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On 15/12/2011 4:51 PM, aiswarya pawar wrote:
<blockquote
cite="mid:CAEa6cRCi6Fy9nqB7eeV=G_cbYCD5yvv=Ni+-9duaGENMryD2qw@mail.gmail.com"
type="cite"><br>
Hi,<br>
<br>
<br>
When i tried running mdrun without mip i received the same error
ie<br>
<br>
when i gave mdrun -deffnm md<br>
<br>
i got=<br>
Back Off! I just backed up md.log to ./#md.log.1#<br>
Getting Loaded...<br>
Reading file md.tpr, VERSION 4.5.4 (single precision)<br>
Loaded with Money<br>
<br>
p0_23443: p4_error: interrupt SIGx: 4<br>
</blockquote>
<br>
The job you ran below with poe did not have the MPI suffix, so I am
not convinced you are doing appropriate things with appropriate
executables. Above, a p4_error is consistent with an MPI-enabled
executable.<br>
<br>
Get an MPI "hello world" program and get it running before worrying
about GROMACS. Follow the user guide for your cluster. Get your
MPI-enabled mdrun suffixed with _mpi like the installation guides
recommend.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEa6cRCi6Fy9nqB7eeV=G_cbYCD5yvv=Ni+-9duaGENMryD2qw@mail.gmail.com"
type="cite"><br>
<br>
Thanks,<br>
Aiswarya<br>
<br>
<div class="gmail_quote">On Wed, Dec 14, 2011 at 5:00 PM, aiswarya
pawar <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:aiswarya.pawar@gmail.com">aiswarya.pawar@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
users,<br>
<br>
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=<br>
<br>
#!/bin/sh<br>
# @ error = job1.$(Host).$(Cluster).$(Process).err<br>
# @ output = job1.$(Host).$(Cluster).$(Process).out<br>
# @ class = ptask32<br>
# @ job_type = parallel<br>
# @ node = 1<br>
# @ tasks_per_node = 4<br>
# @ queue<br>
<br>
echo "_____________________________________"<br>
echo "LOADL_STEP_ID=$LOADL_STEP_ID"<br>
echo "_____________________________________"<br>
<br>
machine_file="/tmp/machinelist.$LOADL_STEP_ID"<br>
rm -f $machine_file<br>
for node in $LOADL_PROCESSOR_LIST<br>
do<br>
echo $node >> $machine_file<br>
done<br>
machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`<br>
echo $machine_count<br>
echo MachineList:<br>
cat /tmp/machinelist.$LOADL_STEP_ID<br>
echo "_____________________________________"<br>
unset LOADLBATCH<br>
env |grep LOADLBATCH<br>
cd /home/staff/1adf/<br>
/usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm
/home/staff/1adf/md -procs $machine_count -hostfile
/tmp/machinelist.$LOADL_STEP_ID<br>
rm /tmp/machinelist.$LOADL_STEP_ID<br>
<br>
<br>
i get an out file as=<br>
_____________________________________<br>
LOADL_STEP_ID=cnode39.97541.0<br>
_____________________________________<br>
4<br>
MachineList:<br>
cnode62<br>
cnode7<br>
cnode4<br>
cnode8<br>
_____________________________________<br>
p0_25108: p4_error: interrupt SIGx: 4<br>
p0_2890: p4_error: interrupt SIGx: 4<br>
p0_2901: p4_error: interrupt SIGx: 15<br>
p0_22760: p4_error: interrupt SIGx: 15<br>
<br>
<br>
an error file =<br>
<br>
Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single
precision)<br>
Sorry couldn't backup /home/staff/1adf/md.log to
/home/staff/1adf/#md.log.14#<br>
<br>
Back Off! I just backed up /home/staff/1adf/md.log to
/home/staff/1adf/#md.log.14#<br>
ERROR: 0031-300 Forcing all remote tasks to exit due to exit
code 1 in task 0<br>
<br>
Please anyone can help with this error.<br>
<br>
Thanks<br>
<br>
<br>
<br>
</blockquote>
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