-- Added 'jobRunnerJobName' definition to QFunction, defaults to value of shortDescription
-- Edited Lsf and Drmaa JobRunners to use this string instead of description for naming jobs in the scheduler
Signed-off-by: Joel Thibault <thibault@broadinstitute.org>
--specifying exception types in cases where none was already specified
----mostly changed to catch Exception instead of Throwable
----EmailMessage has a point where it should only be expecting a RetryException but was catching everything
--changing build.xml so that it prints scala feature warning details
--added necessary imports needed to remove feature warnings
--updating a newly deprecated enum declaration to match the new syntax
Removed some generics from PluginManager for now until able to figure out syntax for requesting explicit subclass.
QStatusMessenger uses a slightly more primitive Map[String, Seq[RemoteFile]] instead of Map[ArgumentSource, Seq[RemoteFile]].
Added an QCommandPlugin.initScript utility method for handling specialized script types.
In addition to outputs, inputs are passed to QStatusMessenger.done()
CloneFunction.cloneIndex has a new CloneFunction.cloneCount companion useful for display purposes.
-- Queue will incrementally now write out its jobReport.txt file whenever jobs finish running (FAIL or DONE)
-- This makes it far easier to track what's going on, or to analyze incrementally performance results coming out of Queue
-- Generally cleaned up the QJobsReporting code, creating a new clean class QJobsReporter that holds all of the information on what to do log and where to put into, which was previously scattered in QCommandLine and QJobReport
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.
Updated HSP to use new padding arguments instead of flank intervals file, plus latest QC evals.
IntervalUtils return unmodifiable lists so that utilities don't mutate the collections.
Added a JavaCommandLineFunction.javaGCThreads option to test reducing java's automatic GC thread allocation based on num cpus.
Added comma to list of characters to convert to underscores in GridEngine job names so that GE JSV doesn't choke on the -N values.
JobRunInfo handles the null done times when jobs crash with strange errors.
QScript accessor to QSettings to specify a default runName and other default function settings.
Because log files are no longer pseudo-random their presense can be used to tell if a job without other file outputs is "done". For now still using the log's .done file in addition to original outputs.
Gathered log files concatenate all log files together into the stdout.
InProcessFunctions now have PrintStreams for stdout and stderr.
Updated ivy to use commons-io 2.1 for copying logs to the stdout PrintStream. Removed snakeyaml.
During graph tracking of outputs the Index files, and now BAM MD5s, are tracked with the gathering of the original file.
In Queue generated wrappers for the GATK the Index and MD5s used for tracking are switched to private scope.
Added more detailed output when running with -l DEBUG.
Simplified graphviz visualization for additional debugging.
Switched usage of the scala class 'List' to the trait 'Seq' (think java.util.ArrayList vs. using the interface java.util.List)
Minor cleanup to build including sending ant gsalib to R's default libloc.
-- Support for collecting resources info from DRMAA runners
-- Disabled the non-standard mem_free argument so that we can actually use our own SGE cluster gsa4
-- NCoresRequest is a testing queue script for this.
-- Added two command line arguments:
-- multiCoreJerk: don't request multiple cores for jobs with nt > 1. This was the old behavior but it's really not the best way to run parallel jobs. Now with queue if you run nt = 4 the system requests 4 cores on your host. If this flag is thrown, though, it will only request 1 and you'll just use 4, like a jerk
-- job_parallel_env: parallel environment named used with SGE to request multicore jobs. Equivalent to -pe job_parallel_env NT for NT > 1 jobs
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
-- General purpose RScript executor in java (please use when invoking RScripts)
-- Removed groupName. This is now analysisName
-- Explicitly added capability to enable/disable individual QFunction
-- onExecutionDone(Map(QFunction, JobRunInfo)) is the new signature, so that you can walk over your jobs and inspect their success/failure and runtime characteristics
- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
Phillip Dexheimer
Louis Bergelson
David Roazen
Francesco
Mauricio Carneiro
Joel Thibault
Johan Dahlberg
kshakir
Mark DePristo