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Peter Amstutz, 09/18/2014 06:02 PM

Everything should be a job


Currently we have tasks, jobs, and pipelines. While this corresponds to a common pattern for building bioinfomatics analysis, in practice we are finding that this design is overly rigid with several unintended consequences:

  1. arv-run-pipeline-instance is currently a special privileged pipeline runner. However, there are potentially many other pipeline frameworks we would like to support, such as bcbio-nextgen, rmake, snakemake, Nextflow, etc. that should be usable by regular users and so can't be privileged processes.
  2. Need to work with batches and pipelines of pipelines. If we have a pipeline that processes a single sample, and we want to run it 100 times, we need to create 100 pipelines by hand or by a script.
  3. Currently, we can create jobs which either 1. submits stages as subtasks or 2. submits stages as additional jobs.
    1. In the first approach, job reuse features are not available with tasks, and all subtasks must be able to run out of the same docker image. There is also (by design) reduced visibility into the inner working of tasks as compared to jobs.
    2. In the second approach, the controller job currently ties up a whole node, even though it is mostly idle. Additionally (and unlike tasks and pipelines) we do not track which job submissions were made by which other jobs, so there's a loss of provenance information.

Proposed solution

  1. Improve job scheduling so that we can have more than one job on a node, with jobs can be allocated to a single core (possibly even fractions of a core).
  2. Remove arv-run-pipeline-instance from its privileged position and run it as a job in a container just like everything else.
  3. Deprecate tasks, prefer to submit jobs instead (enables work reuse)
  4. Track which job submissions were made by the controlling job (add a spawned_by_job_uuid field to the jobs object), possibly using the API token associated with the job.
  5. Workbench summary pages such as dashboard just display jobs that were submitted by a user (spawned_by_job_uuid is null). Unify the display of pipelines and jobs so that a pipeline is just a job that creates other jobs, and permit drilling down through the process tree.
  6. Improve SDK APIs to make it easy to spawn a a bunch of jobs as "futures" and then wait for them all to finish.

Another benefit: supports the proposed v2 Python SDK by enabling users to orchestrate pipelines where "python" is the same whether it runs locally, runs locally and submits jobs, or runs as a crunch job itself and submits jobs.

Related ideas

Currently, porting tools like bcbio or rmake still requires the tool be modified so that it schedules jobs on the cluster instead of running locally. We could use LD_PRELOAD to intercept a whitelist of exec() calls and redirect them to a script that causes the tool to run on the cluster.

Updated by Peter Amstutz almost 10 years ago · 11 revisions