Re: Infiniband and PME gridsize

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Tue Dec 14 2004 - 13:05:45 CST

Hi Gianluca,

 I don't know for sure yet. But we just got MPI installed and running.
 Charm++ now seems to run ok - megatest passed, so will try NAMD next. I
don't expect any major problem of NAMD on inifiband at this point.

Gengbin

Gianluca Interlandi wrote:

>Dear Gengbin,
>
>Many thanks for your answer. Do you think that NAMD would run well on
>infiniband, i.e. any incompatibilities with the MPI-libraries?
>
>Many thanks,
>
> Gianluca
>
>On Tue, 14 Dec 2004, Gengbin Zheng wrote:
>
>
>
>>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 **
>>>*****************************************************************
>>>
>>>
>>>
>>>
>>
>>
>
>-----------------------------------------------------
>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
>-----------------------------------------------------
>
>

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