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 ....................... ....................... WARNING: Writing out atom name (SCSP1) longer than 4 characters to .pd[tya64:04380] [0,0,0]-[0,0,1] mca_oob_tcp_msg_send_handler: writev failed: Broken pipe (32) [tya64:04380] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 188 [tya64:04380] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1198 -------------------------------------------------------------------------- mpirun was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of ORTE_SUCCESS. ========== GROMACS 3.3 was installed from the Debian provided package, LAM option. I also have installed (Intel compiled) OpenMPi in a quite different directory. "which" calls either parallelization support independently. Do the above error messages really imply a conflict LAM OpenMPI or should I better look at elsewhere? thanks francesco pietra _______________________________________________ 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
