Re: [cilib-devel] Patches: Clustering + dynamic environments + more

[Andries E. <en...@cs...>]

Thanks Theuns. We need to discuss the patch at the
next CIlib meeting, unless Gary feels that all is fine,
and can immediately apply.

Theuns Cloete wrote:
> Hi all,
>
> This is the fourth iteration of my set of patches after a rebase from the
> latest 'master'. You can therefore safely ignore the previous set of patches
> that I sent to the mailing list. I would appreciate it if we could apply these
> patches as soon as possible, because each time there is some change to master,
> I have to rebase and sort out a lot of conflicts which takes a considerable
> amount of time. During every rebase it is becoming more difficult to remember
> all the changes that have already been merged and those that still needs to be
> merged. Feel free to comment and send patches. I think it is time that I put
> it out there, so that other people can have a look and suggest or make
> improvements. That's why we switched to Git, right? To make this type of
> collaboration quicker and easier.
>
> The patches include the following:
>
> --- begin clustering branch ---
>
> 1. This patch includes all the changes I had in my Subversion
> repository. It includes various updates that range from clustering
> (mostly) to dynamic environments (less). It also included the dynamic
> environments stuff that Leo sent through, but it was again merged in
> a later patch. Git incorporated this into patch 7. This patch also
> includes the ChargedSwarmInitialisationStrategy which deprecates the
> ChargedParticleInitialisationStrategy.
>
> 2. Renamed a detection strategy.
>
> 3. Small cleanup like removing a super() etc.
>
> 4. Renamed a method and updated some JavaDoc.
>
> 5. Added trivial centroid diversification feature for KMeans.
>
> 6. Rebased from the "tabs to spaces" patch. I also fixed my own white space
> issues. This patch also includes some dynamic environment changes.
>
> 7. Added centroid reinitialisation feature for KMeans, as part of
> centroid initialisation strategy.
>
> 8. Update the kmeans.xml file to show examples of using centroid
> initialisation and diversification.
>
> 9. Implemented methods in StatUtils to calculate a variance vector and
> standard deviation vector. Made use of these methods in clustering
> measurements.
>
> 10. Fixed merge mistakes regarding the pso.dynamic package that were made in
> previous patches.
>
> UPDATE: After another rebase these mistakes were handled correctly in previous
> patches. This patch can probably be squashed into the next patch. This patch
> now only contains renames and minor changes regarding the pso.dynamic package.
>
> 11. Fixed some mistakes regarding the VonNeumannTopology and
> CompetitiveCoevolutionParticleReevaluationResponseStrategy that crept in due
> to the rebase.
>
> UPDATE: After another rebase, these mistakes were handled correctly in
> previous patches. This patch can probably be squashed into the next patch.
>
> 12. Various changes that I had to commit in order to rebase.
>
> --- end clustering branch ---
>
> --- begin multi-threaded-split-coop-alg branch ---
>
> NOTE: Patch 13 is still experimental. I would appreciate some feedback.
>
> 13. Trying something new: Multi-threaded SplitCooperativeAlgorithm. The idea
> is to execute each sub-algorithm in its own thread, thereby improving the
> performance of the SplitCooperateAlgorithm, especially on computers with more
> than one core. This works very nicely, as long as the algorithm you are using
> and the problem you are optimising never uses Algorithm.get(), because the
> algorithm stack is not thread safe. We need some elegant and simple way of
> getting hold of either the main algorithm or the currently executing
> sub-algorithm in a thread safe manner. I hope we can find a way by making use
> of Guice. So try it out and let me know what you think.
>
> NOTE: Patch 14 still needs some work. I would appreciate some feedback.
>
> 14. Big changes regarding clustering as a result of patch 13.
> 14.a. The Pattern class was moved to the type.types.container package as
> Pattern<S extends Vector> and it is now a ForwardingStructuredType<S>.
> 14.b. The Cluster<Vector> class was introduced which is a Set<Pattern<Vector>>,
> i.e. also a Type.
> 14.c. The multi-threaded behaviour of patch 13 caused the entire
> ClusteringUtils class to break, because it was not thread safe, because it
> contained state. The ClusteringUtils class was therefore trimmed down and does
> not contain state anymore. It also makes use of the changes mentioned in 14.a
> to 14.b.
> 14.d. Everything else that depend on the clustering code was updated.
>
> --- end multi-threaded-split-coop-alg branch ---
>
> Look at the commit messages and content of each patch to get a better idea of
> what each patch contains.
>
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