[ensembl-dev] Gene build pipeline SQL deadlock

[arnaud at ebi.ac.uk]

Hi,

I've been getting the same error after migrating our MySQL server where
the default engine became InnoDB.

Switching back to MyISAM instead solved it for us.

There are several tables required for running ensembl pipelines, but
switching just job_status table was sufficient to resolve this.

ALTER TABLE job_status ENGINE=MyISAM;

Hope this helps,
Arnaud

> Dear list,
>
> a pipeline problem again, sorry ;)
> So I fixed my earlier issue (turned out to be related to the logic_name
> and case sensitivity...), but when running a minimal raw compute stage
> (RepeatMasker and tRNAscan), the pipeline deadlocks after a while:
>
> ---------------------------------------------------
> DBD::mysql::st execute failed: Deadlock found when trying to get lock;
> try restarting transaction at
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/DBSQL/JobAdaptor.pm
> line 652.
>
> -------------------- EXCEPTION --------------------
> MSG: ERROR running job 2044 RepeatMasker
> /data2/ensembl-test/test2/output/RepeatMasker/6/contig:vcelegans_test:chrIII_80:1:50000:1.RepeatMasker.0.err
> [
> -------------------- EXCEPTION --------------------
> MSG: Error setting status to SUBMITTED
> STACK Bio::EnsEMBL::Pipeline::DBSQL::JobAdaptor::set_status
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/DBSQL/JobAdaptor.pm:677
> STACK Bio::EnsEMBL::Pipeline::Job::set_status
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:771
> STACK Bio::EnsEMBL::Pipeline::Job::flush_runs
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:505
> STACK Bio::EnsEMBL::Pipeline::Job::batch_runRemote
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/Job.pm:541
> STACK (eval)
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/RuleManager.pm:694
> STACK Bio::EnsEMBL::Pipeline::RuleManager::can_job_run
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/RuleManager.pm:692
> STACK toplevel
> /opt/bioinformatics/ensembl-70/ensembl-pipeline/scripts/rulemanager.pl:336
> Date (localtime)    = Tue May 14 18:14:34 2013
> Ensembl API version = 70
>
>
> Apparently, two processes are trying to update the same entry. How can
> this be avoided? Any suggestions an the level of the pipeline config, or
> using another SQL engine...?
> My setup is a 48-core single-node opteron LSF cluster (for testing
> purposes) and the contig-level jobs finish quite rapidly, of course -
> but I am surprised that there seems to be no checks for this sort of
> thing.
>
> Cheers,
>
> Marc
>
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