hi,
but issue has been reported to us hencee have to sort it out..any
pointers will be helpful
thanks...
On 3/4/12, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> 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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>> >>
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>> >
>> >
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Candidate
>> > 352-392-4032
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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Received on Sat Mar 03 2012 - 19:30:02 PST
