[gmx-users] Problem using MPIRUN MDRUN

fprisch at nimr.mrc.ac.uk fprisch at nimr.mrc.ac.uk
Mon Feb 16 11:00:31 CET 2009

I did not stop the simulation manually and it did not give a segmentation fault message, but something else that I have never seen before (and actually, I am still not understanding the error message).
Now I'm running the dynamics on my machine, instead of running it on the cluster, and there are no problems at all. This means that the problem is not related to my protein or to the parameters of the dynamic, but it must be somewhere else in the mpirun command line or something like that.

grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file.tpr -np 32
mpirun -np 32 /dms/prog/bin/mdrun_mpi_s -s file.tpr -o file.trr -c file.gro  -np 32

----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Date: Friday, February 13, 2009 10:11 pm
Subject: Re: [gmx-users] Problem using MPIRUN MDRUN

> fprisch at nimr.mrc.ac.uk wrote:
> > Thanks a lot, I'll check stderr and stdout, because I think that 
> the log file is correct (it looks like a normal dynamic that has 
> been manually interrupted).
> If you've manually interrupted the simulation, then you cannot 
> expect 
> the buffered I/O to be correctly formed.
> > The system is not exploded cause it does not generate the gro 
> file and step files.
> If there's no final coordinate file (.gro by default), then the 
> simulation did not complete correctly.
> Mark
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