Re: [Swiftng-users] long run times

[Bernd J. <ber...@pa...>]

Here are the associated output-files...
The one with the worst times unfortunately hasn't gotten any stdout/err for
some odd reason. Here is second "best"...


-----Original Message-----
From: Nava Whiteford [mailto:ne...@sg...] 
Sent: Monday, April 27, 2009 4:30 PM
To: Bernd Jagla
Cc: 'Tom Skelly'; Swi...@li...
Subject: Re: long run times

How big is dm3_ucsc.fa? Swifts aligner is very slow and only designed to
deal with 5000bp sequences.

->Dm3 is not being used (too big)...

Are you saying it took 39 hours using the parameters settings in the
svn? That would be a bit odd, if you can send me the stdout/err that
would be useful.

->See attached

Sorry, for the delay in getting back to you on your xml questions. I've
not forgotten! Just snowed under.

->no worries... it is cold here in Paris too today, but not that cold ;)...
Good luck !!

Nav

On Mon, Apr 27, 2009 at 04:07:06PM +0200, Bernd Jagla wrote:
> Nava,
> 
>  
> 
> Here is a list of parameters I tested and associated run-times (143,343.85
> sec = 39hrs!!!!) for one tile.
> 
> Could you please comment on where all the time might be spent?
> 
>  
> 
> I would like to understand the problem to be able to optimize our
protocols.
> 
>  
> 
> It doesn't really seem to be possible to reduce the time without loosing
too
> many clusters.
> 
>  
> 
> Thanks,
> 
>  
> 
> Bernd
> 
>  
> 
> Time  = [sec] user time from time command
> 
> Wc pf = number of lines in *.pf files
> 
> Wc nonpf =  numbe of lines in *.nonpf files
> 
> There is only one parameter changed compared to the standard (normal) call
> of the program. 
> 
>  
> 
> idx   parameter  time  wc pf wc nonpf
> 
> 1     normal     143,343.85 182,256    1,720,580
> 
> 2     --ref dm3_ucsc.fa      27,681.68  110,988    1,809,448
> 
> 3     --correlation_cc_subimage_multiplier 20  114,063.20 179,724
> 1,695,836
> 
> 4     --correlation_cc_subimage_multiplier 10  34,372.92  154,840
> 1,751,684
> 
> 5     --correlation_cc_subimage_multiplier 40  4,732.95   116,920
> 1,801,616
> 
> 6     --threshold_window 3   2,311.50   131,260    664,312
> 
> 7     --threshold_window 4   2,226.00   106,416    261,468
> 
> 8     --segment_cycles 2     3,343.96   143,712    1,301,216
> 
> 9     --segment_cycles 1     2,266.62   142,016    772,496
> 

-- 
Nav

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