gatk-3.8/doc_archive/queue/Queue_with_Grid_Engine.md

Queue with Grid Engine

http://gatkforums.broadinstitute.org/gatk/discussion/1313/queue-with-grid-engine

1. Background

Thanks to contributions from the community, Queue contains a job runner compatible with Grid Engine 6.2u5.

As of July 2011 this is the currently known list of forked distributions of Sun's Grid Engine 6.2u5. As long as they are JDRMAA 1.0 source compatible with Grid Engine 6.2u5, the compiled Queue code should run against each of these distributions. However we have yet to receive confirmation that Queue works on any of these setups.

• Oracle Grid Engine 6.2u7
• Univa Grid Engine Core 8.0.0
• Univa Grid Engine 8.0.0
• Son of Grid Engine 8.0.0a
• Rocks 5.4 (includes a Roll for "SGE V62u5")
• Open Grid Scheduler 6.2u5p2

Our internal QScript integration tests run the same tests on both LSF 7.0.6 and a Grid Engine 6.2u5 cluster setup on older software released by Sun.

If you run into trouble, please let us know. If you would like to contribute additions or bug fixes please create a fork in our github repo where we can review and pull in the patch.

2. Running Queue with GridEngine

Try out the Hello World example with -jobRunner GridEngine.

java -Djava.io.tmpdir=tmp -jar dist/Queue.jar -S public/scala/qscript/examples/HelloWorld.scala -jobRunner GridEngine -run

If all goes well Queue should dispatch the job to Grid Engine and wait until the status returns RunningStatus.DONE and "hello world should be echoed into the output file, possibly with other grid engine log messages.

See QFunction and Command Line Options for more info on Queue options.

3. Debugging issues with Queue and GridEngine

If you run into an error with Queue submitting jobs to GridEngine, first try submitting the HelloWorld example with -memLimit 2:

java -Djava.io.tmpdir=tmp -jar dist/Queue.jar -S public/scala/qscript/examples/HelloWorld.scala -jobRunner GridEngine -run -memLimit 2

Then try the following GridEngine qsub commands. They are based on what Queue submits via the API when running the HelloWorld.scala example with and without memory reservations and limits:

qsub -w e -V -b y -N echo_hello_world \
  -o test.out -wd $PWD -j y echo hello world
qsub -w e -V -b y -N echo_hello_world 

-o test.out -wd $PWD -j y 

-l mem_free=2048M -l h_rss=2458M echo hello world</code class="pre_md">

One other thing to check is if there is a memory limit on your cluster. For example try submitting jobs with up to 16G.

qsub -w e -V -b y -N echo_hello_world \
  -o test.out -wd $PWD -j y \
  -l mem_free=4096M -l h_rss=4915M echo hello world
qsub -w e -V -b y -N echo_hello_world 

-o test.out -wd $PWD -j y 

-l mem_free=8192M -l h_rss=9830M echo hello world
qsub -w e -V -b y -N echo_hello_world 

-o test.out -wd $PWD -j y 

-l mem_free=16384M -l h_rss=19960M echo hello world</code class="pre_md">

If the above tests pass and GridEngine will still not dispatch jobs submitted by Queue please report the issue to our support forum.