[gmx-users] forcefield and run in parallel
spoel at xray.bmc.uu.se
Mon Sep 2 23:02:42 CEST 2002
On Mon, 2002-09-02 at 21:23, Rui Qiao wrote:
> I followed the approach David suggested and I think Gromacs is
> using the new parameters in the simulation. Thanks for all the responses!
> I am now trying to run Gromacs in parallel and somehow the speedup
> is not significant. The basic information is the following:
> # of atom: ~5000 (around 1300 water)
> Forces: PME, 4th order interpolation, FFT grid: 0.11nm,
> vdw cut-off: 1.1nm
> The performance are (on P-III platinuum):
> 1 node : 23.8h/ns
> 4 nodes: 13.9h/ns
> 6 nodes: 12.8h/ns
> 8 nodes: 11.5h/ns
to be honest, it doesn get any better than this for small systems,
unless you have a high speed network or an IBM SP2. Erik and I plan to
work on it, if we get over our need for a couple of hours sleep a day...
> It seems that the performance does not scale nicely with
> increasing nodes for node>=4. I realize that I am using PME and am having
> a small system, but is there a way to somehow boost the performance?
> While checking the log file, I found there are some information
> Total NODE time on node 0: 922.68
> Average NODE time: 153.78
> Load imbalance reduced performance to 600% of max
> My simulation system has about 1200 atoms that are frozen in the
> simulation and they are allocated on node 0 in the simulations. Could this
> cause problems like load im-balancing?
> Rui Qiao
> Research Assistant
> Beckman Institute, UIUC
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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