Re: [Numpy-discussion] numpy + MKL problems
None of that-this is why it has been so frustrating! Only thing I did was remove the folders in the ./build directory in order to get a cleaner slate, and just changed a couple libraries in site.cfg, and got the error, and it persisted even when I went back to the libraries I had given it when I got it to work. So I am really confused as to what could have caused the issue to start with. Anyways, it seems okay now-I had to add mkl_lapack to the library list. Everything isn't 100% yet, but I can now work with it. On Fri, Mar 16, 2012 at 8:35 PM, Francesc Alted wrote: > On Mar 16, 2012, at 8:28 PM, Glen Jenness wrote: > > > Fransesc, > > I don't think that's the problem-I'm working with a version of numpy I > had downloaded back in Dec/Jan and have not updated it since. > > > > However, doing a "LD_PRELOAD" seems to have fixed the problem, but now > whenever I'm running a script I get: > > > > python 2.4.3 GCC 4.1.2 20070626 (Red Hat 4.1.2-14) 64bit ELF on Linux > x86_64 redhat 5.2 Final > > python: symbol lookup error: /opt/intel/mkl/ > 10.0.3.020/lib/em64t/libmkl_lapack.so: undefined symbol: mkl_lapack_dgetrf > > So, if numpy has not changed, then something else does, right? Have you > upgraded MKL? GCC? Installed Intel C compiler? > > -- Francesc Alted > > > > ___ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > -- Dr. Glen Jenness Schmidt Group Department of Chemistry University of Wisconsin - Madison ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy + MKL problems
On Mar 16, 2012, at 8:28 PM, Glen Jenness wrote: > Fransesc, > I don't think that's the problem-I'm working with a version of numpy I had > downloaded back in Dec/Jan and have not updated it since. > > However, doing a "LD_PRELOAD" seems to have fixed the problem, but now > whenever I'm running a script I get: > > python 2.4.3 GCC 4.1.2 20070626 (Red Hat 4.1.2-14) 64bit ELF on Linux x86_64 > redhat 5.2 Final > python: symbol lookup error: > /opt/intel/mkl/10.0.3.020/lib/em64t/libmkl_lapack.so: undefined symbol: > mkl_lapack_dgetrf So, if numpy has not changed, then something else does, right? Have you upgraded MKL? GCC? Installed Intel C compiler? -- Francesc Alted ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy + MKL problems
Fransesc, I don't think that's the problem-I'm working with a version of numpy I had downloaded back in Dec/Jan and have not updated it since. However, doing a "LD_PRELOAD" seems to have fixed the problem, but now whenever I'm running a script I get: python 2.4.3 GCC 4.1.2 20070626 (Red Hat 4.1.2-14) 64bit ELF on Linux x86_64 redhat 5.2 Final python: symbol lookup error: /opt/intel/mkl/ 10.0.3.020/lib/em64t/libmkl_lapack.so: undefined symbol: mkl_lapack_dgetrf Glen On Fri, Mar 16, 2012 at 8:17 PM, Francesc Alted wrote: > On Mar 16, 2012, at 8:00 PM, Glen Jenness wrote: > > > Dear users, > > I was playing around with my numpy configuration, and it is now no > longer working. Whenever I try to run anything with it, I get: > > > > ...MKL FATAL ERROR: /opt/intel/mkl/10.0.3.020/lib/em64t/: cannot read > file data: Is a directory > > > > My site.cfg file is (in case it helps!): > > [DEFAULT] > > library_dirs = /usr/lib > > include_dirs = /usr/include > > [fftw] > > libraries = fftw3 > > [mkl] > > library_dirs = /opt/intel/mkl/10.0.3.020/lib/em64t > > include_dirs = /opt/intel/mkl/10.0.3.020/include > > mkl_libs = mkl_intel_lp64,mkl_intel_thread,mkl_core > > > > I have followed the directions for installing it from source, and it was > working fine earlier today. But I'm not really sure what I had changed so > it would go from working to not working. > > This might be related with: > > http://projects.scipy.org/numpy/ticket/993 > > being fixed in the last few hours. Could you please bisect ( > http://webchick.net/node/99) and tell us which commit is the bad one? > > Thanks! > > -- Francesc Alted > > > > ___ > NumPy-Discussion mailing list > NumPy-Discussion@scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > -- Dr. Glen Jenness Schmidt Group Department of Chemistry University of Wisconsin - Madison ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] numpy + MKL problems
On Mar 16, 2012, at 8:00 PM, Glen Jenness wrote: > Dear users, > I was playing around with my numpy configuration, and it is now no longer > working. Whenever I try to run anything with it, I get: > > ...MKL FATAL ERROR: /opt/intel/mkl/10.0.3.020/lib/em64t/: cannot read file > data: Is a directory > > My site.cfg file is (in case it helps!): > [DEFAULT] > library_dirs = /usr/lib > include_dirs = /usr/include > [fftw] > libraries = fftw3 > [mkl] > library_dirs = /opt/intel/mkl/10.0.3.020/lib/em64t > include_dirs = /opt/intel/mkl/10.0.3.020/include > mkl_libs = mkl_intel_lp64,mkl_intel_thread,mkl_core > > I have followed the directions for installing it from source, and it was > working fine earlier today. But I'm not really sure what I had changed so it > would go from working to not working. This might be related with: http://projects.scipy.org/numpy/ticket/993 being fixed in the last few hours. Could you please bisect (http://webchick.net/node/99) and tell us which commit is the bad one? Thanks! -- Francesc Alted ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy - MKL - build error
My bad, iomp5md is in compiler/lib dir, I copied it to the mkl dir and it worked. From: Igor Ying To: "numpy-discussion@scipy.org" Sent: Wednesday, September 14, 2011 1:07 PM Subject: Re: Numpy - MKL - build error Yes, they all are present in that directory. Also, I tried with root as login. -r-xr-xr-x 1 root root 26342559 Aug 9 22:19 libmkl_avx.so -r--r--r-- 1 root root 1190224 Aug 9 22:26 libmkl_blacs_ilp64.a -r--r--r-- 1 root root 1191496 Aug 9 22:25 libmkl_blacs_intelmpi_ilp64.a -r-xr-xr-x 1 root root 497597 Aug 9 22:25 libmkl_blacs_intelmpi_ilp64.so -r--r--r-- 1 root root 676206 Aug 9 22:21 libmkl_blacs_intelmpi_lp64.a -r-xr-xr-x 1 root root 267010 Aug 9 22:21 libmkl_blacs_intelmpi_lp64.so -r--r--r-- 1 root root 674926 Aug 9 22:22 libmkl_blacs_lp64.a -r--r--r-- 1 root root 1218290 Aug 9 22:28 libmkl_blacs_openmpi_ilp64.a -r--r--r-- 1 root root 703042 Aug 9 22:23 libmkl_blacs_openmpi_lp64.a -r--r--r-- 1 root root 1191152 Aug 9 22:29 libmkl_blacs_sgimpt_ilp64.a -r--r--r-- 1 root root 675854 Aug 9 22:23 libmkl_blacs_sgimpt_lp64.a -r--r--r-- 1 root root 425802 Aug 9 20:44 libmkl_blas95_ilp64.a -r--r--r-- 1 root root 421410 Aug 9 20:44 libmkl_blas95_lp64.a -r--r--r-- 1 root root 144354 Aug 9 22:29 libmkl_cdft_core.a -r-xr-xr-x 1 root root 115588 Aug 9 22:29 libmkl_cdft_core.so -r--r--r-- 1 root root 231886824 Aug 9 22:07 libmkl_core.a -r-xr-xr-x 1 root root 