[khmer] speed up partitioning?

Torsten Seemann torsten.seemann at monash.edu
Tue Feb 18 20:15:49 PST 2014


> > My problem is that it's been running for about a month now, using 90% of
> memory, and 4600% cpu. In other words, it appears to be using available
> resources. If I read the output (pasted below) correctly, I can expect to
> see 6566 partitions. After a month, it is working on partition 2178, so I'm
> only 1/3 of the way through.

My suggestion is to run "sga preqc" on the reads to get an idea if there is
anything unusual about your data set:



> The computer I'm using has 48 cores (AMD 6176 2.3Ghz) and 256GB ram.

PS. We have similar: 64 cores (AMD 6272 2.1 Ghz) and 512GB RAM :-)


*--Dr Torsten Seemann--Victorian Bioinformatics Consortium, Monash
University, AUSTRALIA*

*--Life Sciences Computation Centre, VLSCI, Parkville, AUSTRALIA
--http://www.bioinformatics.net.au/ <http://www.bioinformatics.net.au/>*
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