d6e6b30caf
– Write general NanoScheduler framework in utils.threading. Test with reading via iterator from list of integers, map is int * 2, reduce is sum. Should be efficiency using resources to do sum of 2 * (sum(1 - X)). Done! CPU parallelism is nano threads. Pfor across read / map / reduce. Use work queue to implement. Create general read map reduce framework in utils. Test parallelism independently before hooking up to Locus iterator Represent explicitly the dependency graph. Scheduler should choose the work units that are ready for computation, that are marked as "completing a computation", and then finally that maximize the number of sequent available work units. May be worth measuring expected cost for read read / map / reduce unit and use it to balance the compute As input is single threaded just need one thread to populate inputs, which runs as fast as possible on parallel pushing data to fixed size queue. Each push creates map job and links to upcoming reduce job. Note that there's at most one thread for IO tasks, and all of the threads can contribute to CPU tasks |
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| .. | ||
| alignment | ||
| commandline | ||
| gatk | ||
| jna | ||
| utils | ||
| BaseTest.java | ||
| MD5DB.java | ||
| MD5Mismatch.java | ||
| StingTextReporter.java | ||
| WalkerTest.java | ||