Re: [Swiftng-users] long run times

[Tom S. <ts...@sa...>]

Ouch!

If you go to the run output file (the log, not the xml) and grep out 
'Memstats' lines, that will give you the start/stop and delta times of 
the various processing steps steps. Note that the start/stops are 
nested, so you need to match up a start and a stop with the same label.

That should tell us where to look further.

--TS

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
>
>
>   


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