[ensembl-dev] Gene build pipeline SQL deadlock

[Marc Hoeppner]

Hi,

the conversion to MyISAM seems to have fixed the issue. Thanks!

/Marc
> 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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>
>
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