[gmx-users] grompp results in Segmentation fault

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 31 08:27:27 CEST 2009

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?

Don't you have any more information?
If you run PBS you can run interactively using
qsub -I
and then run grompp on one of your nodes to see what happens.
ldd `which grompp` may also be instructive.
> Best,
> Itamar
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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