[Numpy-discussion] compiling and linking MKL with numpy/scipy

Xavier Barthelemy xabart@gmail....
Tue Nov 22 17:42:11 CST 2011

dear everyone,

I am hard trying to compile numpy / and scipy with mkl.

unfortunately it does not work. i have tried a lot of solution, and the
closest for me to work is:

*I have *

Linux manning 2.6.32-27-server #49-Ubuntu SMP Thu Dec 2 02:05:21 UTC 2010
x86_64 GNU/Linux

python -c 'import os,sys;print os.name,sys.platform' -> posix linux

python 2.6

numpy 1.6.1

scipy 0.10

Intel® Fortran Compiler XE Version 12.1 Update 1, Intel® Debugger Version
12.1 Update 1, Intel® Math Kernel Library (Intel® MKL) Version 10.3 Update 7

*I used this to help me*:

*the relevant part of site.cfg* in numpy:

library_dirs = /opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/
include_dirs = /opt/intel/composer_xe_2011_sp1.7.256/mkl/include/
lapack_libs =
mmkl_libs = mkl_intel_ilp64 ,mkl_core ,mkl_intel_thread,mkl_mc

*i**n distutils/intecompiler.py*

cc_exe = 'icc -m64 -O2 -fomit-frame-pointer -openmp -lpthread -fPIC -xHost
-fp-model strict -DMKL_ILP64 '
ccxx_exe = 'icpc -m64 -O2 -fomit-frame-pointer -openmp -lpthread -fPIC
-xHost -fp-model strict -DMKL_ILP64 '

* in distutils/fcompiler/intel.py*

def get_flags_opt(self):
return ['-O3 -openmp -i8 -fpe0 -L$(MKLROOT)/lib/intel64 -lpthread,']

*I run in .bashrc*

source /opt/intel/composer_xe_2011_sp1.7.256/bin/compilervars.sh intel64
source /opt/intel/composer_xe_2011_sp1.7.256/mkl/bin/mklvars.sh intel64

*and my complation script is:*


python setup.py config --compiler=intelem build_clib --compiler=intelem
build_ext --compiler=intelem install

*I had to use* "-fp-model strict" to pass the simple test of numpy

*but when I run numpy.test('full')*

test_assumed_shape.TestAssumedShapeSumExample.test_all ... Segmentation

*and then with the same config for scipy *


test_definition (test_basic.TestDoubleFFT) ... Segmentation fault
*which obviously come from numpy*

So what do I miss to make it work?

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