On Thu, 2009-10-15 at 21:04 +0200, Francesco Pietra wrote: > $ lamboot > > $ mpirun.lam -np 4 mdrun_mpi.lam -s mod21.tpr -o minim_mod21_traj.trr > -c minim_mod21.gro -e minim_mod21_ener.edr
clip > Program mdrun_mpi.lam, VERSION 3.3.3 > Source code file: ../../../../src/mdlib/init.c, line: 69 > > Fatal error: > run input file mod21.tpr was made for 1 nodes, > while mdrun_mpi.lam expected it to be for 4 nodes. So now it works, you're just using the obsolete version 3.3.3 of Gromacs, which needs the -np argument in grompp, too. > When installing debian-offered gromacs I avoided the OpenMPI version > because of my Intel-installation of OpenMPI. On the other hand, I need > the latter for running amber, so that if I want to use OpenMPI I > should probably compile gromacs by myself. Don't know if the Intel > installation of OpenMPI will be accepted. That is a possibility, even more so if you want to run a modern installation of Gromacs since the Debian packages are _old_. You should be able to install and use the Debian version Open MPI if you didn't use system directories for your Intel version. Remember to check that LD_LIBRARY_PATH isn't set to the Intel version, since otherwise the system will prefer the Intel versions of the libraries instead of the system ones. > Somewhere in gromacs I have read that the command to start a parallel > job is the same for lam- or openmpi-based installation. May be I don't > remember correctly. MPI is a standard so Gromacs works the same on every MPI runtime. Your problem was with the Debian packages. -- ------------------------------------------------------ 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
