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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
