sander gives the message that you have more processors than residues. What
does your sander output say?
It looks like you are getting more MPI threads than the # of cores you
assigned (8).
On Thu, Mar 4, 2010 at 6:05 AM, Nkwe Monama <nmonama.csir.co.za> wrote:
> 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 - 04:30:03 PST
