[gmx-users] Re: gmx-users Digest, Vol 1, Issue 1430
Pim Schravendijk
schraven at mpip-mainz.mpg.de
Tue May 18 21:04:05 CEST 2004
Thanks to the tip from Mike Sullivan (thanx!) to use the 386 rpm I was
able to do runs on a more plausible speed. I did one cpu runs on these
systems:
Type Ghz L2 Cache (I think this is L2)
---------------------------------------------
Mac 2.0 512 kb
Xeon 2.8 512 kb
Opteron 2.0 1024 kb
And here are my results, I added the ones of David from November 2003
System Mac(1) Xeon(2) Optn(3) Optn(4)
-------------------------------------------
Villin 11220 9267 8807 9340
lzm 3048 2878 1801 2541
lzmpme 1438 1529 1281 1600
dppc 143 151 173 185
polymer 3306 3945 3787 4192
(1) With espresso running on other node during most runs.
(2) Using the intel compiler.
(3) With two runs at one 2-cpu node for most runs; using the 386 rpm
binary.
(4) Run with probably better compilation by David v.d. Spoel (gromacs
developer).
I am a bit confused by these results, it seems that the Mac has some
advantage from the altivec loop on the systems with a lot of water, but
really loses when it comes to large amounts of non-water molecules. It
could also be a memory related problem, but it that was the main cause the
polymer should also do well on the Mac.
For the huge bilayer systems the opteron wins I would guess from these
rough statistics, but the medium-sized systems might be handled better by
a xeon or mac.
Do these data look plausible, or are there people with completely other
experiences?
Greetings, Pim
--
Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research
http://www.mpip-mainz.mpg.de/~schraven/
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