Opened 8 months ago

Closed 8 months ago

#1522 closed enhancement (fixed)

Add support for setting more options for submitting jobs to the cluster

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.49.3
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

When submitting jobs to the cluster we need to specify some options regarding the resources that are required, etc. We currently have support for setting number of cores, priority and partition. The cluster is about to be updated and we may have to also specify memory requirements and maybe other things.

We should at least implement support for adding options to reggie-config.xml that are included in the job submission.

It should be possible to manually change defaults via the submission wizards. This doesn't have to be a general functionality that is implemented now, but it should be possible to add it if needed later.

Change History (14)

comment:1 by Nicklas Nordborg, 8 months ago

In 7346:

References #1522: Add support for setting more options for submitting jobs to the cluster

Introduced <submit> and <submit-debug> tags in the reggie-config.xml file. The tags can be used to set options for the queue system. The options must be specified one per line with '=' as a separtor between key and value. Empty lines and lines starting with # are ignored (white-space is removed from the beginning and end of each line first).

The <parallel-environment> should no longer be used. The number of CPUs should be specified with --cpus-per-task=N in the <submit> tag instead. Note that while there was a default value for <parallel-environment> settings, there is no default for <submit> settings.

The configuration has been updated for ASCAT jobs so far.

comment:2 by Nicklas Nordborg, 8 months ago

In 7348:

References #1522: Add support for setting more options for submitting jobs to the cluster

Replaced all <parallel-environment> tags in reggie-config.xml with <submit> tags.

comment:3 by Nicklas Nordborg, 8 months ago

In 7349:

References #1522: Add support for setting more options for submitting jobs to the cluster

Most job creator implementations now use the <submit> tags instead of <parallel-environment> except the demux and FASTQ importer since they are a bit different.

comment:4 by Nicklas Nordborg, 8 months ago

In 7350:

References #1522: Add support for setting more options for submitting jobs to the cluster

The FASTQ importer now uses <submit-import> instead of hard-coded settings.

comment:5 by Nicklas Nordborg, 8 months ago

In 7351:

References #1522: Add support for setting more options for submitting jobs to the cluster

Fixed also for the demux jobs. The possibility to set a different number of slots in the manual start demux wizard has been removed.

comment:6 by Nicklas Nordborg, 8 months ago

In 7353:

References #1522: Add support for setting more options for submitting jobs to the cluster

We need version 1.11 of the job scheduler for supporting options that are flags.

comment:7 by Nicklas Nordborg, 8 months ago

In 7358:

References #1522: Add support for setting more options for submitting jobs to the cluster

Implemented functionality for manually overriding configured job submission options. It has been implemented on the server side for ASCAT, but there is no support yet in the wizard.

comment:8 by Nicklas Nordborg, 8 months ago

In 7359:

References #1522: Add support for setting more options for submitting jobs to the cluster

Implemented functionality for manually overriding configured job submission options on the server side for all other job creator implementations.

comment:9 by Nicklas Nordborg, 8 months ago

In 7360:

References #1522: Add support for setting more options for submitting jobs to the cluster

Implemented functionality for manually overriding job options in the ASCAT wizard.

comment:10 by Nicklas Nordborg, 8 months ago

In 7361:

References #1522: Add support for setting more options for submitting jobs to the cluster

Implemented functionality for manually overriding job options in some more wizards.

comment:11 by Nicklas Nordborg, 8 months ago

In 7362:

References #1522: Add support for setting more options for submitting jobs to the cluster

Fixed an issue with settings when a ParameterSet was specified for the selected software item. This can affect which options that are used from the configuration file.

comment:12 by Nicklas Nordborg, 8 months ago

In 7363:

References #1522: Add support for setting more options for submitting jobs to the cluster

Fixed for the DNA Bwa-mem alignment wizard.

comment:13 by Nicklas Nordborg, 8 months ago

In 7364:

References #1522: Add support for setting more options for submitting jobs to the cluster

Manually overriding the options should work now for all other wizards.

comment:14 by Nicklas Nordborg, 8 months ago

Resolution: fixed
Status: newclosed
Note: See TracTickets for help on using tickets.