Hi everyone
I realize that this e-mail has been written a lot of times before. I
have, however, not been able to make it work even though I have looked
through a lot of e-mails on the mailinglist. I apologize if the solution
is written neatly somewhere.
As many others I would like to install numpy with MKL support on a
cluster. The cluster contains dual core AMD Opteron machines. The reason
for doing this is to enable me to perform multi-threaded
matrix-operations (matrix-multiplications and singular value
decompositions primarily). Additionally I need to integrate some Fortran
code also using Intel MKL into numpy using f2py. I think I need to use
MKL for this, but correct me if I am wrong.
I have tried to follow the guide at
http://www.scipy.org/Installing_SciPy/Linux#head-7ce43956a69ec51c6f2cedd894a4715d5bfff974.
I have compiled my own python and installed it locally using the
LD_RUN_PATH suggested there using gcc (I only have access to the intel
9.1 compilers which seems to have a bug preventing me from compiling
python with it (see http://bugs.python.org/issue1689617)). This works
without any problems.
I have access to Intel MKL 10.2.5.035 and have the following site.cfg
for numpy 1.4.1:
[DEFAULT]
library_dirs = /home/sgamark/usr/lib # for python is installed
with prefix $HOME/usr
include_dirs = /home/sgamark/usr/include
[mkl]
library_dirs = /com/intel/mkl/10.2.5.035/lib/em64t
include_dirs = /com/intel/mkl/10.2.5.035/include
lapack_libs = mkl_lapack
mkl_libs = mkl_intel_lp64, mkl_intel_thread, mkl_core, iomp5, pthread,
mkl_def
and have changes numpy/distutils/intelcompiler.py according to
http://www.scipy.org/Installing_SciPy/Linux#head-7ce43956a69ec51c6f2cedd894a4715d5bfff974
but with cc_exe = 'icc -fPIC -openmp -fomit-frame-pointer -O2 -g'. I
have include openmp since I believe it is necessary for using the
threading features of MKL (correct me if I am wrong).
I have also tried modifiying numpy/distutils/system_info.py as described
in
http://article.gmane.org/gmane.comp.python.numeric.general/18877/match=intel+mkl
but without any effect.
However, executing "python setup.py config" shows that the setup-script
is unable to find any of the libraries I have (see attached file). If I
try to compile anyway MKL is not used and setting OMP_NUM_THREADS have
no effect.
At this point I am a bit frustrated, since it seems that it should not
be too difficult to get to work since it appears that other people have
no problems. Indeed, several people I work with have no problem doing
this with intel 10.1 compilers, MKL 11.1 on Intel Itanium machines. I am
not particularly experienced with this sort of thing but I usually have
few problems compiling a stand-alone Fortran or C/C++ program that uses MKL.
I would greatly appreciate it if anyone could help with this.
Regards
Søren Gammelmark
P.s: The operating system is Linux/CentOS 4.4, x86_64
Running from numpy source directory.
F2PY Version 2
blas_opt_info:
blas_mkl_info:
libraries
mkl_blas95_lp64,mkl_intel_lp64,mkl_intel_thread,mkl_core,iomp5,pthread,mkl_def
not found in /com/intel/mkl/10.2.5.035/lib/em64t
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /home/sgamark/usr/lib
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in /home/sgamark/usr/lib
NOT AVAILABLE
/home/sgamark/tmp/numpy-1.4.1/numpy/distutils/system_info.py:1392: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
libraries blas not found in /home/sgamark/usr/lib
NOT AVAILABLE
/home/sgamark/tmp/numpy-1.4.1/numpy/distutils/system_info.py:1401: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
NOT AVAILABLE
/home/sgamark/tmp/numpy-1.4.1/numpy/distutils/system_info.py:1404: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
NOT AVAILABLE
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries
mkl_blas95_lp64,mkl_intel_lp64,mkl_intel_thread,mkl_core,iomp5,pthread,mkl_def
not found in /com/intel/mkl/10.2.5.035/lib/em64t
NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /home/sgamark/usr/lib
libraries lapack_atlas not found in /home/sgamark/usr/lib
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in /home/sgamark/usr/lib
libraries lapack_atlas not found in /home/sgamark/usr/lib
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/home/sgamark/tmp/numpy-1.4.1/numpy/distutils/system_info.py:1299: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
libraries lapack not found in /home/sgamark/usr/lib
NOT AVAILABLE
/home/sgamark/tmp/numpy-1.4.1/numpy/distutils/system_info.py:1310: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
NOT AVAILABLE
/home/sgamark/tmp/numpy-1.4.1/numpy/distutils/system_info.py:1313: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
running config
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