[gmx-users] grompp results in Segmentation fault

[Mark Abraham]

Itamar Kass wrote:
> Hi,
> 
> I have installed GROMACS 4.0.5 on our cluster (gcc 4.2.1, Open MPI
> 1.2.3) whereas only mdrun was install with -enable-mpi flag. When I
> try to run it via a script (grompp -f pr_complex.mdp -c
> complex_from_EM.gro -p complex.top -n complex.ndx -po
> complex_from_PR.mdp -o complex_for_PR.tpr) I get this:
> 
> /var/spool/torque/mom_priv/jobs/995. ... .SC: line 23:  5128
> Segmentation fault      grompp ...
> 
> When I run grompp out of the script it runs fine.
> 
> Does someone has any idea about this?

Does your local machine have a different architecture from your cluster? 
Executables are not necessarily transferable.

Mark