[gmx-users] grompp results in Segmentation fault

Itamar Kass itamar.kass at gmail.com
Mon Aug 31 07:57:24 CEST 2009


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?


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