Sukit Leekumjorn wrote:
Dear Gmx-developer
This is regard to the CVS version. I came across Erik Lindahl's
presentation on Simulations of Membranes and Membrane Proteins from
Gromacs Workshop at CSC. At the end of the presentation, he mentioned
that the membrane simulations can be scale up to >1000 CPUs in CVS. If
anyone have try this on the CVS version, could u please give me
information on how to run this version of Gromacs. I see that there are
new options implemented in "mdrun" and -shuffle is removed from
"grompp". Below are the new options in "mdrun".
-dd vector 1 1 1 Domain decomposition grid, 1 is particle dec.
-npme int 0 Number of separate nodes to be used for PME
-[no]cart bool no Use a Cartesian communicator
-rdd real 0 The minimum distance for DD communication
-[no]dlb bool no Use dynamic load balancing
just try e.g. mdrun -d 8 8 8 on 512 processors and play with the other
flags. Since these flags are by no means the final ones (that is, we
would like to automate things further) it doesn't make sense to get into
a lot of detail. Also, please beware that this is a development version
and check you results.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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