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Sunday, March 23, 2008

CDK Module dependencies #2

A bit over 2 years ago I published a UML diagram showing the dependencies between CDK modules. Since then I lot of new modules have been defined, added or factored out from the extra module (click to zoom):These kind of diagrams help us maintain the library, and apply some design goals, as explained in the first post on this.

If one compares the two diagrams, one sees that fewer code depends on the data module, but it is also clear that still a lot of them do. Another issue that had not properly addressed yet, is that a lot of modules still depend on the extra module, which aggregates everything that had not been assigned elsewhere.

Parallelism
This diagram also helped me use the Ant <parallel> task to allow compiling CDK modules in parallel, instead of sequentially. Multicore machines can take advantage of that, and reduce the overall computation time. Full parallelism is not possible, and it is well visualized by the above diagram that there basically 12 sequential compilation steps in which one or more modules can be compiled. Further clean up of the module dependencies, will reduce this number, and further reduce the computation time on multicore machines.

Now, graph analysis could pinpoint the most troublesome nodes, but it would not surprise me that extra would be amongst them. But the following items are worth looking at too:
  • why does qsar have to depend on charges?
  • why does sdg (the 2D layout code) depends on io code?
  • can isomorphism and formula be made independent of data?
  • why does reaction depend on sdg?
  • why does forcefield depend on qsaratomic?
Some of these issues are rather practical, but it is these kind of analyses that help us clean up the CDK library.