[gmx-users] Hyper-threading Gromacs 5.0.1

[Johnny Lu]

Does writing frequently (like position, velocity, energy, log every 10
timesteps) significantly slow down the simulation?

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.
>>>
>>
>>
>