Re: [BLAST_ANAWARE] time for crunching

From: Chi Zhang (zhangchi@MIT.EDU)
Date: Tue Sep 28 2004 - 13:00:39 EDT


suspect is the BATS. removed bats handling code from lrd, 7241 has
crunched past 1/3 in 10minutes on dblast09 (niced so don't worry, Compton
people).

the compiled binaries are in cvs_v3.0/BlastLib2 and not yet copied into
bin dir.

Chi

On Tue, 28 Sep 2004, Michael Kohl wrote:

> Hi Chi and others,
>
> when lrd crunches from a dst after introducing v3.3, it takes about ten
> times longer (!) than in a case where the dst had been generated with the
> old online BlastLib version. You see it in the logfiles from the CPUtime
> required, around run 10004 when you introduced the new BlastLib version:
>
> Run CPUtime dst generated
> 9989 331.78 August 10
> 9990 338.6 August 10
> 9991 344.05 August 10
> 9992 353.01 August 10
> 9993 325.46 August 10
> 9994 337.8 August 10
> 9995 321.58 August 10
> 9997 243.95 August 10
> 10003 1077.34 August 14
> 10004 1086.2 August 14
> 10005 11485.2 August 14
> 10007 11367.7 August 14
> 10008 11567.8 August 14
>
> The increased file size effect (500k events instead of 250k) looks
> more like a factor 3 in cputime though, introduced on September 3 (run
> 10826):
>
> Run CPUtime
> 10794 10648.3
> 10795 10907.8
> 10796 11021
> 10797 10847.7
> 10798 10646.7
> 10799 10567.9
> 10801 9200.24
> 10881 2575.81
> 10882 48873.1
> 10883 45581.8
> 10894 25971.6
> 10901 36234.4
> 10902 33244.1
> 10903 33609.9
>
>
> To prove that it is really the BlastLib version of the generated dst, see
> e.g.:
>
> Run CPUtime dst generated on
> 7239 1205.71 May 7
> 7240 1194.63 May 7
> 7241 13215.4 August 11
> 7242 1077.61 May7
>
>
> There are still about 900 runs (> run 10000) to be recrunched. Assuming in
> average 20000 cpusec per run and 24 buds, the remainder will take 750000
> cpusec or 200h (=2 weeks).
>
> There must be a reason why lrd takes so much longer now. Let's figure it
> out quickly!
>
> Regards,
>
> Michael
>
>
> --
>
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