James Cuff wrote: > "Iam running this on SGI multiprocessor(numa)", > > you are running on a single shared (well near unified, and SGI do this > very, very well) memory server with, as you said and appear to understand > shared storage... > > *sigh* > > What on earth are you going to gain from MPI? Standard NCBI threads > should do for you just fine, or maybe I've been smoking the funny stuff. Hi James: 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 much beyond about 10 CPUs on an SMP. The coarser grain of the mpiblast partitioning (the pthread partitioning is very fine grain) will very likely result in better scalability on a NUMA. Not only that, but large multicpu NUMA's have problems with memory hotspots. I remember in the Origin days we used to play games with DPLACE directives and whatnot else to control memory layout, replication of pages, etc. This was under Irix, and there were rich sets of tools to help. I don't think many of them are available under Linux right now (possibly in the SGI propack). You don't see much a problem in 2/4 way systems. It becomes serious when you load data into a page, and you start getting 16 requestors for that page. Page migration is not a win here. readonly page replication can be a huge win here. Luckily, with mpi, all references are local to begin with ... That said, I don't have ready access to one, so I cannot test this hypothesis, though I might just throw together a BBS experiment to test this. I'd love to play with a nice 9MB cache machine. This would be a sweet blast engine :) Expensive... yes, but running out of cache is a "good thing" (TM). > If you _do_ happen to have multiple NUMA's in a cluster, (1) you are very > lucky and (2) you should the still listen to Joe's advice... Local is > only local so far, try: > > Shared=/home/kalyani/toolkit/ncbi > Local=/tmp/kalyani_mpiblast/ > > (or as Joe maybe put better) > > Shared=/home/kalyani/toolkit/ncbi > Local=/mylocalfilesystemthatnoonewillmesswith/kalyani_mpiblast/ 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). > > WFM, YMMV.. 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. Joe > > 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 -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615