aiswarya.pa...@gmail.com wrote:
Mark,
I still the same error.
Check the .log file for any errors, and if you find none, then the problem isn't
from Gromacs and should be investigated with your sysadmin.
-Justin
Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: Mark Abraham <mark.abra...@anu.edu.au>
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 14 Dec 2011 23:03:59
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] submission error
On 14/12/2011 10:30 PM, aiswarya pawar wrote:
Hi users,
I have a submission script for gromacs mdrun to be used on IBM
cluster, but i get an error while running it. the script goes like this=
#!/bin/sh
# @ error = job1.$(Host).$(Cluster).$(Process).err
# @ output = job1.$(Host).$(Cluster).$(Process).out
# @ class = ptask32
# @ job_type = parallel
# @ node = 1
# @ tasks_per_node = 4
# @ queue
echo "_____________________________________"
echo "LOADL_STEP_ID=$LOADL_STEP_ID"
echo "_____________________________________"
machine_file="/tmp/machinelist.$LOADL_STEP_ID"
rm -f $machine_file
for node in $LOADL_PROCESSOR_LIST
do
echo $node >> $machine_file
done
machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
echo $machine_count
echo MachineList:
cat /tmp/machinelist.$LOADL_STEP_ID
echo "_____________________________________"
unset LOADLBATCH
env |grep LOADLBATCH
cd /home/staff/1adf/
/usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md
-procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID
rm /tmp/machinelist.$LOADL_STEP_ID
i get an out file as=
_____________________________________
LOADL_STEP_ID=cnode39.97541.0
_____________________________________
4
MachineList:
cnode62
cnode7
cnode4
cnode8
_____________________________________
p0_25108: p4_error: interrupt SIGx: 4
p0_2890: p4_error: interrupt SIGx: 4
p0_2901: p4_error: interrupt SIGx: 15
p0_22760: p4_error: interrupt SIGx: 15
an error file =
Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
Sorry couldn't backup /home/staff/1adf/md.log to
/home/staff/1adf/#md.log.14#
Back Off! I just backed up /home/staff/1adf/md.log to
/home/staff/1adf/#md.log.14#
ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1
in task 0
Looks like a problem with file writing privileges or maybe disk quota.
Either make a new run directory or clean up before using this job
script, and see how you go.
Mark
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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