Well on top of Burcin's answer and I should add a disclaimer I am working 
here:
http://www.ucsc.canterbury.ac.nz/
as a support person, so I feel for you. I am currently doing installs on 
power7 
hardware from IBM and I want to use a vocabulary that is wholly 
inappropriate 
for a public forum to express my feelings.

I am part of both sage and gentoo science community. Prefix is nice but
doesn't necessarily cover everything because of lack of man power and access
to the hardware. You mention using a mix of compiler and blas/lapack 
libraries,
well we can do that to some extent although the compiler bit may be patchy.
You can customize everything to your liking so long as you are ready to 
invest
some time in it. If you send your stuff back to gentoo we can take some of 
the 
maintenance burden, however you should remember the problem of hardware 
access
(and if you have proprietary compilers, access to that too).

You mention cmake as a build system. Are you thinking of the cmake 
superbuild system
that has touted from time to time on the paraview mailing list? (did I 
mention that
I am also dealing with vtk/paraview.) 

I am not sure how to deal with your number 4 appropriately, I'll have to 
study virtualenv.

Francois

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