Re: Infiniband and PME gridsize

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Dec 14 2004 - 12:16:55 CST

I don't think we have ever run NAMD on infiniband. We are building a
smaller cluster though in the lab and will test the scalability
hopefully soon.

Gengbin

Brian Bennion wrote:

>Can't address number 1 (wish I could!! I would love to try that hardware)
>
>Number 2
>>From my discussions with the developers, the transforms are optimized for
>small factorials of the pme gridsizes. In other words, 99.2 doesn't
>factor well. However, 90 does a bit better 3x3x2x5. Ideally a number
>that factors to prime numbers less than 5 is "optimal". This may have
>changed though. So chose a value that encompasses your system and can be
>factored well...they don't have to be equal to your system dimensions.
>
>Regards
>Brian
>
>
>On Tue, 14 Dec 2004, Gianluca Interlandi wrote:
>
>
>
>>Dear NAMD users,
>>
>>I have two independent questions:
>>
>>1) Are there any experiences about the scalability running NAMD on
>> infiniband? I have been running NAMD on myrinet and, as an example, for
>> a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron
>> 1800+).
>>
>>2) What is recommended for a PME gridsize? One of my boxes has a
>> sidelength of 99.2 A. What is the "ideal" gridsize in this case?
>>
>>Many thanks,
>>
>> Gianluca
>>
>>-----------------------------------------------------
>>Gianluca Interlandi gianluca_at_bioc.unizh.ch
>> +41 (0) 1 635 55 93
>> +41 (0)79 655 73 35
>> http://biocroma.unizh.ch/gianluca/
>>
>>PhD-Student of the Department of Biochemistry
>>at the University of Zurich Irchel, Switzerland
>>-----------------------------------------------------
>>
>>
>>
>
>*****************************************************************
>**Brian Bennion, Ph.D. **
>**Computational and Systems Biology Division **
>**Biology and Biotechnology Research Program **
>**Lawrence Livermore National Laboratory **
>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>**7000 East Avenue phone: (925) 422-5722 **
>**Livermore, CA 94550 fax: (925) 424-6605 **
>*****************************************************************
>
>

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