The user should contact the list herself since she will or should know many
more details that we will need.
On Mar 3, 2012 1:27 PM, "akshar bhosale" <akshar.bhosale.gmail.com> wrote:
> thanks for the detailed info Jason...
>
> however, job is running 100x slower. when she ran job earlier with
> same conf, it was performing fast now this one is slower. other jobs
> are fine using the same MPI and env...i mean non amber jobs. what
> tuning needs to be done?where can be problem? process spawing is aslo
> proper. we have 8 cpu nodes, and cpu load is 8, memory comsumpiton is
> around 3 GB out of 24 GB RAM per node. such 52 nodes.
>
> On 3/3/12, Jason Swails <jason.swails.gmail.com> wrote:
> > On Fri, Mar 2, 2012 at 10:14 PM, akshar bhosale
> > <akshar.bhosale.gmail.com>wrote:
> >
> >> hi,
> >> sorry to give incomplete info but even i dont hv complete info as i am
> >> sysadmin and our client is complying about job running very slow. she
> >> says that when she runs classical amber job, it runs fast but when she
> >> runs replica exchange job, it runs very slow.
> >>
> >
> > There are too many degrees of freedom here. First, the issue could be
> > completely unrelated to Amber (it could be a poorly configured MPI). It
> > could also be that the user doesn't know how to properly run MPI jobs on
> > the cluster (that is, she may be trying to run 16 threads across 2 8-core
> > nodes, for instance, but is binding all 16 threads to the same node).
> >
> > She may also be comparing sander performance to pmemd performance, which
> > accounts for a factor of 2-3 in speed and scaling. She could also be
> > attempting exchanges of replicas every 2 steps, which will cause
> > significant slowdown (around 2x slower or so) but is completely expected.
> >
> > This is only a small sample of the possible things that could be
> happening,
> > all that easily explain the available info. However, "very slow" and
> "runs
> > fast" could mean anything. Is it a 1000x slowdown? Is it a 2x slowdown?
> > Each implies a different set of explanations (but simply giving us that
> > number is still not enough to diagnose).
> >
> > My suggestion would be to rule out factors that are _unrelated_ to Amber
> > first, since those are most likely the root causes of such observations.
> > For instance -- how are her MPI threads distributed? Is she using the
> > correct MPI executables that correspond to the ones that were used to
> build
> > parallel Amber in the first place? Etc.
> >
> > You could also check the Amber installation itself and make sure that the
> > benchmark suite gives results expected based on comparisons to
> > http://ambermd.org.
> >
> > HTH,
> > Jason
> >
> >
> >> On 3/1/12, Cannon, John F. <CannonJ.health.missouri.edu> wrote:
> >> > Dear Akshar,
> >> >
> >> > You have provided practically no useful information about your
> >> > simulation
> >> > for diagnosis. How many atoms? What is the nonbonded cutoff, etc? What
> >> were
> >> > the benchmarks on other simulations on your computer?
> >> >
> >> > John Cannon
> >> > Genetics Program Chair and
> >> > Associate Professor of
> >> > Molecular Microbiology and Immunology
> >> > University of Missouri
> >> > 1 Hospital Drive
> >> > Columbia, Missouri 65212
> >> >
> >> >
> >> > -----Original Message-----
> >> > From: akshar bhosale [mailto:akshar.bhosale.gmail.com]
> >> > Sent: Thursday, March 01, 2012 11:44 AM
> >> > To: amber.ambermd.org
> >> > Subject: [AMBER] slow : amber job
> >> >
> >> > hi,
> >> >
> >> > my amber jobs are running very slow and has completed only 1 ns in 3
> >> days. i
> >> > am using amber 10. job is bigger.
> >> >
> >> > _______________________________________________
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> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Sat Mar 03 2012 - 11:00:03 PST
