Re: [AMBER] error in using pmemd

From: Jason Swails <>
Date: Tue, 10 Jun 2014 11:22:20 -0400

On Tue, 2014-06-10 at 15:13 +0000, Valentina Romano wrote:
> Dear users
> I tried to run a MD simulation in parallel but the output file looked not good.
> The input file to run the parrallel MD was (5ns in total):
> #!/bin/bash -l
> #$ -N PknGAde_md
> #$ -l membycore=1G
> #$ -l runtime=25:00:00
> #$ -pe ompi 32
> #$ -cwd
> ##$ -o $HOME/queue/stdout
> ##$ -e $HOME/queue/stderr
> module load OpenMPI
> #echo "Got $NSLOTS processors."
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md01.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_equil.rst -r PknGAde_md01.rst -x PknGAde_md01.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md02.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md01.rst -r PknGAde_md02.rst -x PknGAde_md02.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md03.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md02.rst -r PknGAde_md03.rst -x PknGAde_md03.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md04.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md03.rst -r PknGAde_md04.rst -x PknGAde_md04.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md05.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md04.rst -r PknGAde_md05.rst -x PknGAde_md05.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md06.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md05.rst -r PknGAde_md06.rst -x PknGAde_md06.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md07.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md06.rst -r PknGAde_md07.rst -x PknGAde_md07.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md08.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md07.rst -r PknGAde_md08.rst -x PknGAde_md08.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md09.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md08.rst -r PknGAde_md09.rst -x PknGAde_md09.mdcrd
> mpirun -v -np $NSLOTS pmemd -O -i -o PknGAde_md10.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md09.rst -r PknGAde_md10.rst -x PknGAde_md10.mdcrd

pmemd executes in serial _only_. If you wish to run in parallel, you
need to use "pmemd.MPI" instead.

> Thus, something wrong append, but I do not know what. It is the first time i try to run MD in parallel.
> Any suggestion?

These symptoms are evidence that you are using a serial executable for
parallel execution. Use pmemd.MPI instead.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 08:30:02 PDT
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