Amazon AWS, RGenoud, Parallel Computing

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Date: Sat, 11 Jun 2011 13:03:10 +0200
From: lui.r.project at googlemail.com
To: r-help at r-project.org
Subject: [R] Amazon AWS, RGenoud, Parallel Computing

Dear R group,

[...]

I am a little bit puzzled now about what I could do... It seems like
there are only very limited options for me to increase the
performance. Does anybody have experience with parallel computations
with rGenoud or parallelized sorting algorithms? I think one major
problem is that the sorting happens rather quick (only a few hundred
entries to sort), but needs to be done very frequently (population
size >2000, iterations >500), so I guess the problem with the
"housekeeping" of the parallel computation deminishes all benefits.

Your sort is part of algorithm or you have to sort results after 
getting then back out of order from async processes? One of 
my favorite anecdotes is how I used a bash sort on huge data
file to make program run faster ( from impractical zero percent CPU
to very fast with full CPU usage and you complain about exactly
a lack of CPU saturation). I guess a couple of comments. First, 
if you have specialized apps you need optimized, you may want
to write dedicated c++ code. However, this won't help if
you don't find the bottleneck. Lack of CPU saturation could
easily be due to "waiting for stuff" like disk IO or VM
swap. You really ought to find the bottle neck first, it
could be anything ( except the CPU maybe LOL). The sort
that I used prevented VM thrashing with no change to the app
code- the app got sorted data and so VM paging became infrequent.
If you can specify the problem precisely you may be able to find
a simple solution.