[Beowulf] cluster softwares supporting parallel CFD computing

Toon Knapen toon.knapen at fft.be
Fri Sep 15 07:05:00 PDT 2006

I agree that in general the quality of the parallelism in most codes is 
rather low, unfortunately. But it is hard to proof that much can be 
gained when the quality would be improved.

Let me elaborate. When developing an app. that needs to run fast, one 
first needs to look at using the best algorithm to get the job done. 
While implementing the algorithm, attention must be paid to the app 
being stable (no use in having a fast app which crashes the whole time). 
And finally you start optimizing. But while using a better algorithm 
might give you a 50% boost, performance increases due to 
code-optimization are generally only marginal. Basically, changes early 
in the development process will have a big effect on performance while 
changes late in the dev.process. will have minor effects.

For instance, I wonder if any real-life application got a 50% boost by 
just changing the switch (and the corresponding MPI implementation). Or, 
what is exactly the speedup observed by switching from switch A to 
switch B on a real-life application?


Patrick Geoffray wrote:
> Hi Mark,
> Mark Hahn wrote:
>> all these points are accurate to some degree, but give a sad impression
>> of the typical MPI programmer.  how many MPI programmers are 
>> professionals,
>> rather than profs or grad students just trying to finish a calculation?
>> I don't know, since I only see the academic side.
> I think that the sample of MPI codes or traces that I have seen so far 
> is a good representation of the academic, labs and commercial sides. 
> It's pretty bad. I am sure they are many reasons, but a few come to mind:
> * a lot of codes in academia and at the labs are written directly by the 
> scientist, physicist, chemist, whatever. They are expert in their 
> domain, but they don't know how to write good code. Doesn't matter if 
> it's parallel or sequential, they don't know how to do it right. For 
> their defense, they never really learned, and they are doing the best 
> they can. However, they really should work with professional 
> programmers. It's paradoxical that physicists would use the service of a 
> statistician to help them make sense of their experimental data, but 
> they don't want help for computer science.
> It's interesting to note that there has always been this push from high 
> in the food chain to bypass the human computer science expertise: it was 
> automagic compilers (OpenMP, HPF and family) in the past, it's 
> "high-productivity" languages now.
> * In the commercial side, the codes are quite old, at least in their 
> design. You can see traces of port from SHMEM to MPI, with Barriers 
> a-lot-and-often. You see collective communications done by hand, I guess 
> because the implementation of the collectives sucked at the time. You 
> see an shameful amount of unexpected messages, the kind where the 
> receive is just a little too late, typical from a code that was designed 
> for a slow network, relatively. In short, it looks like they minimize 
> the investment in code maintenance.
>> for academics, time-to-publish is the main criterion, which doesn't 
>> necessarily mean well-designed or tuned code.  taking a significant 
> I don't know if time is really the constraint here. For grads students, 
> sure, but I would not think that more time would help with profs. A good 
> programing book maybe, but they are too proud to read those :-)
> Patrick

Toon Knapen

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