[gmx-developers] What is the function of 'dd_collect_state' used to ?
wangykoo at gmail.com
Tue Mar 22 10:15:28 CET 2011
I don't know if there is a function in Gromacs that it can get and change a
specific group atom's local information,for example data in the t_state data
structure , when given a group, which is defined and included by command of
grompp -n option.
So I can call this function in the master node and couple severial
simulations simultaneously .
2011/3/22 David van der Spoel <spoel at xray.bmc.uu.se>
> On 2011-03-22 04.42, Mark Abraham wrote:
>> On 22/03/2011 2:38 PM, Yukun Wang wrote:
>>> 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:
>>> 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.
> 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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