Re: [bgl-discuss] File descriptor limits?

[Robert Olson <olson@xxxxxxxxxxx>]

Yes, we should do that. Does anyone know these folks? The approach in  
the paper is much more sophisticated than I'd come up with in a  
quickie attempt at doing this.

--bob

On Mar 14, 2006, at 2:00 PM, Paul Hovland wrote:

> More to the point, see this paper: http://www-users.cs.umn.edu/ 
> ~rangwala/final_bglBLAST.pdf
>
> pioBLAST was extended to better support BG/L.  Doesn't look like  
> this version is publicly available; perhaps we can get the code  
> from IBM.
>
> Paul
>
> Paul Hovland wrote:
> > I was about to suggest the same thing.  And, pioBLAST (~= mpiBLAST- 
> > PIO) is supposed to use collective output, too.  See http:// 
> > mpiblast.lanl.gov/downloads/pubs/IPDPS05-pioBLAST.pdf
> >
> > Paul
> >
> > Robert Olson wrote:
> > > On Mar 14, 2006, at 12:49 PM, Robert Latham wrote:
> > >
> > > > On Tue, Mar 14, 2006 at 11:30:22AM -0600, Robert Olson wrote:
> > > > > The mpiBLAST code is opening up a bunch of files on the nodes,  
> > > > > and is
> > > > > apparently running into a 100 file descriptor limit.
> > > >
> > > > Hi Bob
> > > >
> > > > Is this the same mpiBLAST as mpiblast.lanl.gov ?  if so you may be
> > > > interested in a patch to "allow mpiBLAST to run on IBM BlueGene"
> > > > (http://mpiblast.lanl.gov/Downloads.Patches.html)
> > >
> > >
> > > Yup - I am running with that applied. I think it was mainly  
> > > configuration fixes.
> > >
> > > > More promising is mpiBLAST-pio, which at a quick glance, looks  
> > > > like a
> > > > mpiBLAST that makes use of mpi-io to coordinate client writes.   
> > > > I've
> > > > never played with it, but that sounds like a more correct  
> > > > solution to
> > > > your problem.
> > >
> > > Aha, interesting. I'll have a look. (though this is the database- 
> > > read side, not the client-write side, but I'm sure anything I/O  
> > > related will help).
> > >
> > > --bob
> > >
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