[gmx-users] Error while running starting grompp and mdrun

[Ragothaman Yennamalli]

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 "$qsub test_gromacs", the run terminates with the following message in the log file. Please tell me how to troubleshoot this problem. The error is repeated if the -np option is changed from 4 to 8.
______________________________________________________________________
Fatal error: run input file topol.tpr was made for 4 nodes,
             while mdrun expected it to be for 1 nodes.
[compute-1-30.local:24948] [0,0,0] ORTE_ERROR_LOG: Not found in file base/pls_base_proxy.c at line 189
______________________________________________________________________
The script is as follows:
______________________________________________________________________
#!/bin/bash
#$ -N mpich_gromacs
#$ -S /bin/bash
#$  -cwd
#$ -j yDear 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.

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


Regards,
Ragothaman


      BMR - a key player in weight issues. Know more - http://in.search.yahoo.com/search?&fr=na_onnetwork_mail_taglines&ei=UTF-8&rd=r1&p=basal+metabolic+rate