On Sun, Jul 25, 2010 at 5:18 AM, Jonathan Tu jhtu@princeton.edu wrote:
It shows you don't use either atlas or even simple lapack. If your install used atlas, the atlas libraries would show up on those .so with ldd,
David
Hmm. Ok. What I did for Numpy installation was check out the source code using svn.
Use a released version instead (1.4.1 is the last one as we speak). Although we try to keep a relatively robust trunk, it does not have the QA put in the releases.
Then I did python setup.py build where I changed the site.cfg file so that the [Default] category also contains the path to my local Python 2.6.5 installation, which is /home/jhtu/local.
If you install the atlas libraries in /home/jhtu/local/lib, you need something like:
[atlas] library_dirs = /home/jhtu/local/lib
in your site.cfg
Then I did make install and I think there was probably a prefix type option where I specified that I wanted to install it locally.
I guess you meant python setup.py install ? there is no makefile in numpy
How do I specify that I want to build against ATLAS/LAPACK? I'm certain that they are installed on this cluster.
They are, but they are broken, as showed on the logs you posted. The atlas libraries packaged by RHEL 4 (and even 5 IIRC) are hopelessly broken, you need to build atlas by yourself - preferably into an rpm if you want to deploy on a cluster if you have admin rights.
David