[gmx-users] Hyper-threading Gromacs 5.0.1

[Carsten Kutzner]

On 11 Sep 2014, at 05:03, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Does writing frequently (like position, velocity, energy, log every 10
> timesteps) significantly slow down the simulation?
Probably yes, have a look at the md.log output file
and how much percent is spent in write traj.

Carsten


> 
> On Wed, Sep 10, 2014 at 10:31 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> 
>> tried that, and the result was:
>> 
>> Reading file npt.tpr, VERSION 5.0.1 (double precision)
>> Changing nstlist from 10 to 40, rlist from 1 to 1.028
>> 
>> The number of OpenMP threads was set by environment variable
>> OMP_NUM_THREADS to 48
>> Using 1 MPI thread
>> Using 48 OpenMP threads
>> 
>> WARNING: Oversubscribing the available 24 logical CPU cores with 48
>> threads.
>>         This will cause considerable performance loss!
>> 
>> -------------------------------------------------------
>> Program mdrun_d, VERSION 5.0.1
>> Source code file:
>> /export/data1/kho/software/gromacs5.1/gromacs-5.0.1/src/gromacs/mdlib/nbnxn_search.c,
>> line: 2577
>> 
>> Fatal error:
>> 48 OpenMP threads were requested. Since the non-bonded force buffer
>> reduction is prohibitively slow with more than 32 threads, we do not allow
>> this. Use 32 or less OpenMP threads.
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> 
>> so. i guess that is not a good idea.
>> 
>> On Wed, Sep 10, 2014 at 9:55 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>> 
>>> that 8-20% performance increase was for gromacs 4.6.5
>>> 
>>> On Wed, Sep 10, 2014 at 9:52 PM, Johnny Lu <johnny.lu128 at gmail.com>
>>> wrote:
>>> 
>>>> Is it a good idea to use 48 OpenMP thread, under 1 MPI thread on 24 Xeon
>>>> Processors?
>>>> 
>>>> The mail list say such practice give about 8-20% performance increase
>>>> 
>>>> Should I try g_tune_pme when I searched for "imbalance" in the log file
>>>> and found nothing (24 OMP thread under 1 MPI thread on 24 Xeon Processor)?
>>>> Or is that done automatically?
>>>> 
>>>> Does gromacs support double precision calculation on GPU if the hardware
>>>> supports that?
>>>> 
>>>> The optimize fft option is also obsolete.
>>>> 
>>>> Thanks again.
>>>> 
>>> 
>>> 
>> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa