Re: Infiniband and PME gridsize

From: Gianluca Interlandi (gianluca_at_bioc.unizh.ch)
Date: Tue Dec 14 2004 - 12:54:55 CST

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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