Dear,
I have been trying to run Amber with MOAB script and I get the following messages:
stderr:
********************************************************************************
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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 18 with PID 19339 on
node cnode-1-19 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[cnode-3-23:11079] 47 more processes have sent help message help-mpi-api.txt / mpi-abort
[cnode-3-23:11079] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
*********************************************************************************
stdout:
*********************************************************************************
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
Must have more residues than processors!
***************************************************************************
The following is my MOAB script to run amber:
***************************************************************************
###These lines are for Moab
#MSUB -l nodes=1:ppn=8
#MSUB -l partition=ALL
#MSUB -l walltime=2:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /export/home/nmonama/scratch/amber/amber.out
#MSUB -e /export/home/nmonama/scratch/amber/amber.err
#MSUB -d /export/home/nmonama/scratch/amber
#MSUB -mb
#MSUB -M nmonama.csir.co.za
##### Running commands
cd /export/home/nmonama/scratch/amber
mpirun -nolocal -hostfile hosts /export/home/nmonama/amber/bin/sander.MPI -O -i boxeq.mdin -c 1037.mrst -p 3aibx.prmtop -o tmpmd38.mdout -r 1038.mdrst -x crd100000to110000ps -e en100000to110000ps
****************************************************************************************
Regards,
Nkwe
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Received on Thu Mar 04 2010 - 03:30:03 PST
