cmd on my sytem as:<br>a.<br>[huong@ioitg2 MyPhylo]$ qrsh -verbose -pe make mpirun -np 6 hostname<br>error: Numerical value invalid!<br>The initial portion of string &quot;mpirun&quot; contains no decimal number<br>
[huong@ioitg2 MyPhylo]$ qrsh -verbose -pe orte 2 mpirun -np 6 hostname<br>Your job 36 (&quot;mpirun&quot;) has been submitted<br>waiting for interactive job to be scheduled ...<br>Your interactive job 36 has been successfully scheduled.<br>
Establishing builtin session to host <a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a> ...<br>bash: mpirun: command not found<br>[huong@ioitg2 MyPhylo]$ <br><br>ERROR ! So I try:<br>[huong@ioitg2 MyPhylo]$ qrsh -verbose -pe orte 2 /opt/openmpi/bin/mpirun -np 6 hostname<br>
Your job 38 (&quot;mpirun&quot;) has been submitted<br>waiting for interactive job to be scheduled ...<br>Your interactive job 38 has been successfully scheduled.<br>Establishing builtin session to host <a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a> ...<br>
<a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a><br><a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a><br><a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a><br><a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a><br>
<a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a><br><a href="http://ioitg2.ioit-grid.ac.vn">ioitg2.ioit-grid.ac.vn</a><br>[huong@ioitg2 MyPhylo]$ <br><br>This OK.<br>What is: the PATH points to where mpirun is located.<br>
<br>TRY.<br><br>Good chance<br>HT Cuoc<br><br><br><div class="gmail_quote">On Fri, Apr 9, 2010 at 11:02 AM, Cristobal Navarro <span dir="ltr">&lt;<a href="mailto:axischire@gmail.com">axischire@gmail.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello,<br><br>after some days of work and testing, i managed to install SGE on two machines, also installed openMPI 1.4.1 for each one.<br>
<br>SGE is working, i can submit jobs and it schedules the jobs to the available cores total of 6,<br>

<br>my problem is that im trying to run an openMPI job and i cant.<br><br>this is an example of what i am trying.<br></blockquote><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>$qrsh -verbose -pe pempi mpirun -np 6 hostname<br>Your job 105 (&quot;mpirun&quot;) has been submitted<br>

waiting for interactive job to be scheduled ...<br><br>Your &quot;qrsh&quot; request could not be scheduled, try again later.<br><br>im not sure what this can be, <br>in the ompi_info i have gridengine support.<br><br>where do you recommend to look ??<br>


thanks in advance<br><font color="#888888"><br clear="all">Cristobal<br><br><br>
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