Hey Jonathan, Not sure if it will help, but here is how I got my MKL install working: cd ~/install virtualenv numpy_mkl cd numpy_mkl source bin/activate wget http://downloads.sourceforge.net/project/numpy/NumPy/1.5.1/numpy-1.5.1.tar.g... tar xzvf numpy-1.5.1.tar.gz cd numpy-1.5.1 cat << EOF > site.cfg [DEFAULT] library_dirs = /usr/lib include_dirs = /usr/include# numpy's configuration on resonance [DEFAULT] library_dirs = /usr/lib include_dirs = /usr/include [fftw] libraries = fftw3 [mkl] library_dirs = /opt/intel/Compiler/11.1/073/mkl/lib/em64t:/opt/intel/Compiler/11.1/073/lib/intel64 include_dirs = /opt/intel/Compiler/11.1/073/mkl/include:/opt/intel/Compiler/11.1/073/include lapack_libs = mkl_lapack mkl_libs = mkl_gf_lp64, mkl_gnu_thread, mkl_core, iomp5, guide, irc, mkl_mc, mkl_def EOF wget http://projects.scipy.org/numpy/raw-attachment/ticket/993/system_info.patch patch numpy/distutils/system_info.py < system_info.patch cat > intelccompiler.patch << EOF --- numpy/distutils/intelccompiler.py 2010-11-08 17:58:24.000000000 -0600 +++ numpy/distutils/intelccompiler.py.patched 2011-02-13 02:09:24.247386568 -0600 @@ -8,7 +8,7 @@ """ compiler_type = 'intel' - cc_exe = 'icc' + cc_exe = 'icc -fPIC -O3 -mmse4 -fast' def __init__ (self, verbose=0, dry_run=0, force=0): UnixCCompiler.__init__ (self, verbose,dry_run, force) EOF patch -p0 < intelccompiler.patch python setup.py config python setup.py build_ext --compiler=intel --fcompiler=intel install --prefix=~/local HTH Best, N On Wed, Jan 19, 2011 at 5:24 PM, Jonathan Tu <jhtu@princeton.edu> wrote:
Hi,
I am trying to install numpy with the MKL libraries available on my cluster. Most of the libraries are available in one directory, but the iomp5 library is in another.
/opt/intel/Compiler/11.1/072/mkl/lib/em64t ---> mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_def, mkl_mc /opt/intel/Compiler/11.1/072/lib/intel64 ---> iomp5
Using an older MKL library that was available, I found that when all libraries are in one directory, the install went through fine. But in this case it says the libraries cannot be found, even if I list both under the library_dirs in site.cfg
[mkl] library_dirs = /opt/intel/Compiler/11.1/072/mkl/lib/em64t:/opt/intel/Compiler/11.1/072/lib/intel64 include_dirs = /opt/intel/Compiler/11.1/072/mkl/include lapack_libs = mkl_lapack mkl_libs = mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_def, mkl_mc, iomp5
If I try to install without iomp5, then when I import numpy I get the following error
/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so: undefined symbol: omp_in_parallel
Any ideas? I tried to put symbolic links to both library directories in one place, but that didn't work either. I'm trying to avoid creating a directory of symbolic links to every necessary library.
Jonathan Tu _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
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