Performance of Linux systems for BLAST searching??

Andrew Dalke dalke at bioreason.com
Mon Dec 7 11:33:39 EST 1998


Andrew Martin <amartin at stagleys.demon.co.uk> said:
> Alpha works great if you compile using DEC CC under Digital Unix
> then use the executable.

We've done that before and it works well.  I don't recall serious
crashes on BLAST with that configuration.  There was a bug with
error reporting on exit when using incorrect inputs that I reported
to NCBI last spring.  That's probably fixed by now.

What I wanted to add was:
  1) to do as Andrew suggested you need to statically link the
   executable when compiling under Digital Unix

  2) BLAST can call an external complexity filter and does so with
a call to system().  This requires "sh" to work, and Digitial Unix
hard codes the sh to be in /usr/bin/sh (I think).  Red Hat 5.1 Linux
doesn't have sh in that location (it uses /bin/sh) so we had to make
a symbolic link from one to the other.

						(another) Andrew
						dalke at bioreason.com




More information about the Bio-soft mailing list