[SciPy-User] NumPy error

David Cournapeau david@ar.media.kyoto-u.ac...
Tue Oct 6 01:16:15 CDT 2009


Hi Nitin,

nitin chandra wrote:
> Hello Everyone,
>
> I have a System Configured with P4 1.8GHz, 256 DDR RAM, 80 GB HDD PATA
> which has FC10 with the default kernel 2.6.27 installed.
>
> I have Installed following from source / tar.gz / gz files in /opt/<software>
>
> I Installed Python 2.6.2, LAPACK-3.2.1, XBLAS-1.0.248, ATLAS-3.9.14 (
> Linux_P4ESSE2 ), FFTW-3.2.2, nose-0.11.1,

First, you don't need FFTW, scipy does not use it (anymore).

I would *strongly* recommend against XBLAS and LAPACK 3.2.1. Those
versions cause a lot of trouble and their features (extended precision
support) is not used by numpy/scipy anyway. Use the lapack 3.1.1 (lite
package is enough), and its included BLAS. Make sure you are using
gfortran to compile lapack and not g77 (using the make.inc.gfortran from
lapack should be enough for this). Then rebuild atlas, and run the make
time and make test from atlas. Please do not use atlas 3.9.14: it is a
development version, the last stable version is 3.8.3.

Building atlas
--------------

I assume the path is /usr/src/atlas-3.8.3, change to the right path in
your case.

To build atlas, you may want to use the following command, from atlas
sources:

mkdir /usr/src/atlas-3.8.3/MyObj && cd /usr/src/atlas-3.8.3/MyObj && 
../configure -Fa alg -fPIC --with-netlib-lapack=path_to_lapack

with path_to_lapack the path to your build lapack (e.g. lapack_LINUX.a
or something). Make sure the path exists, atlas does not check that the
path is valid, and create a bogus liblapack.a in that case: check that
the file in MyObj/lib/liblapack.a has a reasonable size (several MB).

Then, just do:

cd /usr/src/atlas-3.8.3/MyObj && make && make test

If this succeeds, you have a working atlas.

Building numpy
--------------

Edit your site.cfg as follows:

[atlas]
library_dirs = /usr/src/atlas-3.8.3/MyObj/lib

And then build numpy and scipy with the python setup.py build command.
It is a good idea to run the config step separately:

python setup.py config

To check that the correct library is detected.

cheers,

David


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