[gmx-users] Problem using MPIRUN MDRUN

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 13 14:41:37 CET 2009

fprisch at nimr.mrc.ac.uk wrote:
> Dear users,
> I'm trying to run gromacs v.3.3.3. on a cluster of 4 machines with 8 CPUs each. I've checked the mailing list and the manual in order to find the correct way to write the command line and I've found that the commands listed below are supposed to be correct and to work.
>> grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file_md.tpr -np 32
>> mpirun -np 32 /dms/prog/bin/mdrun_mpi_d -s file_md.tpr -o file_md.trr -c file_md.gro -np 32
> The dynamics starts, but after few minutes it crushes and I've got this message of error: 
> One of the processes started by mpirun has exited with a nonzero exit code.  This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application.
> PID 24320 failed on node n0 ( with exit status 1.
> Does anyone can help me to sort out this problem?Does anyone know what I'm doing wrong? 

That's just a generic mpirun error message. You'll need to look at the 
end of the .log file, or further back in stderr or stdout to find any 
diagnostic messages from GROMACS.


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