vivek sharma wrote:
Hi Carsten,
I have also tried scaling gromacs for a number of nodes ....but was not
able to optimize it beyond 20 processor..on 20 nodes i.e. 1 processor
per node..
I am not getting the point of optimizing PME for the number of nodes, is
it like we can change the parameters for PME for MDS or using some other
coulomb type for the same, please explain.
This is something I played with for a while; see the thread I started here:
http://www.gromacs.org/pipermail/gmx-users/2008-October/036856.html
I got some great advice there. A big factor is the PME/PP balance, which grompp
will estimate for you. For simple rectangular boxes, the goal is to shoot for
0.25 for the PME load (this is printed out by grompp). In the thread above,
Berk shared with me some tips on how to get this to happen.
Then you should be able to set -npme using mdrun to however many processors is
appropriate. I believe mdrun will try to guess, but I'm in the habit of
specifying it myself just for my own satisfaction :)
-Justin
and suggest me the way to do it.
With Thanks,
Vivek
2008/11/10 Carsten Kutzner <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Hi,
most likely the Ethernet is the problem here. I compiled some
numbers for the DPPC
benchmark in the paper "Speeding up parallel GROMACS on high-latency
networks",
http://www3.interscience.wiley.com/journal/114205207/abstract?CRETRY=1&SRETRY=0
<http://www3.interscience.wiley.com/journal/114205207/abstract?CRETRY=1&SRETRY=0>
which are for version 3.3, but PME will behave similarly. If you did
not already use
separate PME nodes, this is worth a try, since on Ethernet the
performance will drastically
depend on the number of nodes involved in the FFT. I also have a
tool which finds the
optimal PME settings for a given number of nodes, by varying the
number of PME nodes
and the fourier grid settings. I can send it to you if you want.
Carsten
On Nov 9, 2008, at 10:30 PM, Yawar JQ wrote:
I was wondering if anyone could comment on these benchmark results
for the d.dppc benchmark?
Nodes Cutoff (ns/day) PME (ns/day)
4 1.331 0.797
8 2.564 1.497
16 4.5 1.92
32 8.308 0.575
64 13.5 0.275
128 20.093 -
192 21.6 -
It seems to scale relatively well up to 32-64 nodes without PME.
This seems slightly better than the benchmark results for Gromacs
3 on www.gromacs.org <http://www.gromacs.org/>.
Can someone comment on the magnitude of the performance hit and
lack of scaling with PME is worrying me.
For the PME runs, I set rlist,rvdw,rouloumb=1.2 and the rest set
to the defaults. I can try it with some other settings, larger
spacing for the grid, but I'm not sure how much more that would
help. Is there a more standardized system I should use for testing
PME scaling?
This is with GNU compilers and parallelization with OpenMPI 1.2.
I'm not sure what we're using for the FFTW The compute nodes are
Dell m600 blades w/ 16GB of RAM and dual quad core Intel Xeon 3GHz
processors. I believe it's all ethernet interconnects.
Thanks,
YQ
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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