Khalid Shakir 22b4466cf5 Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error. ... 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.		2012-08-13 15:43:05 -04:00
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org/broadinstitute/sting/queue	Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.	2012-08-13 15:43:05 -04:00