[InterMine Dev] postprocessing speedup?

Dr. Intikhab Alam intikhab.alam at kaust.edu.sa
Wed Mar 28 16:07:42 BST 2012


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
--
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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
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