Ragothaman Yennamalli wrote:
Dear all,
I get an error while running grompp or mdrun in a Sun cluster. Each node has 4
processors. I am submitting the job via a SGE script.
After, I submit the job by "$qsub test_gromacs", the run terminates with the
following message in the log file. Please tell me how to troubleshoot this problem. The
error is repeated if the -np option is changed from 4 to 8.
Since there's three different usages of -np you'd need to be more
precise to make a good description of your problem.
Fatal error: run input file topol.tpr was made for 4 nodes,
while mdrun expected it to be for 1 nodes.
[compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file
base/pls_base_proxy.c at line 189
The script is as follows:
#!/bin/bash
#$ -N mpich_gromacs
#$ -S /bin/bash
#$ -cwd
#$ -j y
#Set the Parallel Environment and number of procs.
#$ -pe mpich
#Set the Parallel Environment and number of procs.
#$ -pe mpich 4
#$ -l h_rt=01:00:00
echo Running on host `hostname`
echo Directory is `pwd`
echo This job runs on the following processors:
cat $TMPDIR/machines | tee machinefile
echo This job has allocated $NSLOTS processors
export MDRUN=/home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/mdrun
export MPIRUN=/opt/mpich/gnu/bin/mpirun
##running directory
cd /home/raghu/quad_md/case1
#add -v to create more verbose comments
#-nice 0 needs to be before the -s and other arguments; this corrects the
default of 19 (lowest priority)
/home/raghu/gromacs/x86_64-unknown-linux-gnu/bin/grompp -f em.mdp -c
box_sol.gro -p master.top -v -np 4
$MPIRUN -v -np 4 $MDRUN -v -nice 0 -np $NSLOTS -s topol.tpr -o traj.trr -e ener.edr
-x traj.xtc -g md.log -c confout.gro >&em_run.log
The symptoms you observe make sense if $NSLOTS==1. Since all three -np
flags need the same value after them, you should use the same variable
each time. You should verify that the "echo" line tells you that has
$NSLOTS==4 like you need.
Mark
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