[gmx-users] mpirun error?

Justin Kat justin.kat at mail.mcgill.ca
Wed Feb 16 22:37:30 CET 2011

Dear Gromacs,

My colleague has attempted to issue this command:

mpirun -np 8 (or 7) mdrun_mpi ...... (etc)

According to him, he gets the following error message:

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec.c, line: 5888

Fatal error:
There is no domain decomposition for 7 nodes that is compatible with the
given box and a minimum cell size of 0.955625 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS

However, when he uses say, -np 6, he seems to get no error. Any insight on
why this might be happening?

Also, when he saves the output to a file, sometimes he sees the following:

NOTE: Turning on dynamic load balancing

Is this another flag that might be causing the crash? What does that line

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