Need for Speed (postscript)
stephenREVOLUTION at barncard.com
Sun Jul 15 16:50:16 EDT 2007
Has someone benchmarked this?
I could easily stand corrected on this (not tested by me), but I'd
look for a way to touch the variable outPutData "by reference" (in
other words touching as little as possible).
"Put into", I think, has more overhead. In a situation with so much
data, every little bit helps.
I know that in HC, when you put somevariable into tOutVariable, that
the entire tOutVariable gets recreated, not just appended.
Ken Ray has a demonstration of the the use of "by reference" but does
not allude to any speed improvement.
Also again I could be corrected, but perhaps moving the data from
field "massList" into a variable might speed things up a bit. I'm
wondering that ANY referring to any field from inside such a long
loop is a possible time consumer.
another thing -- the last line in the loop
put "====================" & return after outputData
perhaps that could be a constant, defined at the top of the script
constant kBarDisplay = "===================="
then use this in the loop
put kBarDisplay & return after outputData
this one might have negligible difference, but I haven't tested this.
>Thanks to everyone who responded (Mark Schonewille, Mark Smith,
>Viktoras Didziulis, Robert Brenstein, apologies if I forgot anyone)
>- a whole range of solutions, including arrays, databases and 'just'
>variables. Anyway, I coded up the brute force method without any
>finess... here's the business bit of the script with some frippery...
> put "NEW SEARCH, MASS = " & pepMass & " at " & ppm & " ppm
>error" & return after outputData
>I ran a brutal test, of 45,000 lines in massList and 16,000 lines in seqDB
>My crude attempt seems to be capable, even running within the Rev
>IDE, of completing the 720million comparisons in about 30minutes
>(OK, admittedly CoreDuo 2.66GHz, 2GB RAM). That's 24million a
>minute! (I deliberately put some searches that would match at the
>end of seqDB, to be sure I searched through most of the file each
>time). I am pretty happy with this, and I'd be looking for at least
>a 10-fold gain in speed to code up a harder solution.
>Do you experts thing a 10-fold gain is feasible? 100-fold?
>Prof R J Beynon[h]
>Proteomics and Functional Genomics Group
>Faculty of Veterinary Science
>University of Liverpool
>Crown Street, Liverpool L69 7ZJ
>Phone: +44 151 794 4312
>Fax: +44 151 794 4243
>Email: r.beynon at liv.ac.uk
>This email was sent on Sun, 15 Jul, 2007 at 8:58 PM.
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