Anyone: NCBI BLAST2 on >1 CPU on Solaris?

Roland Mainz roland.mainz at informatik.med.uni-giessen.de
Thu May 4 02:01:08 EST 2000


mike4 at cris.com wrote:

> I'm having trouble getting BLAST2 (executable: blastall) to run on more
> than one processor (i.e., when I specify the number of processors as 4
> with the '-a' command line option).  It could have something to do with
> my local environment, although I can get other programs (e.g. Perl) to
> utilize all 4 processors.

This heavily depends on the executable. Unless the program or interpreter
(perl, JAVA) was designed to use multiple CPUs the program will only use
one CPU. You can always run multiple instances of the program which will
distribute over all available CPUs (=available means also that you can
restrict this via pbind (1m) - which may be usefull for interactive
machines which should be shared between many users).

If you have the Sun Workshop compiler you can do some magic to turn any
(uhm... most...) single-CPU-apps. into multi-CPU-apps. but this is little
bit tricky (=if the program was written portable and uses itself no
threading (this excludes the usage of GUI libraries like GTK+ etc., too)
it works, otherwise you'll see some weired crashes =:-)


> Has anyone observed BLAST-2 running on more
> than one processor in a 64-bit Solaris environment?  Does anyone know
> of a trick to get BLAST2 to compile so that it can use all the
> processors?

Uhm, I think we need little more information
Which Solaris version (64bit==Solaris 7, right ?), kernel patch rev,
hardware, compiler used ?

----

Bye,
Roland

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