Re: [GUSDEV] PostLoadGenome.proteomeAnalysis.loadLowComplexityFile

[Brian B. <br...@pc...>]

Adhemar, my memory is that the default max is 10000 object in memory at once which is usually sufficient as there is seldom transactions that would exceed that.  You can increase this default in the plugin by adding the following line .. actually can use any of the objects for this but the context has the algorighmInvocation object so this uses that.

$ctx->{'self_inv'}->setMaximumNumberOfObjects(50000);

This will increase the limit to 50,000 .. could make it larger if you need to do so.  Now that machines have more memory we should probably consider increasing the default limit.  It is there to keep developers from not removing from the cache in each loop since the objects can't be garbage collected until that is done.

-Brian


On Jun 24, 2011, at 2:35 PM, Adhemar wrote:

> Hi, 
> The plugin ApiCommonData::Load::Plugin::InsertLowComplexityFeature also has the problem with the maximum number of objects in the memory. 
> How can I fix this?
> 
> The full log is attached and here is the error message:
> 
> ERROR MESSAGE:  You have exceeded the maximum number of allowable objects in memory:
>   You must use the method 'undefPointerCache()' in each loop 
>     to clear the cache and allow garbage collection!!
>  If you need > 10000 objects at one time, 
>    then increase the default number with the method 'setMaximumNumberOfObjects(<number>)' at /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 483
> 
> Thanks,
> -Adhemar
> 
> 
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Brian P. Brunk, Ph.D.
EuPathDB Manager
1403 Blockley Hall
Penn Center For Bioinformatics
University of Pennsylvania
Philadelphia PA 19104-6021
Tel: 215-573-3118
Fax: 215-573-3111