Bioaccelerator advise?

William R. Pearson wrp at alpha0.bioch.virginia.edu
Wed Nov 25 17:03:48 EST 1998

greg at franklin.burnham-inst.org (Dr. Greg Quinn) writes:
> Does anyone have any recommendations or experience about the current 
> dedicated sequence analysis computing systems (eg. Paracel, etc) in
> terms of effectiveness/maintenance/expandability in relation to cost.

I cannot say anything about dedicated sequence analysis systems, but
I did recently look at some timings for conventional unix workstations.

Here are the numbers on Work/Mhz for the different architectures for
the ssearch3 (Smith-Waterman) program.

Smith-Waterman cells/sec/Mhz:	cells*10^-6/sec/proc	OS	cost

PowerPC 604e (300 Mhz):	58,365	17.5	(MkLinux)	$1800 (300 Mhz G3*)
Alpha EV4 (275 Mhz):	54,777	15.1	(DUnix)
Alpha EV5 (533 Mhz):	65,448	34.9	(DUnix)
Alpha EV5 (533 Mhz):	57,305	30.5	(Linux)		$3500 (linux only)
SGI R10K (180 Mhz):	72,277	13.0	(Irix)
Intel PPro (200 Mhz):	86,336	17.3	(Linux)		$2000 (450 Mhz PII**)

*A 300 Mhz G3 machine is probably 1.5 - 2.0X as fast. **The 450 PII is
probably 2X as fast as the 200 Mhz PPro.

At the moment, a dual processor 450 MHz PII Linux machine for $4,000
should provide about 70*10^6 cells/sec - impressive. 30-40*10^6
cells/sec is available on PowerPC G3's and 450 MHz PII's for $2,000.

Bill Pearson

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