Created attachment 419850 [details] emerge --info Hello, when MKL blas implementation (mkl64-gfortran-openmp in my case) is being used by numpy-1.10.2-r1 it is not linked properly. Numpy itself builds fine, but fails to load at runtime: $ python Python 3.3.5 (default, Mar 28 2014, 19:31:48) [GCC 4.7.3] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib64/python3.3/site-packages/numpy/__init__.py", line 180, in <module> from . import add_newdocs File "/usr/lib64/python3.3/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/lib64/python3.3/site-packages/numpy/lib/__init__.py", line 18, in <module> from .polynomial import * File "/usr/lib64/python3.3/site-packages/numpy/lib/polynomial.py", line 20, in <module> from numpy.linalg import eigvals, lstsq, inv File "/usr/lib64/python3.3/site-packages/numpy/linalg/__init__.py", line 51, in <module> from .linalg import * File "/usr/lib64/python3.3/site-packages/numpy/linalg/linalg.py", line 29, in <module> from numpy.linalg import lapack_lite, _umath_linalg ImportError: /opt/intel/composerxe-2013.2.144/mkl/lib/intel64/libmkl_gnu_thread.so: undefined symbol: mkl_blas_dgemm_blk_info_hi_thr_bdz Diagnostics shows: $ symlookup -p /opt mkl_blas_dgemm_blk_info_hi_thr_bdz symlookup: warning: directory '/opt/intel/composerxe-2013.1.106/licenses' cannot be read: Permission denied /opt/intel/composerxe-2013.2.144/mkl/lib/ia32/libmkl_core.so: mkl_blas_dgemm_blk_info_hi_thr_bdz /opt/intel/composerxe-2013.2.144/mkl/lib/intel64/libmkl_core.so: mkl_blas_dgemm_blk_info_hi_thr_bdz MKL pkg-config file contains proper information: $ pkg-config --libs mkl64-gfortran-openmp -L/opt/intel/composerxe-2013.2.144/mkl/lib/intel64 -L/opt/intel/composerxe-2013.2.144/compiler/lib/intel64 -Wl,--start-group -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp -lpthread Please notice -lmkl_core — this library contains required symbol. My version of MKL is rather old (11.1.2.144), but I can't use newer one due to license restrictions. As one can see from above, MKL pkg-config setup is correct itself, so the problem is somewhere in the numpy: it should link with mkl_core as well, but: # ldd /usr/lib64/python3.3/site-packages/numpy/linalg/lapack_lite.cpython-33.so linux-vdso.so.1 (0x00007fff6edff000) /opt/intel/composerxe-2013.2.144/compiler/lib/intel64/libimf.so (0x00007fc43df4f000) libmkl_gf_lp64.so => /opt/intel/composerxe-2013.2.144/mkl/lib/intel64/libmkl_gf_lp64.so (0x00007fc43d7ef000) libmkl_gnu_thread.so => /opt/intel/composerxe-2013.2.144/mkl/lib/intel64/libmkl_gnu_thread.so (0x00007fc43cd0a000) libpython3.3.so.1.0 => /usr/lib64/libpython3.3.so.1.0 (0x00007fc43c894000) libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.2/libgomp.so.1 (0x00007fc43c684000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fc43c467000) libc.so.6 => /lib64/libc.so.6 (0x00007fc43c0c4000) libintlc.so.5 => /opt/intel/composerxe-2013.2.144/compiler/lib/intel64/libintlc.so.5 (0x00007fc43be6d000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fc43bc69000) libutil.so.1 => /lib64/libutil.so.1 (0x00007fc43ba66000) libm.so.6 => /lib64/libm.so.6 (0x00007fc43b76b000) /lib64/ld-linux-x86-64.so.2 (0x00007fc43e617000) $ ldd /usr/lib64/python3.3/site-packages/numpy/linalg/_umath_linalg.cpython-33.so linux-vdso.so.1 (0x00007fff47f75000) /opt/intel/composerxe-2013.2.144/compiler/lib/intel64/libimf.so (0x00007f460fff6000) libmkl_gf_lp64.so => /opt/intel/composerxe-2013.2.144/mkl/lib/intel64/libmkl_gf_lp64.so (0x00007f460f896000) libmkl_gnu_thread.so => /opt/intel/composerxe-2013.2.144/mkl/lib/intel64/libmkl_gnu_thread.so (0x00007f460edb1000) libpython3.3.so.1.0 => /usr/lib64/libpython3.3.so.1.0 (0x00007f460e93b000) libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.2/libgomp.so.1 (0x00007f460e72b000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f460e50e000) libc.so.6 => /lib64/libc.so.6 (0x00007f460e16b000) libintlc.so.5 => /opt/intel/composerxe-2013.2.144/compiler/lib/intel64/libintlc.so.5 (0x00007f460df14000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f460dd10000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f460db0d000) libm.so.6 => /lib64/libm.so.6 (0x00007f460d812000) /lib64/ld-linux-x86-64.so.2 (0x00007f46106e0000) Please note, that libmkl_core is absent in the listings. (The whole setup is quite old, but in production and can't be @world updated till the next maintenance window.)
Oops, should be "when MKL *lapack* implementation"
commit 1a7d2ff6d7c7473e44b2d76e954a4b279b083a09 Author: Justin Lecher <jlec@gentoo.org> Date: Sun Dec 27 17:15:52 2015 +0100 sci-libs/mkl: Update link flags according to intel's suggestions Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=568826 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
