[gmx-users] Affinity setting for 1/16 threads failed. Version 5.0.2

[Siva Dasetty]

Thank you Mark. Yes I have already taken this issue to gordon and while am
awaiting for their response I am just wondering if this issue has anything
to do with the bug#1184: http://redmine.gromacs.org/issues/1184.


Thank you again for your quick response.

On Wed, Nov 18, 2015 at 10:31 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> These are good issues to take up with the support staff of gordon. mdrun
> tries to be a good citizen and by default stays out of the way if some
> other part of the software stack is already managing process affinity. As
> you can see, doing it right is crucial for good performance. But mdrun -pin
> on always works everywhere we know about.
>
> Mark
>
> On Wed, Nov 18, 2015 at 3:28 PM Siva Dasetty <sdasett at g.clemson.edu>
> wrote:
>
> > Dear all,
> >
> > I am running simulations using version 5.0.2 (default in gordon) and I am
> > having a performance loss from 180 ns/day to 8 ns/day compared to the
> same
> > simulations that I previously ran in a different cluster.
> >
> > In both the clusters I am using a single node and 16 cpus (no gpus) and
> the
> > following is the command line I used:
> >
> > mdrun_mpi -s <tpr file> -v -deffnm <output file> -nb cpu -cpi <cpt file>
> > -append -pin on
> >
> >
> > Following is reported in the log file:
> >
> >
> > WARNING: Affinity setting for 1/16 threads failed.
> >
> >          This can cause performance degradation! If you think your
> setting
> > are correct, contact the GROMACS developers.
> >
> >
> > I even tried running a simulation without the flag -pin on and there is
> no
> > change in the performance.
> >
> >
> > Are there any other options that I can try to recover the performance?
> >
> >
> >
> > Additional Information:
> >
> >
> > The other difference I could see is in the compilers:
> >
> >
> > In gordon (8ns/day):
> >
> >
> > C compiler: /opt/mvapich2/intel/ib/bin/mpicc Intel 13.0.0.20121010
> >
> > C compiler flags:    -mavx    -std=gnu99 -w3 -wd111 -wd177 -wd181 -wd193
> > -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418
> > -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346
> > -wd11074 -wd11076  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const
> > -ansi-alias
> >
> > C++ compiler:       /opt/mvapich2/intel/ib/bin/mpicxx Intel
> 13.0.0.20121010
> >
> > C++ compiler flags:  -mavx    -w3 -wd111 -wd177 -wd181 -wd193 -wd271
> -wd304
> > -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572
> > -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076
> > -wd1782 -wd2282  -O3 -DNDEBUG -ip -funroll-all-loops -alias-const
> > -ansi-alias
> >
> >
> > In our cluster (180 ns/day):
> >
> >
> > C compiler: /software/openmpi/bin/mpicc GNU 4.8.1
> >
> > C compiler flags:    -msse4.1    -Wno-maybe-uninitialized -Wextra
> -Wno-miss
> >
> > ing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
> -Wno-unused
> >
> > -Wunused-value -Wunused-parameter  -O3 -DNDEBUG -fomit-frame-pointer
> -funro
> >
> > ll-all-loops -fexcess-precision=fast  -Wno-array-bounds
> >
> > C++ compiler: /software/openmpi/bin/mpicxx GNU 4.8.1
> >
> > C++ compiler flags:  -msse4.1    -Wextra -Wno-missing-field-initializers
> -W
> >
> > pointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG
> -fomit-frame-pointer
> >
> >  -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
> >
> >
> >
> >
> > Thanks in advance for your help,
> >
> > --
> > Siva Dasetty
> > --
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-- 
Siva Dasetty