[gmx-developers] VsiteN in parallel problem
David van der Spoel
spoel at xray.bmc.uu.se
Mon Aug 18 21:55:02 CEST 2014
On 2014-08-18 21:41, Berk Hess wrote:
> 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.
> On 08/18/2014 05:23 PM, David van der Spoel wrote:
>> 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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