[SciPy-user] Problem importing scipy compiled with intel compiler (/opt/intel/fc/9.0/lib/libifcore.so.5: undefined symbol: __subq)

Albert Strasheim fullung at gmail.com
Mon Nov 13 19:32:44 CST 2006


Hey Sourish

I managed to build a working Python + NumPy + SciPy + Intel CC + Intel FC + 
Intel MKL configuration over the weekend. I built everything in my home 
directory under opt since I don't have root access to the machines I'm 
using.

The main trick was to set LD_RUN_PATH before I built anything (including 
Python itself) so that the linker included the paths to the Intel libraries 
in all the executables I built. If I built Python without these paths, I had 
unresolved symbols turning up as the NumPy test suite was running.

If you don't want to go this route (and use LD_LIBRARY_PATH instead), you 
might check that you included the right libraries for MKL in library_dirs in 
site.cfg. I think one wants mkl, vml. Check the README that comes with MKL 
for details on these libraries.

I recommend the LD_RUN_PATH way -- I think one can run into problems when 
you try to invoke NumPy scripts through non-login shells if you need 
LD_LIBRARY_PATH to find your libraries.

You might also want to tune the Intel CC flags.

I've attempted to document most of this stuff here:

http://www.scipy.org/Installing_SciPy/Linux#head-7ce43956a69ec51c6f2cedd894a4715d5bfff974

I still have to sort out the Intel FC flags -- the defaults currently in 
numpy.distutils give some warnings with Intel FC 9.1. I see it's also trying 
to link in the 32-bit and 64-bit LAPACK libraries. Don't know if this is 
right.

Anyway, good luck. ldd is your friend to check that the various NumPy and 
SciPy binary modules are linked against the right Intel libraries and that 
they can be found in your environment.

Cheers,

Albert

P.S. You'll probably see a few NumPy test failures in test_ufunclike.py due 
to sign-of-NaN issues. I also see a few test failures in the weave stuff. 
Here's a snippet to run all the tests:

python -c "import numpy as N; import scipy as S; 
[N.testing.NumpyTest(x).testall(level=4,verbosity=9999) for x in [N,S]]"

For NumPy: Ran 666 tests in 3.889s
For SciPy: Ran 1723 tests in 8.527s, FAILED (failures=2)

----- Original Message ----- 
From: "Sourish Basu" <sbasu at physics.cornell.edu>
To: <scipy-user at scipy.org>
Sent: Sunday, November 12, 2006 3:55 AM
Subject: [SciPy-user] Problem importing scipy compiled with intel compiler 
(/opt/intel/fc/9.0/lib/libifcore.so.5: undefined symbol: __subq)


>I compiled both numpy and scipy with intel compilers on a Xeon (4 cpu-s)
> which has ATLAS. It appears that numpy works fine, but scipy does not :(
> In IPython, I see the following

> <snip> 



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