Enhance TaskArrayCollector to support configurable timeout-based array submission #6647
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Add defensive copy of task array before passing to createTaskArray() to prevent concurrent modification during iteration in prepareLauncher(). The race condition occurred when: 1. Timer thread flushes array and calls submitAndReset() 2. createTaskArray() iterates over tasks outside the lock 3. prepareLauncher() modifies the collection during iteration This fix ensures createTaskArray() works on its own copy of the list.
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Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
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@johnoooh I went ahead and cleaned up the PR to get it ready for merging. I also pushed a temporary fix that might fix the error you are getting, let me know if it works |
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Currently, TaskArrayCollector submits a job array only when the array reaches its configured size. In pipelines with slower task generation or variable workloads, small batches may remain in memory indefinitely if the array never fills, delaying execution. This is especially a problem in pipelines with hanging channels, like channels made by watchPath. We have a few pipelines that run forever, watching a samplesheet for new entries, and processing them as they come in. We would like to use array jobs to reduce strain on the slurm scheduler as much as possible as this has been a problem on our cluster.
My proposal is to create a maximum amount of time to wait for more jobs before submitting the array of jobs. Then the pipeline would work like this:
The first 10 jobs are submitted as an array job as expected. The next 6 jobs are added into the task array. Then, the time specified by executorSubmitTimeout elapses. At this point the remaining 6 jobs are put into a job array and submitted to the cluster.
Discussion of this feature was originally started here:
#5924
Then I further described the issue here: #6465
I'm currently having an issue with java.util.ConcurrentModificationException when running hundreds of jobs.