On Sat, Feb 16, 2013 at 11:27 PM, Tomek Wlodarski <[email protected] > wrote:
> Hi! > > I have problem in running gromacs 4.6 in PBS queue... > I end up with error: > > > [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv > failed: Connection reset by peer (104) > -------------------------------------------------------------------------- > mpirun noticed that process rank 18 with PID 616 on node n344 exited on > signal 4 (Illegal instruction). > -------------------------------------------------------------------------- > [n370:03036] 3 more processes have sent help message > help-opal-shmem-mmap.txt / mmap on nfs > [n370:03036] Set MCA parameter "orte_base_help_aggregate" to 0 to see all > help / error messages > 3 total processes killed (some possibly by mpirun during cleanup) > > I run the same pbs files with older gromacs 4.5.5 (installed with the same > openmpi, gcc and fftw) and everything is working.. > > also when I am running gromacs directly on the access node: > > mpirun -np 32 /home/users/didymos/gromacs/bin/mdrun_mpi -v -deffnm > protein-EM-solvated -c protein-EM-solvated.gro > > it is running OK. > Any ideas? > Nope. Those messages are all from mpirun after GROMACS already wrote any of its diagnostic messages. We'd need what GROMACS wrote to stderr, stdout and the head and tail of the .log file. Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
