On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote: > Hi: I was trying to minimize in vacuum a pure CG protein on a four > core (two dual operons), getting errors: > > $ lamboot > > $ mpirun -np 4 mdrun -s mod21.tpr -o minim_mod21_traj.trr -c > minim_mod21.gro -e minim_mod21_ener.edr > ................... > ................... > > WARNING: Writing ompirun noticed that job rank 2 with PID 4385 on node > tya64 exited on signal 11 (Segmentation fault). > 3 processes killed (possibly by Open MPI) > Writing out atom name (SCSP1) longer than 4 characters to .pdb file
This looks like you are trying to run the LAM binary with Open MPI's mpirun command. Use the LAM version instead (mpirun.lam in Debian). Furthermore, the Debian packages use suffixes, for instance the binaries in the gromacs-lam package are /usr/bin/mdrun_mpi.lam and /usr/bin/mdrun_mpi_d.lam, so you should switch mdrun to mdrun_mpi.lam . So all in all: $ mpirun.lam -np 4 mdrun_mpi.lam -s mod21.tpr -o minim_mod21_traj.trr -c minim_mod21.gro -e minim_mod21_ener.edr What is also possible is that your installation of the Intel compiled Open MPI is visible in your environment, which may quite well lead into problems. (Also, LAM has been obsoleted by Open MPI years ago, so you might just try switching from LAM to Open MPI, then you wouldn't have to run lamboot at the beginning.) -- ------------------------------------------------------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------------------------------------------------------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi ------------------------------------------------------ _______________________________________________ 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
