StarCluster - Mailing List Archive

[Starcluster] How to update numpy / rebundle Starcluster

From: Dan Yamins <no email>
Date: Fri, 30 Oct 2009 00:10:00 -0400

Hi Starcluster list:

I've just installed starcluster, and it looks great! I'm really looking
forward to using it.

Something that I've run into is that I 'd like to numpy the version of numpy
to 1.3, and rebundle the AMI. I have a couple of questions about doing

1) In building numpy, how do I tell it where the optimized LAPACK libraries
are? I have a general sense of the environment variables that I'd have to
set, but I don't specifically understand which optimized libraries you guys
have built on Starcluster, and how I would exactly tell numpy configuration
where those libraries are? I have just tried to install numpy 1.3, withou
setting any environment variables, ... and I get output like this during the

       Setting PTATLAS=ATLAS
       libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
       libraries lapack_atlas not found in /usr/local/lib
       libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/atlas

      libraries lapack not found in /usr/local/lib
      libraries lapack not found in /usr/lib64
      libraries lapack not found in /usr/lib

... even though I can clearly see that there are lots of lapack and atlas
libraries in those directories. Any suggestions on this would be great.

2) Even though I've installed numpy 1.3, this doesn't seem to be
"registering" with the python install, e.g. 1.2.1 still seems to be the one
that python is linked to:

In [1]: import numpy
In [2]: numpy.version.version
Out[2]: '1.2.1'

Why is this, and how do I resolve it? (Sorry for asking here ... I know
this is probably a really dumb question that's more about Python than
StarCluster, but I've never encountered this issue before. I figured I'd
ask here first before writing to the Python list.)

3) Finally, do you expect that I'll have any problems in rebundling the
AMI? Is this a common procedure that others have used? What issues should
I expect to encounter (esp. with SSH keygen), if any? I have had serious
problems re-bundling other AMIs, so I'm just wondering whether people have
much experience with this AMI.

Thanks -- and I apologize for the long email with multiple parts!

Received on Fri Oct 30 2009 - 00:10:15 EDT
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