[gmx-users] submission error

[Justin A. Lemkul]

aiswarya.pawar at 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.Abraham at anu.edu.au>
> Sender: gmx-users-bounces at gromacs.org
> Date: Wed, 14 Dec 2011 23:03:59 
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Reply-To: Discussion list for GROMACS users <gmx-users at 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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