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Subject: [OMPI users] OpenMPI 1.3 and SGE 6.2u1
From: Malone, Scott (Scott.Malone_at_[hidden])
Date: 2009-03-19 11:07:17

I am having two problem with the integration of OpenMPI 1.3 and SGE 6.2u1, which we are new with both. The troubles are getting jobs to suspend/resume and collect cpu time correctly.

For suspend/resume I have added the following to my mpirun command:

--mca orte_forward_job_control 1 --mca plm_rsh_daemonize_qrsh 1

and adjusted the suspend_method for the queue that it's running in. I have not gotten it to place any process into the T state. Although this is not a huge problem, I hope to have this working in the future.

My main problem is getting the cpu time correct. On a multiple cpu job only the master nodes shows the cpu time correct for that process, the others are very short and not sure what they are measuring. (I believe startup time). Here's and example:

cpu 0.360
cpu 0.480
cpu 0.470
cpu 0.490
cpu 0.530
cpu 0.470
cpu 0.680
cpu 464.305

And from watching the runs that time is close to the wall clock time and match what I see for that single process. Now I have gotten it to give what I believe are correct values, but I have to include --debug-daemons option to our mpirun command. With that I get the following:

cpu 73.146
cpu 72.982
cpu 73.381
cpu 73.142
cpu 73.029
cpu 73.183
cpu 73.117
cpu 73.265
cpu 73.236

I have noticed that when I get the cpu time correctly I get qrsh process that startup (my understanding is that this is what starts the processes on the remote machines) and they stay running until the jobs is finished. When I don't get the correct cpu time, I see the qrsh processes start on the master node, but die off once they start the process on the remote nodes. The PE environment looks like the following:

pe_name orte
slots 560
user_lists NONE
xuser_lists NONE
start_proc_args /bin/true
stop_proc_args /bin/true
allocation_rule $round_robin
control_slaves TRUE
job_is_first_task FALSE
urgency_slots min
accounting_summary FALSE

Please let me know if I can provide any more information to help figure this out.


Scott Malone
Manager, High Performance Computing Facility
Information Sciences - Research Informatics
St. Jude Children's Research Hospital
332 North Lauderdale
Memphis, TN 38105

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