This work was done by summer interns
working at IBM, we are planning to provide any improvements back to the
developers. We just downloaded
the mpiBLAST-pio version to identify and implement differences.
Robert Olson <olson@xxxxxxxxxxx> Sent by: owner-discuss@xxxxxxxxxxxxxxx
03/14/2006 02:08 PM
To
Paul Hovland <hovland@xxxxxxxxxxx>
cc
Robert Latham <robl@xxxxxxxxxxx>,
discuss@xxxxxxxxxxxxxxx
Subject
Re: [bgl-discuss] File descriptor limits?
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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