[gmx-developers] VsiteN in parallel problem

Berk Hess hess at kth.se
Mon Aug 18 21:57:41 CEST 2014

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?

>> 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?

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