16730033 Aug 9 22:18 libmkl_core.so -r-xr-xr-x 1 root root 21474555 Aug 9 22:18 libmkl_def.so -r--r--r-- 1 root root 14974574 Aug 9 22:06 libmkl_gf_ilp64.a -r-xr-xr-x 1 root root 7008828 Aug 9 22:48 libmkl_gf_ilp64.so -r--r--r-- 1 root root 15140998 Aug 9 22:06 libmkl_gf_lp64.a -r-xr-xr-x 1 root root 7055304 Aug 9 22:48 libmkl_gf_lp64.so -r--r--r-- 1 root root 16435120 Aug 9 22:07 libmkl_gnu_thread.a -r-xr-xr-x 1 root root 9816940 Aug 9 22:49 libmkl_gnu_thread.so -r--r--r-- 1 root root 14968130 Aug 9 22:06 libmkl_intel_ilp64.a -r-xr-xr-x 1 root root 7008368 Aug 9 22:48 libmkl_intel_ilp64.so -r--r--r-- 1 root root 15134406 Aug 9 22:06 libmkl_intel_lp64.a -r-xr-xr-x 1 root root 7053588 Aug 9 22:48 libmkl_intel_lp64.so -r--r--r-- 1 root root 2472940 Aug 9 22:07 libmkl_intel_sp2dp.a -r-xr-xr-x 1 root root 1191479 Aug 9 22:20 libmkl_intel_sp2dp.so -r--r--r-- 1 root root 27642508 Aug 9 22:07 libmkl_intel_thread.a -r-xr-xr-x 1 root root 17516608 Aug 9 22:49 libmkl_intel_thread.so -r--r--r-- 1 root root 5350948 Aug 9 20:44 libmkl_lapack95_ilp64.a -r--r--r-- 1 root root 5413476 Aug 9 20:44 libmkl_lapack95_lp64.a -r-xr-xr-x 1 root root 29543829 Aug 9 22:19 libmkl_mc3.so -r-xr-xr-x 1 root root 25428037 Aug 9 22:19 libmkl_mc.so -r-xr-xr-x 1 root root 22888659 Aug 9 22:18 libmkl_p4n.so -r--r--r-- 1 root root 19232716 Aug 9 22:07 libmkl_pgi_thread.a -r-xr-xr-x 1 root root 12243062 Aug 9 22:49 libmkl_pgi_thread.so -r-xr-xr-x 1 root root 4984870 Aug 9 22:49 libmkl_rt.so -r--r--r-- 1 root root 10367758 Aug 9 22:49 libmkl_scalapack_ilp64.a -r-xr-xr-x 1 root root 6574928 Aug 9 22:50 libmkl_scalapack_ilp64.so -r--r--r-- 1 root root 10292432 Aug 9 22:49 libmkl_scalapack_lp64.a -r-xr-xr-x 1 root root 6452627 Aug 9 22:50 libmkl_scalapack_lp64.so -r--r--r-- 1 root root 9958444 Aug 9 22:07 libmkl_sequential.a -r-xr-xr-x 1 root root 5926347 Aug 9 22:48 libmkl_sequential.so -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_ilp64.a -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_ilp64_sequential.a -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_lp64.a -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_lp64_sequential.a -r-xr-xr-x 1 root root 6711968 Aug 9 22:48 libmkl_vml_avx.so -r-xr-xr-x 1 root root 2795928 Aug 9 22:47 libmkl_vml_def.so -r-xr-xr-x 1 root root 5476786 Aug 9 22:48 libmkl_vml_mc2.so -r-xr-xr-x 1 root root 5778052 Aug 9 22:48 libmkl_vml_mc3.so -r-xr-xr-x 1 root root 5382511 Aug 9 22:48 libmkl_vml_mc.so -r-xr-xr-x 1 root root 4235841 Aug 9 22:48 libmkl_vml_p4n.so drwxr-xr-x 3 root root 4096 Aug 18 11:43 locale Y you can reach the person managing the list at numpy-discussion-ow...@scipy.org Message: 1 Date: Tue, 13 Sep 2011 09:58:27 -0400 From: Olivier Delalleau Subject: Re: [Numpy-discussion] Numpy - MKL - build error To: Discussion of Numerical Python Message-ID: Content-Type: text/plain; charset="iso-8859-1" Sorry if it sounds like a stupid question, but are the files listed in the error message present in that directory? If yes, maybe try running the command with sudo, just in case it would be some weird permission issue. -=- Olivier 2011/9/13 Igor Ying > Hi, > > I am very new to Numpy and trying to build Numpy 1.6.1 with Intel MKL > 10.3.6 and getting the following errors. > > $python setup.py config --compiler=intel build_clib --compiler=intel > build_ext
