[Biopython-dev] Building Biopython with ICC instead of GCC (intel compiler)

[João Rodrigues]

Hi all,

This is more of a curiosity rather than a necessity. I'm setting up a new
cluster and we are preferring ICC (intel compiler) over the usual GCC. When
I run "python setup.py build" the output shows ICC being used quite a lot
but some lines still use GCC.

Example:

*gcc -pthread -shared build/temp.linux-x86_64-2.6/Bio/KDTree/KDTree.o
build/temp.linux-x86_64-2.6/Bio/KDTree/KDTreemodule.o -L/usr/lib64
-lpython2.6 -o build/lib.linux-x86_64-2.6/Bio/KDTree/_CKDTree.so*
building 'Bio.Motif._pwm' extension
creating build/temp.linux-x86_64-2.6/Bio/Motif
icc -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv
-fPIC
-I/home/software/python-libs/lib64/python2.6/site-packages/numpy/core/include
-I/usr/include/python2.6 -c Bio/Motif/_pwm.c -o
build/temp.linux-x86_64-2.6/Bio/Motif/_pwm.o
icc: command line warning #10006: ignoring unknown option '-fwrapv'
icc: command line warning #10006: ignoring unknown option '-fwrapv'
/home/software/python-libs/lib64/python2.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h(15):
warning #1224: #warning directive: "Using deprecated NumPy API, disable it
by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  #warning "Using deprecated NumPy API, disable it by " \
   ^

I guess this has to do with distutils? Any idea on how to force it to use
only the intel compilers?

Cheers,

João