[InterMine Dev] postprocessing speedup?

Richard Smith richard at flymine.org
Wed Mar 28 16:18:11 BST 2012


Hi Intikhab,
Sorry we didn't get to this sooner.  That doesn't seem right at all,
can you send more of the log from the postprocess directory?

Can you explain a bit more about the situation?  How many chromosome
objects do you have loaded?  Or have you created each read as a
chromosome feature?  What are the feature types loaded?

Regards,
Richard.









On 28/03/2012 16:07, Dr. Intikhab Alam wrote:
> Dear Richard/Julie,
>
> My post-processing (the transfer-sequences) is still running since March
> 18, last write:
> 2012-03-28 18:01:05 INFO org.intermine.bio.postprocess.TransferSequences
> - Starting transfer for AT0200m01A1 chromosome AT0200m01A1.GATTB1C02HV5CP
> 2012-03-28 18:01:05 INFO
> org.intermine.sql.precompute.PrecomputedTableManager - Creating new
> precomputed table CREATE TABLE precomp_1827553
>
> Is there a way to speedup post-processing e.g. Using multiple processors?
>
> Thanks,
>
> Intikhab
>
>
> From: Intikhab Alam <intikhab.alam at kaust.edu.sa
> <mailto:intikhab.alam at kaust.edu.sa>>
> Date: Sat, 24 Mar 2012 17:20:32 +0300
> To: "dev at intermine.org <mailto:dev at intermine.org>" <dev at intermine.org
> <mailto:dev at intermine.org>>
> Subject: [InterMine Dev] postprocessing speedup?
>
> Hi,
>
> I am developing a mine for a metagenomic project, containing 4 million
> DNA reads and similar amount of predicted ORFs and related
> attributes/features. Post-processing (transfer-sequences) started
> 2012-03-18 04:38 and still going on.
> Is there a way to paralellize post-processing to speed up these steps
> e.g. On a multiprocessor machine?
>
> Thanks,
>
> Intikhab
> --
> --
> Intikhab Alam, PhD
>
> Research Scientist
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4336
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, KSA
> W: http://www.kaust.edu.sa
> T +966 (0) 2 808-2423 F +966 (2) 802 0127




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