[Bioclusters] error while running mpiblast

kalyani goli kalyanigoli at gmail.com
Wed Mar 2 07:15:19 EST 2005

HI all!
I gave Shared and Local same and able to run mpiBlast1.3.0. I did nt
get exactly what u are saying .Whether to continue like this or change
the Local ..

Iam getting the following error repeated for 200 times while running
mpiblast with the  following command. Iam attaching the sequence file.
Could u help me in telling where could be the error. Iam able to
execute other sequence files with the same command , same database and
same database fragments and indexes.

time mpirun -np 4 ~/bin/mpiblast -p blastp -d pir.fasta -i seqnew2  -o

[blastall] ERROR: ncbiapi [000.000]  ObjMgrNextAvailEntityID failed
with idx 2048

On Wed, 2 Mar 2005 00:59:11 -0500 (EST), James Cuff <jcuff at broad.mit.edu> wrote:
> On Wed, 2 Mar 2005, Joe Landman wrote:
> >    it is quite possible that mpiblast will scale better than NCBI blast
> > on this system.  mpi forces you to pay attention to locality of
> > reference, so you tend to do a good job partitioning your code (that is,
> > if it scales).  NCBI is built with pthreads, and I haven't seen it scale
> *snip*
> See - I told you that Joe knew his stuff...  (old school, with a touch of
> new)
> > Lucas sent me a note indicated that in 1.3.0 they allow for shared and
> > local to coexist.  Aaron/Lucas, if you are about, could you clarify some
> > of this?  I don't want to lead people astray (and I will need to update
> > the SGE tool).
> *blush* it did actually work for me with (local/local) on our cluster, but
> it did keep moaning about this darn thing called 'blossom'...  if only I
> knew what a 62 year old flower had to do with genome analysis ;-)
> Sorry in all seriousness, a couple of weeks ago, I pushed through one of
> "them there lazy, throw in a genome get out an answer, I just can't be
> bothered to chunk and overlap this sucker" problems on 200 nodes.  I got
> about 147 nodes worth of 'throughput', but I got the answer in really
> short time, well 147 times shorter (factoring in my lazyness) to be
> precise :-).
> mpiblast works.  Really very well for certain problems.  There I said it.
> Guy and Tim will probably never forgive me...  I think I may have been the
> original 'embarrassingly parallel is the only way, nothing else will ever
> give the throughput, yada, yada' advocate...
> > Note: We have not built the mpiblast RPM for Itanium (nor for that
> > matter, any of our RPMs).  Is there any interest in this?  Curious.
> Shame they cost so darn much, well ours do, but folk keep demanding me to
> cram 64GB in them for something called whole genome assembly.  I just
> can't for the life of me understand why they cost so much :-)
> Best,
> J.
> --
> James Cuff, D. Phil.
> Group Leader, Applied Production Systems
> Broad Institute of MIT and Harvard. 320 Charles Street,
> Cambridge, MA. 02141.  Tel: 617-252-1925  Fax: 617-258-0903
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
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