For your information, the procedure is: $ grompp ... (to generate minimize.tpr)
$ lamboot $ l$ mdrun_mpi -np 4 -v -s minimize.tpr -o mod21_traj.trr -c mod21.gro -e mod21_ener.edr It worked nicely, exactly as the serial run "mdrun -v -s minimize.tpr ...". No interference with installed openmpi, no need to mention lam in the md command line. Forget about the Debian compilation, it does not require any special command. Have a nice day francesco On Thu, Oct 15, 2009 at 7:55 PM, Jussi Lehtola <jussi.leht...@helsinki.fi> wrote: > 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-us...@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 > > _______________________________________________ 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
