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I would be happy to help troubleshoot, but I am not much of a programmer to know how. The hang is reproducible, and -mca btl ^sm is about 15% faster.
if you want to shoot me some instructions off list, I can give it a go.
The application that I am working with, primarily, is ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
On Dec 15, 2009, at 11:55 AM, Eugene Loh wrote:
> Matthew MacManes wrote:
>> On my system, mpirun -np 8 -mca btl_sm_num_fifos 7 is much slower (and appeared to hang after several thousand interations) than -mca btl ^sm
> If the hang is reproducible, we should perhaps have a look. Also, the fact that it's much slower is interesting. Can you characterize the message pattern? Increasing the number of FIFOs means that there are more places to look to find messages, but this should make a difference mainly only for very large on-node process counts (more than 8 I would have thought) and very latency-sensitive applications (but perhaps that's what you have).
>> Is there another better way I should be modifying fifos to get better performance?
> Actually, there have some been some promising developments on the trac-2043 front. So, maybe 1-3 days of patience could payoff here. But, I'm not in a position to promise anything.
>> On Dec 11, 2009, at 4:04 AM, Terry Dontje wrote:
>>>> Date: Thu, 10 Dec 2009 17:57:27 -0500
>>>> From: Jeff Squyres <jsquyres_at_[hidden]>
>>>> On Dec 10, 2009, at 5:53 PM, Gus Correa wrote:
>>>>>> How does the efficiency of loopback
>>>>>> (let's say, over TCP and over IB) compare with "sm"?
>>>> Definitely not as good; that's why we have sm. :-) I don't have any quantification of that assertion, though (i.e., no numbers to back that up).
>>> However, as Eugene wrote earlier you can actually increase the number of fifos used by the SM and avoid the hang that way. Unless you are really strapped for memory I think that would be the best way to go.
> users mailing list
University of California- Berkeley
Museum of Vertebrate Zoology
Lab Website: http://ib.berkeley.edu/labs/lacey
Personal Website: http://macmanes.com/