[gmx-users] Hyper-threading Gromacs 5.0.1

Johnny Lu johnny.lu128 at gmail.com
Thu Sep 11 04:31:44 CEST 2014

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
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:
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.

More information about the gromacs.org_gmx-users mailing list