Re^2: use dual-core or quad-core

well,

i'm trying to replicate the idea behind the the BLAST program(it is an alignment program - it realy doesn't matter what kind a algorithm it is). the program is written i c and it has an option to use one, tow ... or number of cores. the program calculates the similarity of the alignment. i'm also calculating something similarly to the things BLAST calculates, and in some segments my program is even faster than blast, but i cannot compare myself to BLAST algorithm when multiple core system is turned on. so i'm looking for a way to speed up my performance.

i now that perl is not intended for hard core calculations and lot of people told me not to do this in perl, but everything is in the approach.

Comment on Re^2: use dual-core or quad-core

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Re^3: use dual-core or quad-core by lima1 (Curate) on May 20, 2008 at 12:03 UTC
blast is optimized to hell. If you say you are faster in perl under some circumstances, you are doing something that is not comparable ;) Honestly, it makes not much sense to use perl for huge scientific calculations and even less trying it on multiple CPUs. In C (even without OpenMP), you are magnitudes (much more than 2,4,8 times) faster. Here are a lot of bioinformatic guys, what do you want to do?	[reply]
Re^4: use dual-core or quad-core by baxy77bax (Deacon) on May 20, 2008 at 13:25 UTC
i'm not aligning, i'm not using the heuristics behind finding matches between two sequences. only the calculation after scoring is interesting to me. i gave the example , because this was the only program i could use to see differences between parallel and linear computing	[reply]
Re^3: use dual-core or quad-core by moritz (Cardinal) on May 20, 2008 at 09:09 UTC
I think the "number of cores" is just the number of parallel threads or processes used, which shouldn't be too hard to in perl. Beware that threads can have nasty pitfalls in perl, so if you don't have a lot of data to share between the parallel calculations you could try to start separate processes instead.	[reply]
Re^4: use dual-core or quad-core by BrowserUk (Patriarch) on May 20, 2008 at 09:23 UTC
It's a perfectly legitimate thing to do. See http://en.wikipedia.org/wiki/Processor_affinity Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. "Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."	[reply]


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