On 15/12/2011 4:51 PM, aiswarya pawar wrote:
Hi,
When i tried running mdrun without mip i received the same error ie
when i gave mdrun -deffnm md
i got=
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file md.tpr, VERSION 4.5.4 (single precision)
Loaded with Money
p0_23443: p4_error: interrupt SIGx: 4
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.
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.
Mark
Thanks,
Aiswarya
On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar
<aiswarya.pa...@gmail.com <mailto:aiswarya.pa...@gmail.com>> 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
Please anyone can help with this error.
Thanks
--
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