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Job Processing Was RE: Parallel Merge

From: Nathan Watson-Haigh
Subject: Job Processing Was RE: Parallel Merge
Date: Tue, 23 Aug 2011 16:08:56 +0930

Hi Ole,

I'm in the middle of optimising the processing of such file. While I'm at it I 
have a quick question:

I'm processing my input file with -N 2500 as it seems to give me the best 
processing time. My CPU usage and disk IO are well below their maximum capacity 
and wondered how GNU parallel processes/submits new jobs as others are 
completed? I'm thinking that GNU parallel is somehow stalling my pipeline. 
Could you provide some information on this aspect of GNU parallel?



Nathan Watson-Haigh
Senior Bioinformatician | The Australian Wine Research Institute
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-----Original Message-----
> From: [] On Behalf Of Ole
> Tange
> Sent: Saturday, 20 August 2011 11:49 PM
> To: Nathan Watson-Haigh
> Cc:
> Subject: Re: Parallel Merge
> On Sat, Aug 20, 2011 at 12:54 AM, Nathan Watson-Haigh
> <> wrote:
> >
> > What I'm actually doing is using the ABySS genome assembler. Part of
> the pipeline is:
> >
> > KAligher | ParseAligns | sort | DistanceEst
> >
> > KAligner takes sequences from one file (queries) and finds alignments
> agianst sequences in another file (targets), outputting these in
> Sequence Alignment/Map (SAM) format. ParseAligns takes the SAM format
> and filters out some alignments. It is the ParseAligns step which is
> slowest and I'm looking at how best to split up the work to make use of
> more cores. A job for early next week!
> The most obvious way seems to be:
>   cat queries | parallel --pipe --files 'KAligher | ParseAligns |
> sort' | parallel -Xj1 sort -m {}\;rm {} | DistanceEst
> Would that work?
> /Ole

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