22b4466cf5
Implemented a mixin called "RetryMemoryLimit" which will by default double the memory. GridEngine memory request parameter can be selected on the command line via '-resMemReqParam mem_free' or '-resMemReqParam virtual_free'. Java optimizations now enabled by default: - Only 4 GC threads instead of each job using java's default O(number of cores) GC threads. Previously on a machine with N cores if you have N jobs running and java allocates N GC threads by default, then the machines are using up to N^2 threads if all jobs are in heavy GC (thanks elauzier). - Exit if GC spends more than 50% of time in GC (thanks ktibbett). - Exit if GC reclaims lest than 10% of max heap (thanks ktibbett). Added a -noGCOpt command line option to disable new java optimizations. |
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| .. | ||
| examples | ||
| lib | ||
| DataProcessingPipeline.scala | ||
| GATKResourcesBundle.scala | ||
| MethodsDevelopmentCallingPipeline.scala | ||
| PacbioProcessingPipeline.scala | ||