[gmx-users] limit of number of processors ??
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 21 22:59:50 CET 2006
이 선주 wrote:
> Hello All,
> I have been doing membranes simulations using the computer nodes in
> UTEXAS supercomputing center. Each board contains two Xeon Intel
> Duo-Core 64-bit processors (4 cores in all) and nodes are interconnected
> with InfiniBand technology.
> The performance is great. However, I have got weird results if I
> increase the number of processors more than 12. Even though the bilayer
> is still intact, one or two lipids were popped out of the membrane not
> long after the simulation was started.
> To make sure that it is not the problem due to different initial
> conditions, I ran two separate md simulations starting from the same
> structure and velocities on each atom but only with different number of
> processors, 8 and 16.
> As expected, the job with 8 processors resulted in the intact membrane
> but a lipid was pulled out of the membrane in the job run with 16
> So far, I could not find out the cause of this problem. Does anyone have
> any thought about this problem?
> Thank you
Please check bugzilla to see if your problem is listed there. It looks a
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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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