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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>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sat Mar 03 2012 - 10:30:02 PST
