[gmx-users] mdrun_mpi segmentation fault for run in vacuum

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 12 12:53:14 CEST 2012

On 6/12/12 5:54 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I tried to run a minimization just of the hydrogen of a membrane protein.
> I want to do this in vacuum.
> But when I started the run with
> mpirun mdrun_mpi -deffnm protein -v -nt 2
> I get the error that there is a segmentation fault.

Threading and MPI parallelization are independent.  You can't use both.  If 
you've compiled with MPI support, you can't invoke the -nt option.

> But when I only type
> mpirun mdrun_mpi
> there is no problem so I guess that my already produced input files are
> the problem. For example I am not completely sure about the .mdp file. Can
> you please give me an example for a .mdp file for a minimization of only
> the hydrogen but not the whole protein in a vacuum.

It would be far more useful for you to post what you're using so we can provide 
feedback.  The fact that the second command works while the first fails should 
lead to the opposite conclusion - your input is fine, but your invocation of 
mdrun was incorrect.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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