Thank you, Szilárd, for this list of options!
2014-10-13 22:00 GMT+04:00 Szilárd Páll :
> Hi,
>
> As the log file points out, you picked a combinations of settings that
> do not have corresponding optimized non-bonded kernels:
>
> "LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels,
Hi,
As the log file points out, you picked a combinations of settings that
do not have corresponding optimized non-bonded kernels:
"LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels,
falling back to plain-C kernels
Using plain C 4x4 non-bonded kernels
WARNING: Using the slow plai
Good day,
Here is the .log file
https://drive.google.com/file/d/0B3p_uIrSkPysS2kweC1QWUVfaTA
Regards
Oleg Titov
2014-10-13 13:31 GMT+04:00 Mark Abraham :
> Hi,
>
> Very likely that simulation is too small to make good use of that many
> cores (though if there's hyper-threading going on, then th
What about trying a larger system, ~10,000 interaction centers?
The performance which you report is much below natural expectations for GROMACS.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Mon, Oct 13, 2014 at 10:55 AM, Олег Титов wrote:
> Thanks for you reply.
>
> On a different machi
Hi,
Very likely that simulation is too small to make good use of that many
cores (though if there's hyper-threading going on, then there may only be 8
real cores, and you may do better with hyper-threading off...). Gromacs use
of OpenMP does not do very well with lots of threads and few atoms. If
Thanks for you reply.
On a different machine I've recompiled GROMACS with icc version 13.1.0 (gcc
version 4.4.6 compatibility).
cmake command:
I_MPI_CC=nvcc CC=icc CXX=icpc cmake ../gromacs-src
-DCMAKE_INSTALL_PREFIX=~/gromacs-5.0.2/ -DGMX_FFT_LIBRARY=MKL -DGMX_MPI=OFF
-DGMX_GPU=OFF -DGMX_BUILD_MD
On Fri, Oct 10, 2014 at 8:16 PM, Олег Титов
wrote:
> Good day.
>
> I've got sigmificant performance degradation when trying to use Verlet
> cutoff-scheme for free energy calculation. My system contains 1
> bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on
> 8-core CPU resulte
Good day.
I've got sigmificant performance degradation when trying to use Verlet
cutoff-scheme for free energy calculation. My system contains 1
bromobenzene molecule and 543 TIP3P waters. 16 hours of calculation on
8-core CPU resulted in 2.5 ns trajectory. With group scheme i've got 6.5 ns
trajec
