Dear gromacs users, I am trying to run a replica exchange simulation using the files you find in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz
The 4 replicas have been generated, as following: grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp The simulation was started with command, using gromacs 4.5.5 with the latest bug fix: mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out1 giving the following error: [etna:10799] *** An error occurred in MPI_comm_size [etna:10799] *** on communicator MPI_COMM_WORLD [etna:10799] *** MPI_ERR_COMM: invalid communicator [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 10796 on node etna exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [etna:10795] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [etna:10795] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages The nice thing is that the same error doesn't appear either if I use the 4.5.5 without applying tha patches!!! mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out2 or the bug fixed with multiple processors per replica: mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out3 Since I have to use more then 4 replicas, I need to run 1cpu/replica. Has someone any idea of the probem? Francesco -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
