On 11/30/2010 03:32 AM, David Brodbeck wrote:

I'm trying to install NumPy 1.5.1 on RedHat 5.5 and I'm having trouble getting it to find the ATLAS libraries. I did a lot of Googling but didn't find anything that helped...also looked through the install instructions, but they focus mainly on Ubuntu.

The problem I'm having is it's looking for the libraries in the right location, but not finding them. e.g.:

atlas_blas_info: libraries f77blas,cblas,atlas not found in /opt/python-2.5/lib libraries f77blas,cblas,atlas not found in /usr/local/lib64 libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib64/atlas libraries f77blas,cblas,atlas not found in /usr/lib64/sse2 libraries f77blas,cblas,atlas not found in /usr/lib64 libraries f77blas,cblas,atlas not found in /usr/lib/sse2 libraries f77blas,cblas,atlas not found in /usr/lib NOT AVAILABLE

...and yet...

brodbd@patas:~/numpy-1.5.1$ locate libf77blas /usr/lib64/atlas/libf77blas.so.3 /usr/lib64/atlas/libf77blas.so.3.0 brodbd@patas:~/numpy-1.5.1$ locate libcblas /usr/lib64/atlas/libcblas.so.3 /usr/lib64/atlas/libcblas.so.3.0 brodbd@patas:~/numpy-1.5.1$ locate libatlas /usr/lib64/atlas/libatlas.so.3 /usr/lib64/atlas/libatlas.so.3.0

the *.so.N.M are enough for binaries, but you need the *.so to link against a library. Those are generally provided in the -devel RPMS on RH distributions,

cheers,

David

So the libraries are there, and they're where NumPy is looking for them, but it's still not finding them? Clearly I'm missing something, but I'm not sure what.

On Tue, Nov 30, 2010 at 9:38 AM, David Brodbeck brodbd@uw.edu wrote:

On Mon, Nov 29, 2010 at 9:08 PM, David david@silveregg.co.jp wrote:

...

the *.so.N.M are enough for binaries, but you need the *.so to link against a library. Those are generally provided in the -devel RPMS on RH distributions,

Ah, right. Thank you for filling in that missing piece of information for me.  I'll see if I can find development RPMs.

I could have sworn I got this to build once before, too.  I should have taken notes.

Turns out there is no atlas-devel package, so I changed tactics and installed blas, blas-devel, lapack, and lapack-devel, instead. This was enough to get both NumPy and SciPy built. However, now SciPy is segfaulting when I try to run the test suite:

brodbd@patas:~$ python2.5 Python 2.5.5 (r255:77872, May 17 2010, 14:07:05) [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2 Type "help", "copyright", "credits" or "license" for more information.

...

...

import scipy; scipy.test();

Running unit tests for scipy NumPy version 1.5.1 NumPy is installed in /opt/python-2.5/lib/python2.5/site-packages/numpy SciPy version 0.8.0 SciPy is installed in /opt/python-2.5/lib/python2.5/site-packages/scipy Python version 2.5.5 (r255:77872, May 17 2010, 14:07:05) [GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] nose version 0.11.2 ................................................................................................................................................................................/opt/python-2.5/lib/python2.5/site-packages/scipy/fftpack/tests/test_basic.py:404: ComplexWarning: Casting complex values to real discards the imaginary part y1 = fftn(x.astype(np.float32)) /opt/python-2.5/lib/python2.5/site-packages/scipy/fftpack/tests/test_basic.py:405: ComplexWarning: Casting complex values to real discards the imaginary part y2 = fftn(x.astype(np.float64)).astype(np.complex64) /opt/python-2.5/lib/python2.5/site-packages/scipy/fftpack/tests/test_basic.py:413: ComplexWarning: Casting complex values to real discards the imaginary part y1 = fftn(x.astype(np.float32)) /opt/python-2.5/lib/python2.5/site-packages/scipy/fftpack/tests/test_basic.py:414: ComplexWarning: Casting complex values to real discards the imaginary part y2 = fftn(x.astype(np.float64)).astype(np.complex64) ......................K.............................................................................................................................K..K............................................................Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply .........Warning: divide by zero encountered in log Warning: invalid value encountered in multiply Warning: divide by zero encountered in log Warning: invalid value encountered in multiply ......................................................................................................................................................................................................................................................................................................./opt/python-2.5/lib/python2.5/site-packages/scipy/io/recaster.py:328: ComplexWarning: Casting complex values to real discards the imaginary part test_arr = arr.astype(T) ../opt/python-2.5/lib/python2.5/site-packages/scipy/io/recaster.py:375: ComplexWarning: Casting complex values to real discards the imaginary part return arr.astype(idt) ......................................................................................F..FF.........................................../opt/python-2.5/lib/python2.5/site-packages/scipy/lib/blas/tests/test_fblas.py:86: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ....../opt/python-2.5/lib/python2.5/site-packages/scipy/lib/blas/tests/test_fblas.py:196: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) .................../opt/python-2.5/lib/python2.5/site-packages/scipy/lib/blas/tests/test_fblas.py:279: ComplexWarning: Casting complex values to real discards the imaginary part self.blas_func(x,y,n=3,incy=5) ..................................................................SSSSSS......SSSSSS......SSSS...................................................F.Segmentation fault