mpiBLAST release announcement

David Mathog mathog at caltech.edu
Mon Feb 17 05:27:09 EST 2003


On 13 Feb 2003 10:16:15 -0000
darling at cs.wisc.edu (Aaron Darling) wrote:

> The mpiBLAST team anounces the release of mpiBLAST, an MPI based parallel
> implementation of NCBI BLAST.  mpiBLAST is a pair of programs that replace
> formatdb and blastall with versions that execute BLAST jobs in parallel on
> a cluster of computers with MPI installed. 

Is your "blastall" a shell that calls regular blastall on the compute
nodes or did you actually manage to make the merge function coexist with the
NCBI code?  If the latter I'm really, really, really, impressed, because
for those of you who have not had the joy of modifying blastall let me tell
you that the code is hideously complex.  I looked into that approach and
gave up and took the easy way out - postprocessing the blastall
output in a separate program.  My parallel blast version has many more
programs (and scripts) but otherwise sounds like it does pretty much what
yours does.  It may be obtained here:

  ftp://saf.bio.caltech.edu/pub/software/molbio/parallelblast.tar

This version uses PVM instead of MPI for running the compute node
jobs.  It doesn't do any message passing other than "start job" and
"job is completed".  There is a cgi front end which is designed for
on site use - it would need minor modifications to allow off site users.
The merge step is not built into blastall but carried out separately by
"blastmerge", a program which was announced here some time ago.

There are also some patches to the BLAST distribution (2.2.3) which
fix a few problems in rpsblast and extend the "gi" mechanism so that
searches of nr/nt may be restricted by taxon id using only two files.
(Ie, not a separate gi file for each taxon).

PHIBLAST isn't supported here.  Does yours include it?

> Because each node's segment of the database is smaller it can
> usually reside in the buffer-cache, yielding a significant
> speedup due to the elimination of disk I/O. 

Right.  The benefits of file caching are not irrelevant for folks
with just one machine sitting on their desk.  My package may also
be used for "serial parallelization" to take advantage of this effect.
That is, if a researcher has a 10000 entry query and wants to find
those hits in the human genome on his workstation the database typically
won't fit into memory and the search will take forever.  This same
search can be speeded up immensely by fragmenting the database, running
the same query to completion on each fragment, and then merging the
results with blastmerge.  The fragmented method is faster so long as:

  number of database fragments < ratio (uncached run time / cached run time)

Ie, if splitting the database 3 ways makes it small enough to stay in
cache, and the ratio is 30, searching the fragments sequentially will
be 10x faster than searching the entire database at once.

The other advantages to fragmenting N ways are that if the database does
need to load from local disk it does so N times faster than it would have
on a single node.  Also, and this is the primary reason I wrote my version,
you can run databases which do not fit into a single node's memory.  Our
20 node cluster has 20Gb of memory.  Subtract 50 Mb for the OS and 100Mb
for blastall (roughly) and it leaves 17 Gb to cache databases.  That's
more than big enough to hold nt, nr, and a couple of mammalian genomes.
But 850Mb (the free amount on each node) isn't. When the databases
finally outgrow cluster memory then you can add more nodes. With
unfragmented databases you have to add memory to each machine, and
if they won't support enough memory, replace the lot of them with a model
that does.

> It does not require a dedicated cluster.

I can't speak for your implementation but here if any other jobs run
at the same time their load must be exceedingly well balanced.
Since the merge step cannot complete until all nodes
finish a CPU hog on just one node will bog down the BLAST system.
Moreover, these other jobs can't use too much memory either or they'll
bump the blast databases out of cache.  Since parallel blast itself is
pretty well balanced we allow two blastalls to run at once on each node,
one at higher precedence (for shorter jobs) and another at lower precedence
(for longer jobs).  No adverse interactions from doing so have shown
up so far. 

There is one other minor "gotcha" for potential users of
either parallel BLAST.  Some linux distributions come with "locate"
which puts "slocate.cron" into /etc/daily.  Even on our 1Gb compute
nodes when slocate.cron runs it throws everything out of cache.  That
was causing the first job that ran afterwards to be abnormally
slow since it had to reload the database fragments from local disk. 
Had the fragments been NFS mounted the hit would have been
even greater.  Compute nodes usually don't need reindexing that often
so move that file to /etc/monthly.  It would probably make sense to
take it out of cron entirely.

Regards,
 
David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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