Dear Bob, Ros, amber community,
So, as Bob suggested it looks like the pmemd segmentation fault that I
reported some days ago had something to do with the i8 and i4 versions
of amber9 that people at the PNNL compiled. As soon as I changed to the
i4 version the problem dissapeared. I am currently trying to fix the
problem for the i8 version together with the people responsible.
I started a meticulous benchmarking (pmemd9) of my system (65 k atoms)
by running 5000 steps of MD (10 ps) on 8, 16, 32, 64, 128, and 512 cpus.
The first results for the total time are:
8 cpus - 775 s,
16 cpus - 463 s,
32 cpus - 277 s,
64 cpus - 402 s.
Since I do not have experience with benchmarking, I was confused by the
differnce between 32 cpus and 64 cpus and I noticed that the difference
comes from "DataDistrib" at the end of the pmemd output (see outputs for
32 and 64 cpus below). My question is what does actually "DataDistrib"
mean? Is this action done only once at the beginning of the simulation,
therefore being independent of the number of MD steps ? Could you tell
me which are the actions in the output table done only once at the
beginning of the simulation and which are done each step (obvously the
energy terms are calculated each step but for instance RunMD seems ta
take the same time on different numbers of CPUs?
I am asking this because I would like to use these 5000 steps benchmark
runs to estimate the numebr of ns/day for each run ... Is this actually
possible?
Thanks a lot for help on this!!
Best wishes
vlad
Output 32 cpus
| DataDistrib 87.84 32.06
| Nonbond 166.87 60.90
| Bond 0.08 0.03
| Angle 0.96 0.35
| Dihedral 2.81 1.02
| Shake 2.27 0.83
| RunMD 13.09 4.78
| Other 0.10 0.04
| ------------------------------
| Total 274.02
Output 64 cpus
| DataDistrib 306.89 77.25
| Nonbond 71.37 17.96
| Bond 0.03 0.01
| Angle 0.47 0.12
| Dihedral 1.37 0.34
| Shake 1.54 0.39
| RunMD 15.36 3.87
| Other 0.24 0.06
| ------------------------------
| Total 397.27
--
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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Received on Sun Apr 01 2007 - 06:07:23 PDT
