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

[Mark Abraham]

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