Playing with HMMER on a number of servers and workstations.
I grabbed the binary distribution of 2.3.2 from the web site for Intel/FreeBSD, MacOS X, and Sparc/Solaris. On single CPU boxes, the MacOS X port is the fastest, by about 13 seconds in the hmmcalibrate routine. It’s only slightly slower than the Sparc and Intel dual CPU boxes. On a dual CPU Apple Xserve G4, hmmcalibrate is all of about 3 seconds - compared to 11 to 28 seconds on all the other machines. I guess those Altivec extensions do some good, as I doubt that we’re seeing plain CPU comparisons here. I suspect that if someone put their mind to it, they could produce some Sparc or Intel specific extensions that would make them run a lot faster as well.
I’m curious to see what this would do on a dual CPU G5 system…
Posted by Rowan Littell at February 5, 2004 11:41 AM