Hi,
I am trying to run xplor-NIH (version 2.16.0) on a cluster computer, but
having problems.
Here's what I did do:
1) I installed xplor-NIH in my own user directory, and manipulated the
PBS script mentioned at the xplor-NIH site to match the cluster here.
In the script I specified the number of cpus to be used #PBS -l ncpus=##
2) When I submit the job:
qsub myjob.pbs
The task starts running (confirmed by mail to my account)
Then the timer locks at the value of 00:00:00 but somehow indicates a
running status, output of qstat:
Job id Name User Time Use S Queue
------------------- ---------------- ---------------- -------- - -----
14474.beoclus RDC_short ramon 00:20:57 R
dque
14477.beoclus RDC_short_NIH ramon 00:00:00 R
dque
First job is the one I am running with the 'old' xplor (working
perfectly, but can only use one cpu per script)
The last one is with xplor-NIH after 10 minutes of running.
On the Node that is running two processes named xplor are spawned by
xplor-NIH. Both processes generate output PDBs, whereas I only want one.
(Just like I would like to run ONE xplor-NIH on this node)
The logfile remains empty. Probably because writing is hampered by two
processes trying to write to this file.
When I type qdel 14477 (delete the xplor-NIH process)
The process is eliminated from the queue, but both processes keep on
running on the node.
My questions:
1) How can I run a single xplor-NIH processes via PBS-scripting (on a
cluster) ?
2) How can I make the processes write to a logfile ?
3) How can I make the process respond correctly to my PBS-commands?
(So qdel actually deletes the process, not deleting just the name from
the queue)
Regards,
Ramon
