Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun

From: Jason Swails <>
Date: Mon, 20 Aug 2012 00:07:09 -0400


On Sun, Aug 19, 2012 at 9:53 PM, Catein Catherine <>wrote:

> Dear Sir/Madam,
> I have a cpptraj input file as follows:
> parm xxx.prmtoptrajin xxx.mdcrd.gzaverage xxx.pdb pdb
> I then run $AMBERHOME/bin/cpptraj < cpptraj
> It works perfectly. However, when I run the same command in mpirun and
> queuing the job at supercomputer system, it did not work. Following are
> some of the error message that I got.

By "the same command", do you mean:

mpirun -np X $AMBERHOME/bin/cpptraj < cpptraj


If so, this will not work for any of Amber's MPI programs. Every program
in Amber that is MPI-parallelized has a separate MPI-enabled executable
(such as cpptraj.MPI). I don't think cpptraj.MPI is ever built (not sure
if it would even work if you could build it...)

If you want parallel support for cpptraj, I think you need to do an OpenMP
build (note, this is NOT OpenMPI). Before doing this, though, you should
check the AmberTools manual for the specific actions that are
parallelizable to see if it is worthwhile.

Otherwise, just run cpptraj in serial.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Sun Aug 19 2012 - 21:30:03 PDT
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