Hi all I have installed gromacs-4.0.7-parallel with open mpi. I have successfully ran a few short simulations on 2,3 and 4 nodes using pbc. I am now interested in simulating a cluster of 32 molecules with no pbc in parallel and the simulation doe not proceed. I have set by box vectors to 0 0 0 in the conf.gro file, pbc = no in the mdp file, and use dparticle decomposition. The feedback I get from the following command
nohup mpirun -np 2 /local1/gromacs-4.0.7-parallel/bin/mdrun -pd -s & is Back Off! I just backed up md.log to ./#md.log.1# Reading file topol.tpr, VERSION 4.0.7 (single precision) starting mdrun 'test of 32 hexylcage molecules' 1000 steps, 0.0 ps. [emerald:22662] *** Process received signal *** [emerald:22662] Signal: Segmentation fault (11) [emerald:22662] Signal code: Address not mapped (1) [emerald:22662] Failing at address: (nil) [emerald:22662] [ 0] /lib64/libpthread.so.0 [0x7fbc17eefa90] [emerald:22662] [ 1] /local1/gromacs-4.0.7-parallel/bin/mdrun(nosehoover_tcoupl+0x74) [0x436874] [emerald:22662] [ 2] /local1/gromacs-4.0.7-parallel/bin/mdrun(update+0x171) [0x4b2311] [emerald:22662] [ 3] /local1/gromacs-4.0.7-parallel/bin/mdrun(do_md+0x2608) [0x42dd38] [emerald:22662] [ 4] /local1/gromacs-4.0.7-parallel/bin/mdrun(mdrunner+0xe33) [0x430973] [emerald:22662] [ 5] /local1/gromacs-4.0.7-parallel/bin/mdrun(main+0x5b8) [0x431128] [emerald:22662] [ 6] /lib64/libc.so.6(__libc_start_main+0xe6) [0x7fbc17ba6586] [emerald:22662] [ 7] /local1/gromacs-4.0.7-parallel/bin/mdrun [0x41e1e9] [emerald:22662] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 22662 on node emerald exited on signal 11 (Segmentation fault). p.s I have ran several of these non pbc simulations with the same system in serial and have never experienced a problem. Has anyone ever come across this sort of problem before? and if so could you please provide some advice. Many Thanks Gavin -- 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