[gmx-users] Specifying the number of OpenMP threads that g_hbond uses

[Justin Lemkul]

On 4/19/14, 1:51 PM, Andrew DeYoung wrote:
> Hi,
>
>  From the web page
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x ,
>
> it looks like parallelization for g_hbond (via OpenMP) was added in version
> 4.6.x.
>
> What is a typical command to run g_hbond in parallel?  Since I mostly have
> experience with Gromacs 4.5.5 (which for mdrun has auto MPI threading as the
> default parallelization, which means I only have to specify the number of
> threads with -nt), I am not sure how to launch OpenMP for g_hbond in 4.6.x.
>
>
> When I just run g_hbond in 4.6.1 with no extra flags, the output says,
> "Frame loop parallelized with OpenMP using 8 threads."  Is there any way to
> change the number of OpenMP threads that g_hbond uses?
>

g_hbond -nthreads.  See description in g_hbond -h.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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