gatk-3.8/public
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
..
R Fix for missing formatter in R 2.15 2012-08-17 11:49:02 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
doc
java Initial implementation of GSA-515: Nanoscheduler 2012-08-24 14:07:44 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release. 2012-07-23 16:32:31 -04:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running 2012-08-21 14:44:18 -04:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00