From: Bernd J. <ber...@pa...> - 2009-04-27 14:07:25
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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 |