gatk-3.8/public/java/test/org/broadinstitute/sting
Mark DePristo 295455eee2 NanoScheduler optimizations and simplification
-- The previous model was to enqueue individual map jobs (with a resolution of 1 map job per map call), to track the number of map calls submitted via a counter and a semaphore, and to use this information in each map job and reduce to control the number of map jobs, when reduce was complete, etc.  All hideously complex.
-- This new model is vastly simply.  The reducer basically knows nothing about the control mechanisms in the NanoScheduler.  It just supports multi-threaded reduce.  The NanoScheduler enqueues exactly nThread jobs to be run, which continually loop reading, mapping, and reducing until they run out of material to read, when they shut down.  The master thread of the NS just holds a CountDownLatch, initialized to nThreads, and when each thread exits it reduces the latch by 1.  The master thread gets the final reduce result when its free by the latch reaching 0.  It's all super super simple.
-- Because this model uses vastly fewer synchronization primitives within the NS itself, it's naturally much faster at getting things done, without any of the overhead obvious in profiles of BQSR -nct 2.
2012-12-24 13:35:57 -05:00
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commandline Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
gatk Added functionality of outputting sorted GATKReport Tables 2012-12-20 14:02:21 -05:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils NanoScheduler optimizations and simplification 2012-12-24 13:35:57 -05:00
BaseTest.java Extensive unit tests, contacts, and documentation for RecalDatum 2012-07-31 08:11:03 -04:00
MD5DB.java Finalizing BCF2 mark III commit 2012-06-21 15:16:27 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
TestNGTestTransformer.java Add custom TestNGTestTransformer that adds a maximum test runtime of 10 minutes to all testng tests 2012-11-01 15:34:12 -04:00
WalkerTest.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00