Linux vs Unix for doing bioinformatics

Aaron J Mackey ajm6q at virginia.edu
Wed Mar 1 13:53:32 EST 2000


On Wed, 1 Mar 2000, Steffen Schmidt wrote:

> Stephane Bortzmeyer wrote:
> > 
> >  Keith Bradnam <keith at thale.nott.ac.uk> writes:
> > 
> > > Does anybody have any experience of performing intensive bioinformatics
> > > tasks (e.g. running blast searches, serving databases to the outside
> > > world) on PCs running linux as oppposed to Suns or DECs?

> We are running BLAST searches on Linux based PentiumIII-Servers - we
> have severe problems (i.e. the server crashes) when we use e.g. blastpgp
> and a database which is accessed via NFS. This is a known bug to Linux
> as far as I know (If someone knows better please answer). So the best
> way to use BLAST is by using locally stored databases and everything is
> fine!

We have found that for the fasta package, threaded memory allocation is
flakey under Linux.  We have not experienced these memory problems under
any other OS version (and note that the Linux problems are sporadic and
specific only to threaded versions of the fasta programs).

On the otherhand, our PVM- and MPI-enabled versions of the fasta programs
work great on a distributed linux clusters (ours is quite big, and the
databases are shared via NFS with no problems).

So Linux may not yet be the best solution for everyone.

-Aaron

-- 
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/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
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