[Mpiblast-users] [Bioclusters] mpiblast users, I got your help, thanks

[Mike Cariaso]

--- Aaron Darling <darling at cs.wisc.edu> wrote:
>If large exact matches aren't problematic for
standard NCBI blast onyour machine then they shouldn't
be troublesome for mpiblast either. One thing you
could try is disabling the distributed bioseq lookup. 
Itmay be that one of the database sequences is
particularly large and thewriter crashes when trying
to receive a very large message using MPI. Use the
command line switch --disable-mpi-db to shut off
distributedbioseq lookups.  Beware that
--disable-mpi-db should only be used with blastn
searches...



Fortunately, I'm only doing blastn searches. Even more
fortunately, --disable-mpi-db seems to have solved the
problem. A full run takes about 2 days, and I've only
just been able to take a stab at it. But its currently
cruising through sequences that  used to make it
crash.

A great big thanks to Alan Kilian and Chris Dwan for
offering more insight to the problem.



>  For what it's worth (maybe not much), this query
didn't 
> ...

Its worth a heck of a lot. Certainly a few more
drinks, if you can wait about 6 months.


And just for the archives, some of you would have seen
my earlier messages about a message 'Error allocating
X bytes for Dynamic Programming'. This issue was only
happening on machines using the 2.6 kernel. I hope to
continue to play with configurations and isoate that
problem a bit better. But if anyone else sees
something comparable, you may want to roll back to
2.4.

Mike 

"I've been chasing this bug off-an-on for 4 months
now. In 60 days we have to deliver to the customer." 

Cariaso

=====
Mike Cariaso