bugGNU Parallel - Bugs: bug #37325, Inefficiency of --pipe -L

 
 

bug #37325: Inefficiency of --pipe -L

Submitter:  Ole Tange <tange>
Submitted:  Tue 11 Sep 2012 08:39:02 AM UTC
   
 
Category:  None Severity:  3 - Normal
Item Group:  None Status:  Fixed
Privacy:  Public Assigned to:  tange
Open/Closed:  Closed
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Sun 25 Nov 2012 11:20:36 PM UTC, comment #1: 

Fixed in [6921d28]

Ole Tange <tange>
Group administrator
Tue 11 Sep 2012 08:39:02 AM UTC, original submission:  


The NEWS file mentions that '-L n --pipe' is useful for fastq.  I tried this, and it works, but extremely slowly.  On the other hand, using '-N' instead of '-L' works and is much faster.

I'm using GNU parallel 20120822.  Here is how to reproduce the problem:

seq 100000 > fake.fastq

# This works and is fast:
time parallel --pipe -N10000 cat < fake.fastq > out1

# These work but are extremely slow:
time parallel --pipe -L10000 cat < fake.fastq > out2a
time parallel --pipe -L4 cat < fake.fastq > out2b
time parallel --pipe -L4 --block 1M cat < fake.fastq > out2c

(As you can see, I'm also not certain how -L is supposed to be used.)

I hope this is useful,
Martin Frith
http://www.cbrc.jp/~martin/

Ole Tange <tange>
Group administrator

 

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    Date Changed by Updated Field Previous Value => Replaced by
    2012-11-25 tange StatusConfirmed Fixed
        Open/ClosedOpen Closed

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