[Numpy-discussion] another numpy/ATLAS problem

David Warde-Farley dwf@cs.toronto....
Thu Nov 26 19:53:58 CST 2009


It seems like I've done this enough times on enough machines but I'm  
still running into problems...

After installing what I'm pretty sure is a complete ATLAS+LAPACK and  
building numpy against it (appropriately editing site.cfg, etc.) I'm  
faced with this when building numpy-1.3.0:

dwf@mirage:~/tmp$ python
Python 2.6.4 (r264:75706, Nov  2 2009, 14:44:17)
[GCC 4.4.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ 
__init__.py", line 130, in <module>
     import add_newdocs
   File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ 
add_newdocs.py", line 9, in <module>
     from lib import add_newdoc
   File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ 
lib/__init__.py", line 13, in <module>
     from polynomial import *
   File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ 
lib/polynomial.py", line 18, in <module>
     from numpy.linalg import eigvals, lstsq
   File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ 
linalg/__init__.py", line 47, in <module>
     from linalg import *
   File "/home/dwf/virtualenv/stable/lib/python2.6/site-packages/numpy/ 
linalg/linalg.py", line 22, in <module>
     from numpy.linalg import lapack_lite
ImportError: /home/dwf/virtualenv/stable/lib/python2.6/site-packages/ 
numpy/linalg/lapack_lite.so: undefined symbol: dlamc3_

FWIW these are the files that ATLAS has installed:

dwf@mirage:~/Downloads$ ls /opt/sw/ATLAS/lib/ -al
total 23472
drwxr-xr-x 2 root root     4096 2009-11-26 20:36 .
drwxr-xr-x 4 root root     4096 2009-11-26 20:36 ..
-rw-r--r-- 1 root root 12963138 2009-11-26 20:36 libatlas.a
-rw-r--r-- 1 root root   466244 2009-11-26 20:36 libcblas.a
-rw-r--r-- 1 root root   572812 2009-11-26 20:36 libf77blas.a
-rw-r--r-- 1 root root  8979016 2009-11-26 20:36 liblapack.a
-rw-r--r-- 1 root root   466678 2009-11-26 20:36 libptcblas.a
-rw-r--r-- 1 root root   573196 2009-11-26 20:36 libptf77blas.a

liblapack.a looks big enough for it to be a complete LAPACK.

ATLAS (3.9.17) was configured with the following:

../configure -Ss kern /usr/bin/gcc-4.2 --prefix=/opt/sw/ATLAS --with- 
netlib-lapack-tarfile=/home/dwf/tmp/lapack-lite-3.1.1.tgz -Fa alg - 
fPIC -D c -DPentiumCPS=2668 -t 4 -b 64

I tried a few different things, including building dylibs, in which  
case I get an undefined symbol error for ATL__zttrsm.

Any help would be appreciated. To be honest I'm not sure why  
lapack_lite is getting involved at all; I thought that was what got  
used in case of no detected LAPACK, but config definitely does detect  
ATLAS/LAPACK.

David


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