Hi All,
As many of you know, NCBI released a new blastall last week. The new
release includes a re-implemented blast core and various support code.
This represents the most significant and sweeping change to the NCBI
BLAST codebase since mpiBLAST has been under development. As such, it
will likely take time before mpiBLAST can fully support the new core
implementation.
In the meantime, I have updated the mpiBLAST toolbox patch to allow the
current mpiBLAST implementation to work with the new toolbox release
(12062005), using the old core blast search implementation. I just
committed these changes to the sourceforge CVS and they should appear on
the public server some time tomorrow.
In addition the new patch, I also tried to address a few of the
outstanding issues that various people have raised. In particular, part
of blast_hooks.c appeared to overload an NCBI object cache when a given
query had several thousand hits. This problem can manifest itself
either in the form of error messages like: "ObjMgrNextAvailEntityId
failed with idx 2048" or by simply using up all available memory. The
offending code was actually a workaround for a bug in the NCBI toolbox
that prevents the -m 1 through -m 6 options from working correctly with
mpiBLAST. The workaround is now only enabled when one of those output
options are selected.
Note that in general this workaround may be unrelated to the
"ObjMgrNextAvailEntityId failed" error messages. There are many other
ways to trigger such an error.
Several other important changes have trickled in during the last few
months. One notable change (courtesy of Jason Gans) is a bugfix for a
race-condition in mpiblast.cpp. I've also added to Lucas' code to
resume a crashed run. It now handles both html and text output and
saves the effective search space in a checkpoint file.
The new changes will be available from CVS tomorrow:
http://mpiblast.lanl.gov/Downloads.Unstable.html
Be sure to use the new toolbox:
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20051206
If anybody is interested in a windows binary please e-mail me directly.
-Aaron
-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems? Stop! Download the new AJAX search engine that makes
searching your log files as easy as surfing the web. DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
Mpiblast-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mpiblast-users
