[gmx-developers] VsiteN in parallel problem

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 18 22:01:54 CEST 2014

On 2014-08-18 22:03, Berk Hess wrote:
> On 08/18/2014 09:54 PM, David van der Spoel wrote:
>> On 2014-08-18 21:41, Berk Hess wrote:
>>> Hi,
>>> I don't understand what the issue is exactly.
>>> When you use OpenMP only one thread creates the vsite, but after a
>>> thread barrier (which is implicitly present when exiting an OpenMP
>>> parallel region) after all threads will have the new vsite position,
>>> since they all share the same memory.
>> Thanks, I was looking for the communication code but of course it is
>> not needed. It seems the problem is in the initiation of thread
>> structures specific for vsiteN. There are tons of if (ftype != VSITEN)
>> in the code. I'll figure it out.
> But do I understand correctly that there is a bug with vsiteN and OpenMP
> in 4.6 and 5.0 then?
That could well be. I will try to investigate that tomorrow with a 
simpler test system.

> Berk
>>> Cheers,
>>> Berk
>>> On 08/18/2014 05:23 PM, David van der Spoel wrote:
>>>> Hi,
>>>> I'm working on a branch where I have one vsiteN per amino acid in my
>>>> protein, and all vsites interact with each other. When running mdrun
>>>> using OpenMP the vsite positions do not get created on all threads,
>>>> despite listing the interaction type as a bonded type in ifunc.c.
>>>> Before diving into domain decomposition code I wonder whether there
>>>> may be a quick workaround?

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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