Hi,
before running parallel job, i type mpd & then setenv DO_PARALLEL 'mpirun
-np 8'
is there anything wrong?
i compile amber parallel with:
./configure_amber -mpich2 gfortran
make parallel
mpich2version:
MPICH2 Version: 1.2.1p1
MPICH2 Release date: Unknown, built on Wed Feb 16 10:26:18 MYT 2011
MPICH2 Device: ch3:nemesis
MPICH2 configure: --prefix=/opt/mpich2
MPICH2 CC: gcc -O2
MPICH2 CXX: c++ -O2
MPICH2 F77: g77 -O2
MPICH2 F90: f95 -O2
I tried using lam following the manual but it turned out to be the same,
when top, there are 8 sander.MPI but the output indicate that running in one
node.
Pls assist.
Thanks and regards,
Colvin
On Wed, Mar 9, 2011 at 3:27 AM, Jason Swails <jason.swails.gmail.com> wrote:
> What command did you use to spawn all 8 threads? I've seen this happen
> before when, for instance, I compile sander.MPI with OpenMPI compiler
> wrappers, yet use an mpich2 mpirun/mpiexec script to launch sander.MPI.
> This is bad because then you have 8 separate 1-thread MPI jobs trying to
> read from and write to the same files.
>
> Try recompiling Amber, taking care that you're using the right mpicc/mpif90
> (make sure PATH is set up correctly to use the proper compilers, or modify
> the compilers with absolute paths in config.h).
>
> Hope this helps,
> Jason
>
> On Tue, Mar 8, 2011 at 1:11 AM, colvin <colvin4367.gmail.com> wrote:
>
> > Hi all,
> >
> > I tried to run my simulations on a machine with 2 quad core processors (8
> > in
> > total). When i top, it shows 8 running sander.MPI.
> >
> > But when i open the .out file from md run, it stated that:
> >
> > "Running AMBER/MPI version on 1 nodes"
> >
> > and this actually explained why my simulation taken such a long time,
> even
> > for 200 ps (about 3 days).
> >
> > Pls assist and comment. Thanks.
> >
> > Thanks and regards,
> > Colvin
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 08 2011 - 22:30:03 PST
