NONMEM Users Network Archive

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NONMEM and PsN on a Cluster with TORQUE

From: Ahmed Suleiman <ahmed.suleiman>
Date: Sat, 15 Sep 2012 12:30:06 +0200 (CEST)

Dear NM users,

I have just installed NONMEM successfully on a cluster together with perl
and PsN. Our cluster uses TORQUE as the resource manager. I have been
running some tests to check the installation and came with 2 questions:

1. When I submit a bootstrap using a batch script requesting 10 nodes and
10 ppn for example, with a command at the end of the script saying

"bootstrap run1.mod -samples=100 -threads=100 -nodes=10",

the run times of the bootstrapped samples are a couples of times longer
than the run time of the original fit. Apparently the multi-node operation
doesn't work as it should have been working and the processes run only on
the first node. When I omit the "threads option", 5 threads are used (as
specified in the psn.conf) and the run times drop to their usual values,
which further proves the over commitment of the executing node. How can I
solve this within the batch script ?

2. It would be easier if I were able to run PsN without having to write
batch scripts, however I am not aware of the options which would allow me
to request resources other than those set as default by the administrator.
For example the default wall time in our cluster is 1 hour, and the only
option which I found to change this was -max_runtime, but unfortunately
this works only with SLURM. Is it possible to specify different resources
from the command interface ?

Kind Regards,

Ahmed Abbas Suleiman, MSc
PhD Candidate at Bonn University
Institute of Pharmacology - Clinical Pharmacology Unit
Hospital of the University of Cologne
Gleueler Str. 24, 50931 Cologne
Germany
Received on Sat Sep 15 2012 - 06:30:06 EDT

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