weird gcc error when building python numpy from source

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weird gcc error when building python numpy from source

Postby sccolbert on Fri Mar 27, 2009 1:01 pm

Hey all,

New to this distro, great work by the way!

I do a lot of scientific work with python and so last night I built lapack 3.1.1 and Atlas 3.8.3 from source against gfortran and gcc 4.3.1 and running into a weird error.

Atlas and Lapack build and test fine according to the test suites in the make files.

Then I build Python numpy 1.3.0b1 from sources linking it to Atlas/lapack. This also works "fine" and I can use the numpy routines and verify the calls are passing to the atlas .so's

I run into a problem when trying to use the eigenvalue solver in numpy (which calls a lapack routine). The function hangs and never returns.

Now, I have been on the numpy developers board all morning and they think they have the issue narrowed down to a problem with ggc. The brought my attention to the following lines the build log and suggested I hop on over to the Distro's board and see if anyone is familiar with this error. So without further adieu, here is what we're seeing in the log:

...
compile options: '-c'

gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/local/atlas/lib -llapack -lptf77blas -lptcblas -latlas -o _configtest
/usr/bin/ld: _configtest: hidden symbol `__powidf2' in /usr/lib/gcc/i486-linux-gnu/4.3.2/libgcc.a(_powidf2.o) is referenced by DSO
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status
/usr/bin/ld: _configtest: hidden symbol `__powidf2' in /usr/lib/gcc/i486-linux-gnu/4.3.2/libgcc.a(_powidf2.o) is referenced by DSO
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: ld returned 1 exit status
failure.


anyone have experience with this? This package is routinely built by the ubuntu guys with no problems, and I didnt think that gcc was recompiled for mint. but its worth a shot.
Any help would be appreciated.

Thanks!

Chris
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Re: weird gcc error when building python numpy from source

Postby el_b on Fri Mar 27, 2009 2:58 pm

I haven't been trough that, but,
What is it written on? Are you using make? If it's on c++ you have to apt-get install build-essential if you haven't already.
It is giving a linking error, probably to libraries. Maybe you're using a different version of a library than what it is designed for.
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Re: weird gcc error when building python numpy from source

Postby sccolbert on Fri Mar 27, 2009 3:13 pm

I have all the required libs, build essentials, etc...

The weird thing about all of it, is that the same gcc version is used to build this by people on Ubuntu with no problems...
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