[Numpy-discussion] Linux numpy 1.0.1 install failed - undefined symbol: pthread_join

[Gong, Shawn (Contractor)]

Hi Robert,
I have tried both suggestions and got the same error message when
"import numpy"

Try #1) changed site.cfg to have only these 3 lines
[atlas]
library_dirs = /usr/local/lib/atlas
libraries = lapack, f77blas, cblas, atlas

result: did not work

Try #2) changed site.cfg to have only these 3 lines
[atlas]
library_dirs = /home/sgong/dev/dist/lib/atlas
libraries = lapack, f77blas, cblas, atlas

  copy the above 4 files onto /home/sgong/dev/dist/lib/atlas
  /usr/local/lib/atlas/ has all 7 files: lapack, f77blas, cblas, atlas,
ptcblas, ptf77blas, statlas
  ranlib (in /home/sgong/dev/dist/lib/atlas)

result: did not work

the install screen capture "out" from Try #2 is attached for your
reference. Note that both library_dirs = ['/usr/local/lib/atlas',
'/home/sgong/dev/dist/lib/atlas'] are found.  
But '/usr/local/lib/atlas' is ahead of '/home/sgong/dev/dist/lib/atlas'.

Is it a problem?

Thanks,
Shawn



---------------------------
>python
Python 2.3.6 (#9, May 18 2007, 10:22:59) [GCC 3.2.3 20030502 (Red Hat
Linux 3.2.3-53)] on linux2 Type "help", "copyright", "credits" or
"license" for more information.
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File
"/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/__init__.py",
line 40, in ?
    import linalg
  File
"/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/linalg/__init__.
py", line 4, in ?
    from linalg import *
  File
"/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/linalg/linalg.py
", line 25, in ?
    from numpy.linalg import lapack_lite
ImportError: 
/home/sgong/dev/dist/lib/python2.3/site-packages/numpy/linalg/lapack_lit
e.so: undefined symbol: pthread_join



-----Original Message-----
From: numpy-discussion-bounces at scipy.org
[mailto:numpy-discussion-bounces at scipy.org] On Behalf Of Robert Kern
Sent: Friday, May 25, 2007 1:24 PM
To: Discussion of Numerical Python
Subject: Re: [Numpy-discussion] Linux numpy 1.0.1 install failed -
undefined symbol: pthread_join

Gong, Shawn (Contractor) wrote:
> Hi Robert and list,
> 
> My colleague said that it certainly looks like a missing thread
library.
> It looks like the problem is that lapack_lite was compiled
> multi-threaded and can't find the thread library.

Okay, it looks like ATLAS's multithreaded libraries are being picked up
before
the single-threaded libraries. Try the following site.cfg:

[atlas]
library_dirs = /usr/local/lib/atlas
libraries = lapack, f77blas, cblas, atlas

If that doesn't work, copy the single-threaded libraries named above to
somewhere else (like /home/sgong/dev/dist/lib/), and use the following
site.cfg:

[atlas]
library_dirs = /home/sgong/dev/dist/lib
libraries = lapack, f77blas, cblas, atlas

You may have to run ranlib on the libraries after you copy them.

-- 
Robert Kern

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