[Beowulf] Please help to setup Beowulf

Reuti reuti at staff.uni-marburg.de
Wed Feb 18 04:42:19 EST 2009


Am 18.02.2009 um 07:32 schrieb Mark Hahn:

>> searches. Without array task scheduling this would require 500,000  
>> individual job submissions. The fact that I never met a serious  
>> PBS shop that had not
>
> what's wrong with 500k job submissions?  to me, the existence of  
> "array jobs"
> is an admission that the job/queueing system is inefficient.

When I compare this e.g. to C:

- a loop like:

     for (i=1;i<=100000;i++)
         printf("Hello from run %d.\n", i);

- and you can guess: 100,000 times:

     printf("Hello from run %d.\n", i++);


While the execution time is nearly the same, compilation of the first  
one is faster by far. So, that a "for"-instruction in C exists is  
also an admission that it can't compile sequential code very well and  
generates a big executable? The compiler must read the source, and  
SGE has to read the job requirements for every job again and again  
and store it.

-- Reuti

(PS: not to mention, that a for-loop/array-job is easier to handle  
for the user)


>   if you're saying that the issue is not per-job overhead of  
> submission, but rather that jobs are too short, well, I think  
> that's a user problem.  I think it's entirely reasonable to require  
> user jobs to consume some minimum cpu time
> (say, few minutes).
>
>> - Policy and resource allocation features are very important to  
>> people deploying these systems
>
> so I'm curious what that means.  things like "dept A needs to be  
> guaranteed
> N cpus, but dept B gets to use whatever is left over"?  or node  
> choice based on amount of free disk?  I don't really see why these  
> sorts of issues
> would be less important to more parallel environments.
>
>> - Storage speed is often more important than network speed or  
>> latency in many cases
>
> which makes me wonder: do bio types consider using map-reduce-like
> frameworks?  that is, basically distributing the work to the data.
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