On Sun, Dec 21, 2014 at 9:02 AM, Fabian Glaser <fabian.glaser.gmail.com>
wrote:
> Hi Amber experts,
>
>
> We had pmemd.MPI (amber 14) installed correctly and running, but after a
> disk addition to our cluster it fails to run, we try to run pmemd.MPI with
> the following setup
>
> > source /usr/local/amber14/setup.csh
> which contains the following definitions
>
> > more /usr/local/amber14/setup.csh
> #!/bin/csh -f
> #
> # Setup for Amber 14
> #
> setenv AMBERHOME /usr/local/amber14
> setenv PATH $AMBERHOME/bin:$PATH
> setenv LD_LIBRARY_PATH $AMBERHOME/lib:$LD_LIBRARY_PATH
>
> and sets the MPI path as follows:
>
> > which mpirun
> /usr/local/amber14/bin/mpirun
>
> we get the following error message:
>
> > mpirun -np 12 pmemd.MPI
> -------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> it seems that the "numtasks" parameter is not passed to the pmemd.MPI
> executable.
>
> We would quite appreciate any help, and are ready to provide any additional
> information regarding the AMBER 14 installation and compilation on our
> system.
>
> All the other non-MPI programs including pmemd or sander run fine.
>
This happens when you compile Amber with one MPI and try to use the
"mpirun" from a different MPI. This is true of every MPI program, not just
Amber.
You need to make sure that Amber is compiled with the same MPI installation
you intend on using to run it.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 21 2014 - 08:00:04 PST
