Hi Mark,
Mark Abraham wrote:
Terminology - GROMACS is not threaded, but uses MPI processes for
parallelism.
Yes, I gathered that.
I have an MPI-compiled version of gromacs v4.0 and am attempting to
get parallel execution on a 2x2 core AMD Opteron system via:
$ lamboot
$ mdrun -np 4 -s ../1WOM.tpr -v -N 4
-N does nothing, and -np is no longer accepted - as you'd know from
reading mdrun -h, right?
That is a bit of a condecending way of putting it. If I knew -N did
nothing and -np was no longer accepted, then of course I would not have
used them. In fact, I was reading the documentation from a file called
"manual-4.0.pdf" which stated:
"
If you have a single machine with multiple processors you don’t have to
use the mpirun com-
mand, but you can do with an extra option to mdrun:
% mdrun -np 8 -s topol -v -N 8
"
so that is where I took the example from. I think this PDF was linked
from the gromacs "documentation" section of the website.
Like most MPI parallel codes, you need to use mpirun. If your lam
environment is correctly configured, then I think you will not need
-np 4 as an argument to mpirun.
Also, probably you are actually running a non-MPI gromacs, since by
default, using --enable-mpi will suffix mdrun to be mdrun_mpi.
Doesn't look like it:
$ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi
$ make
$ make install
$ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun
mdrun
Anyway, thanks for your suggestions because I now have it working via:
$ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4
and I see 4 processes running at 100% and an estimated run time 25% of
the serial version.
Ian.
--
Ian Stokes-Rees, Research Associate
SBGrid, Harvard Medical School
http://sbgrid.org
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