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<TITLE>RE: [torqueusers] Torque environment problem</TITLE>
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<P><FONT SIZE=2>Hi<BR>
<BR>
I did figure out the issue, or at least I am on the path to a solution.<BR>
<BR>
I was assuming that when I submit a job via torque with the PBS parameter: #PBS -l nodes=12:ppn=12 that the PBS_NODEFILE parameter would have the correctly formatted hosts file for openmpi. <BR>
<BR>
What I am seeing is that torque will generate a hosts file that looks like this:<BR>
<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node164<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
node163<BR>
....<BR>
<BR>
<BR>
But from what I can see, openmpi expects a hostfile list likethis:<BR>
<BR>
node164 slots=12<BR>
node163 slots=12<BR>
<BR>
So what I had to do in my script is add the following code:<BR>
<BR>
np=$(cat $PBS_NODEFILE | wc -l)<BR>
<BR>
for i in `cat ${PBS_NODEFILE}|sort -u`; do<BR>
echo $i slots=12 > /home/admins/rsvancara/nodes<BR>
done<BR>
<BR>
/usr/mpi/intel/openmpi-1.4.3/bin/mpiexec $RUN $MCA -np $np -hostfile /home/admins/rsvancara/nodes /home/admins/rsvancara/TEST/mpitest<BR>
<BR>
I guess I was expecting openmpi to do the right thing but apparently torque and openmpi are not on the same page in terms of formatting for a hosts file. I am using version 2.4.7 of torque. Would newer versions of torque correctly generate a hosts file?<BR>
<BR>
The strange thing is that why would openmpi just simply tell me it may be a LD_LIBRARY_PATH problem seems rather vague. A better response would be "What the .... am I supposed to do with this hosts file you idiot, please format it correctly". <BR>
<BR>
Best regards<BR>
<BR>
Randall<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: torqueusers-bounces@supercluster.org on behalf of Shenglong Wang<BR>
Sent: Fri 3/18/2011 8:45 PM<BR>
To: Torque Users Mailing List<BR>
Subject: Re: [torqueusers] Torque environment problem<BR>
<BR>
Have you set LD_LIBRARY_PATH in your ~/.bashrc file? Did you try to include LD_LIBRARY_PATH to mpirun or mpiexec?<BR>
<BR>
np=$(cat $PBS_NODEFILE | wc -l)<BR>
<BR>
mpiexec -np $np -hostfile $PBS_NODEFILE env LD_LIBRARY_PATH=$LD_LIBRARY_PATH XXXX<BR>
<BR>
Best,<BR>
<BR>
Shenglong<BR>
<BR>
<BR>
<BR>
<BR>
On Mar 18, 2011, at 11:36 PM, Svancara, Randall wrote:<BR>
<BR>
> I just wanted to add that if I launch a job on one node, everything works fine. For example in my job script if I specify<BR>
><BR>
><BR>
> #PBS -l nodes=1:ppn=12<BR>
><BR>
> Then everything runs fine.<BR>
><BR>
><BR>
> However, if I specify two nodes, then everything fails.<BR>
><BR>
><BR>
> #PBS -l nodes=1:ppn=12<BR>
><BR>
> This also fails<BR>
><BR>
><BR>
> #PBS -l nodes=13<BR>
><BR>
> But this does not:<BR>
><BR>
><BR>
> #PBS -l nodes=12<BR>
><BR>
> Thanks,<BR>
><BR>
> Randall<BR>
><BR>
> -----Original Message-----<BR>
> From: torqueusers-bounces@supercluster.org on behalf of Svancara, Randall<BR>
> Sent: Fri 3/18/2011 7:48 PM<BR>
> To: torqueusers@supercluster.org<BR>
> Subject: [torqueusers] Torque environment problem<BR>
><BR>
><BR>
> Hi,<BR>
><BR>
> We are in the process of setting up a new cluster. One issue I am experiencing is with openmpi jobs launched through torque.<BR>
><BR>
> When I launch a simple job using a very basic mpi "Hello World" script I am seeing the following errors from openmpi:<BR>
><BR>
> **************************<BR>
><BR>
> [node164:06689] plm:tm: failed to poll for a spawned daemon, return status = 17002<BR>
> --------------------------------------------------------------------------<BR>
> A daemon (pid unknown) died unexpectedly on signal 1 while attempting to<BR>
> launch so we are aborting.<BR>
><BR>
> There may be more information reported by the environment (see above).<BR>
><BR>
> This may be because the daemon was unable to find all the needed shared<BR>
> libraries on the remote node. You may set your LD_LIBRARY_PATH to have the<BR>
> location of the shared libraries on the remote nodes and this will<BR>
> automatically be forwarded to the remote nodes.<BR>
> --------------------------------------------------------------------------<BR>
> --------------------------------------------------------------------------<BR>
> mpirun noticed that the job aborted, but has no info as to the process<BR>
> that caused that situation.<BR>
> --------------------------------------------------------------------------<BR>
> --------------------------------------------------------------------------<BR>
> mpirun was unable to cleanly terminate the daemons on the nodes shown<BR>
> below. Additional manual cleanup may be required - please refer to<BR>
> the "orte-clean" tool for assistance.<BR>
> --------------------------------------------------------------------------<BR>
> node163 - daemon did not report back when launched<BR>
> Completed executing:<BR>
><BR>
> *************************<BR>
><BR>
> However when launch a job running mpiexec, everything seems to work fine using the following script:<BR>
><BR>
> /usr/mpi/intel/openmpi-1.4.3/bin/mpirun -hostfile /home/admins/rsvancara/hosts -n 24 /home/admins/rsvancara/TEST/mpitest<BR>
><BR>
> The job runs on 24 nodes with 12 processes per node.<BR>
><BR>
> I have verified that my .bashrc is working. I have tried to launch from an interactive job using qsub -I -lnodes=12:ppn12 without any success. I am assuming this is an environment problem, however, I am unsure as the openmpi error includes "MAY". <BR>
><BR>
> My question is:<BR>
><BR>
> 1. Has anyone had this problem before (I am sure they have)<BR>
> 2. How would I go about troubleshooting this problem.<BR>
><BR>
><BR>
> I am using torque version 2.4.7.<BR>
><BR>
> Thanks for any assistance anyone can provide.<BR>
><BR>
><BR>
> _______________________________________________<BR>
> torqueusers mailing list<BR>
> torqueusers@supercluster.org<BR>
> <A HREF="http://www.supercluster.org/mailman/listinfo/torqueusers">http://www.supercluster.org/mailman/listinfo/torqueusers</A><BR>
<BR>
<BR>
</FONT>
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