[ensembl-dev] pipeline run with status 'VOID'

Susan Fairley sf7 at sanger.ac.uk
Fri Jun 10 16:18:53 BST 2011

江JWK wrote:
> Hi
> the problem is that the rulemanager script continue to run on the cluster, although all other jobs have been finished (except these VOID jobs).
> In normal situations, when all jobs are successfully completed, the rulemanager script will be terminated automatically, 
> so it seems likely that these VOID jobs cause the rulemanager script consider some jobs still not finished yet, so it continues to run.
> Should i terminate the rulemanger script manually?

Yes. When you can see that all jobs have run as far as they can,
terminating rule_manager can be sensible.

Rule_manager can also continue running for a short period after all jobs
have successfully completed, especially if the input_id_analysis table
has become large and rule manager needs to check lots of jobs to see if
anything should be run. If you don't want to wait for rule_manager, you
may want to kill it in these circumstances too.

After you terminate rule_manager, remember to check the meta table for a
pipeline.lock, which may be left behind and will prevent you running
rule_manager again until it is removed.

You should also remove the void Genscan jobs from the pipeline, or at
least make sure that their settings are such that rule_manager won't
pick them up next time you run it.


> monitor output:
> Pipeline current status
> Name     Status Count   Analysis-id
> Genscan  VOID  3      3
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