I believe that I have identified the problem: I was
using sander instead of sander.MPI.
JF
--- Ross Walker <> wrote:
> Hi Joseph
>
> > I have recently upgraded to amber9/mpich2. To my
> > dismay, I found a significant hit in performance
> when
> > using sander9, such that jobs running with sander8
> are
> > up to 5 times faster. I compiled mpich2 with
> Intel
> > compiler8.1, and then compiled amber9 in parallel
> with
> > the same compiler. I realize that something must
> have
> > gone wrong, but it is not clear to me what it is.
>
> > Any help on this matter would be greatly
> appreciated.
> > I am running on a cluster with Intel xeon
> processors
> > and Red Hat Linux Entreprise 3.0.
>
> This is a tough one to help out on due to all the
> variables. However, a few
> questions. Are you using sander or pmemd? What type
> of simulation are you
> running? I you are doing periodic boundary PME or
> Generalized Born implicit
> solvent you should be using PMEMD as you will get
> better performance.
>
> Secondly have you compiled up amber 8 with mpich2?
> Does this show slower
> performance that with mpich v1?
>
> What about single processor speed, without mpich.
> Run a few of the
> benchmarks in $AMBERHOME/benchmarks as single
> processor with amber 8 and
> amber 9. Amber 9 should come out faster than amber
> 8. If it does then the
> problem is definately with your mpich2 installation.
> If it comes out much
> slower then you possibly have an issue with your
> compilers / libraries you
> are linking to etc.
>
> Anyway, I suspect it is a problem with the mpich2
> installation. What is the
> interconnect on your cluster? Be careful that you
> haven't done something
> like compile up mpich2 to use the ethernet
> interconnect instead of say
> myrinet or infiniband. Run some of the mpich2 test
> cases that come with it
> to check.
>
> The essential thing here is, like with any
> scientific experiment, to reduce
> the problem down to a set of independent variables
> that you can test one at
> a time.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:-
> ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
> Note: Electronic Mail is not secure, has no
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> be read every day, and should not be used for urgent
> or sensitive issues.
>
>
>
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Received on Sun May 14 2006 - 06:07:15 PDT
