Re: [gmx-users] Running GROMACS on mini GPU cluster

[Szilárd Páll]

The message is perfectly normal. When you do not use all available
cores/hardware threads (seen as CPUs by the OS), to avoid potential
clashes, mdrun does not pin threads (i.e. it lets the OS migrate
threads). On NUMA systems (most multi-CPU machines), this will cause
performance degradation as without pinning the OS can move tightly
coupled threads belonging to the same process/MPI rank to different
NUMA regions (e.g. cores on different CPU sockets).

With four physical cores the machines in question are most probably
single-processor and for these pinning will not improve performance by
much (if at all).

Cheers,
--
Szilárd


On Fri, Jul 26, 2013 at 12:09 AM, Tim Moore tcmoo...@gmail.com wrote:
 I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am 
 trying to bench mark some systems, and I am getting this message:

 NOTE: The number of threads is not equal to the number of (logical) cores
   and the -pin option is set to auto: will not pin thread to cores.
   This can lead to significant performance degradation.
   Consider using -pin on (and -pinoffset in case you run multiple jobs).

 Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set 
 -nt 2. But since we have a queuing system, there is no way to know which 
 cores will be available to set -pinoffset. Does anyone have a solution, or 
 should I even be worrying about that at all?

 Thanks,
 Tim--
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Re: [gmx-users] Running GROMACS on mini GPU cluster

[Justin Lemkul]

On 7/25/13 6:09 PM, Tim Moore wrote:

I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying 
to bench mark some systems, and I am getting this message:

NOTE: The number of threads is not equal to the number of (logical) cores
   and the -pin option is set to auto: will not pin thread to cores.
   This can lead to significant performance degradation.
   Consider using -pin on (and -pinoffset in case you run multiple jobs).

Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set -nt 
2. But since we have a queuing system, there is no way to know which cores will 
be available to set -pinoffset. Does anyone have a solution, or should I even 
be worrying about that at all?



You're probably not invoking mdrun correctly for your configuration.  The wiki 
page has some useful examples:


http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Heterogenous_parallelization.3a_using_GPUs

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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