fpri...@nimr.mrc.ac.uk wrote:
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.
OK, so there's probably some problem with file system availability on
the cluster, and/or returning output files to the user. We can't help
you there.
This sort of detail and differential diagnosis would have been a good
thing to say the first time you described your problem. See the final
link here - http://wiki.gromacs.org/index.php/Support
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
This looks like asking for trouble, if _s and _d are your suffixes for
single and double. Don't mix them. If you've erroneously retyped them,
then that's not helpful information for us. Computers are literal, and
we can only help you work out what you've told it wrongly if you tell us
the same thing - so write a script and/or copy-paste things so that you
are reproducible.
Mark
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