gatk3的最后一个经典版本3.8
 
 
 
 
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Mark DePristo d6e6b30caf Initial implementation of GSA-515: Nanoscheduler
– 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
2012-08-24 14:07:44 -04:00
licensing Revert unintentional license change 2012-08-09 17:10:47 -04:00
protected/java HaplotypeCaller forbids BAQ 2012-08-24 13:25:05 -04:00
public Initial implementation of GSA-515: Nanoscheduler 2012-08-24 14:07:44 -04:00
settings Updating cofoja to the latest version 2012-08-09 16:36:18 -04:00
.gitignore Minor additions to the shared .gitignore file, now that Mark has checked one in. 2011-10-26 12:24:28 -04:00
build.xml Convert external.build.dir and external.dist.dir back to paths 2012-08-15 23:04:10 -04:00
ivy.xml Updating cofoja to the latest version 2012-08-09 16:36:18 -04:00