-- Closes GSA-515 Nanoscheduler GSA-542 Good interface to nanoScheduler
-- Old -nt means dataThreads
-- New -cnt (--num_cpu_threads_per_data_thread) gives you n cpu threads for each data thread in the system
-- Cleanup logic for handling data and cpu threading in HMS, LMS, and MS
-- GATKRunReport reports the total number of threads in use by the GATK, not just the nt value
-- Removed the io,cpu tags for nt. Stupid system if you ask me. Cleaned up the GenomeAnalysisEngine and ThreadAllocation handling to be totally straightforward now
-- Invert logic in GATKArgumentCollection to disable monitoring, not enable. That means monitoring is on by default
-- Fix testing error in unit tests
-- Rename variables in ThreadAllocation to be clearer
-- See https://jira.broadinstitute.org/browse/GSA-502
-- New command line argument -mt enables thread monitoring
-- If enabled, HMS uses StateMonitoringThreadFactory to create monitored threads, and prints out an efficiency report when HMS exits, telling the user information like:
for BQSR – known to be inefficient locking
INFO 17:10:33,195 StateMonitoringThreadFactory - Number of activeThreads used: 8
INFO 17:10:33,196 StateMonitoringThreadFactory - Total runtime 90.3 m
INFO 17:10:33,196 StateMonitoringThreadFactory - Fraction of time spent blocked is 0.72 ( 64.8 m)
INFO 17:10:33,197 StateMonitoringThreadFactory - Fraction of time spent running is 0.26 ( 23.7 m)
INFO 17:10:33,197 StateMonitoringThreadFactory - Fraction of time spent waiting is 0.02 ( 112.8 s)
INFO 17:10:33,197 StateMonitoringThreadFactory - Efficiency of multi-threading: 26.19% of time spent doing productive work
for CountLoci
INFO 17:06:12,777 StateMonitoringThreadFactory - Number of activeThreads used: 8
INFO 17:06:12,777 StateMonitoringThreadFactory - Total runtime 43.5 m
INFO 17:06:12,778 StateMonitoringThreadFactory - Fraction of time spent blocked is 0.00 ( 4.2 s)
INFO 17:06:12,778 StateMonitoringThreadFactory - Fraction of time spent running is 1.00 ( 43.3 m)
INFO 17:06:12,779 StateMonitoringThreadFactory - Fraction of time spent waiting is 0.00 ( 6.0 s)
INFO 17:06:12,779 StateMonitoringThreadFactory - Efficiency of multi-threading: 99.61% of time spent doing productive work
Mark DePristo
Matt Hanna