GCG on DEC AXP info

Tim Bolling bollingt at ugene1.abbott.com
Tue May 17 09:35:37 EST 1994

David Mathog writes:


>Some recent Alpha AXP performance benchmarks that may be of interest are:

>FASTA Benchmark (run with cooperation of MIT/Whitehead)
>SPARC10/40	 		1.20 sec
>AlphaAXP OSF/1 3000-600	 .37 sec
>AlphaAXP OSF/1 3000-800	 .31 sec


Not that I'm refuting this data but I have to say that the actual times seem
a bit suspicious to me.  At our site, the most common use of FASTA is to query
a sequence against one of the public databanks.  The time necessary to do this
search on a 690MP is more on the order of 20 min not 1.20 sec.  Much of that 
time is spent reading data from the disk so the type of disk, its controller,
and the amount of memory, etc., in addition to the CPU factor into the real-time
that elapses when one executes a search program.  Any search done in 1.2
sec. is obviously not searching one of the public databanks (ie. GenBank, EMBL, 
etc) and thus, is not representative a typical "real-life" use of FASTA.

On the otherhand, the BLAST times (not included in this message) look pretty
representative of actual times I've experienced.  If the FASTA results were
to hold in a more extensive search, then it would appear that the Alpha 
might indeed be 2-4 times faster than the SPARC10.

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