[Swiftng-users] long run times

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

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