[gmx-developers] What is the function of 'dd_collect_state' used to ?

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 22 08:26:35 CET 2011

On 2011-03-22 04.42, Mark Abraham wrote:
> On 22/03/2011 2:38 PM, Yukun Wang wrote:
>> Hi
>> What is the function of 'dd_collect_state' used to ?
> It collects the state of the simulation system, which was distributed
> across the parallel nodes, into a single structure.
>> In the md.c there is a function as:
>> dd_collect_state(cr->dd,state,state_global)
>> I don't know what' the mean of it,and where was it defined.
>> I want to realize a work by gromacs, that there are several
>> simulations which coulped weakly only by exchanging position
>> information of a group of atoms for every n steps, and for each
>> simulation I want to run parallelly. So the trouble is coming for each
>> simulation with domain decomposition parallelizing that this group of
>> atoms would be distributed in different node.
>> How can I get those data from different nodes in the running time? If
>> I put the self-written coulping code in the master node for each
>> simulation how I do this data gathering job?
> Either you need to collect on the master node and communicate between
> them before redistributing, or write complex (but ultimately more
> scalable) code to communicate between all the processors. The REMD
> implementation should be a good model for the former.
Indeed, or the more general -multi option.
> Mark

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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