[gmx-users] Restart REMD

Min Wu min.wu at chem.gu.se
Fri Aug 16 15:05:29 CEST 2013

Hi gmx-users

I had an error as followed when I restart my REMD with commands:

mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend
-replex 250 in gromacs version 4.5.5


[glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce
[glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD
[glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator
[glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will
now abort
mpirun has exited due to process rank 53 with PID 17572 on
node glenn26-3 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
[glenn25-3.int.private:22036] 17 more processes have sent help message
help-mpi-errors.txt / mpi_errors_are_fatal
[glenn25-3.int.private:22036] Set MCA parameter "orte_base_help_aggregate"
to 0 to see all help / error messages

Is this a bug? how to fix it?

Best regards


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