Re: [Numpy-discussion] Numpy - MKL - build error
It seems you are missing libiomp5.so, which is sound if you re using the whole Composer package: the needed libs are split in two different locations, and unfortunately, Numpy cannot cope with this last time I checked (I think it was one of the reasons David Cournapeau created numscons and bento). Matthieu 2011/9/14 Igor Ying > Yes, they all are present in that directory. Also, I tried with root as > login. > > -r-xr-xr-x 1 root root 26342559 Aug 9 22:19 libmkl_avx.so > -r--r--r-- 1 root root 1190224 Aug 9 22:26 libmkl_blacs_ilp64.a > -r--r--r-- 1 root root 1191496 Aug 9 22:25 libmkl_blacs_intelmpi_ilp64.a > -r-xr-xr-x 1 root root497597 Aug 9 22:25 > libmkl_blacs_intelmpi_ilp64.so > -r--r--r-- 1 root root676206 Aug 9 22:21 libmkl_blacs_intelmpi_lp64.a > -r-xr-xr-x 1 root root267010 Aug 9 22:21 libmkl_blacs_intelmpi_lp64.so > -r--r--r-- 1 root root674926 Aug 9 22:22 libmkl_blacs_lp64.a > -r--r--r-- 1 root root 1218290 Aug 9 22:28 libmkl_blacs_openmpi_ilp64.a > -r--r--r-- 1 root root703042 Aug 9 22:23 libmkl_blacs_openmpi_lp64.a > -r--r--r-- 1 root root 1191152 Aug 9 22:29 libmkl_blacs_sgimpt_ilp64.a > -r--r--r-- 1 root root675854 Aug 9 22:23 libmkl_blacs_sgimpt_lp64.a > -r--r--r-- 1 root root425802 Aug 9 20:44 libmkl_blas95_ilp64.a > -r--r--r-- 1 root root421410 Aug 9 20:44 libmkl_blas95_lp64.a > -r--r--r-- 1 root root144354 Aug 9 22:29 libmkl_cdft_core.a > -r-xr-xr-x 1 root root115588 Aug 9 22:29 libmkl_cdft_core.so > -r--r--r-- 1 root root 231886824 Aug 9 22:07 libmkl_core.a > -r-xr-xr-x 1 root root 16730033 Aug 9 22:18 libmkl_core.so > -r-xr-xr-x 1 root root 21474555 Aug 9 22:18 libmkl_def.so > -r--r--r-- 1 root root 14974574 Aug 9 22:06 libmkl_gf_ilp64.a > -r-xr-xr-x 1 root root 7008828 Aug 9 22:48 libmkl_gf_ilp64.so > -r--r--r-- 1 root root 15140998 Aug 9 22:06 libmkl_gf_lp64.a > -r-xr-xr-x 1 root root 7055304 Aug 9 22:48 libmkl_gf_lp64.so > -r--r--r-- 1 root root 16435120 Aug 9 22:07 libmkl_gnu_thread.a > -r-xr-xr-x 1 root root 9816940 Aug 9 22:49 libmkl_gnu_thread.so > -r--r--r-- 1 root root 14968130 Aug 9 22:06 libmkl_intel_ilp64.a > -r-xr-xr-x 1 root root 7008368 Aug 9 22:48 libmkl_intel_ilp64.so > -r--r--r-- 1 root root 15134406 Aug 9 22:06 libmkl_intel_lp64.a > -r-xr-xr-x 1 root root 7053588 Aug 9 22:48 libmkl_intel_lp64.so > -r--r--r-- 1 root root 2472940 Aug 9 22:07 libmkl_intel_sp2dp.a > -r-xr-xr-x 1 root root 1191479 Aug 9 22:20 libmkl_intel_sp2dp.so > -r--r--r-- 1 root root 27642508 Aug 9 22:07 libmkl_intel_thread.a > -r-xr-xr-x 1 root root 17516608 Aug 9 22:49 libmkl_intel_thread.so > -r--r--r-- 1 root root 5350948 Aug 9 20:44 libmkl_lapack95_ilp64.a > -r--r--r-- 1 root root 5413476 Aug 9 20:44 libmkl_lapack95_lp64.a > -r-xr-xr-x 1 root root 29543829 Aug 9 22:19 libmkl_mc3.so > -r-xr-xr-x 1 root root 25428037 Aug 9 22:19 libmkl_mc.so > -r-xr-xr-x 1 root root 22888659 Aug 9 22:18 libmkl_p4n.so > -r--r--r-- 1 root root 19232716 Aug 9 22:07 libmkl_pgi_thread.a > -r-xr-xr-x 1 root root 12243062 Aug 9 22:49 libmkl_pgi_thread.so > -r-xr-xr-x 1 root root 4984870 Aug 9 22:49 libmkl_rt.so > -r--r--r-- 1 root root 10367758 Aug 9 22:49 libmkl_scalapack_ilp64.a > -r-xr-xr-x 1 root root 6574928 Aug 9 22:50 libmkl_scalapack_ilp64.so > -r--r--r-- 1 root root 10292432 Aug 9 22:49 libmkl_scalapack_lp64.a > -r-xr-xr-x 1 root root 6452627 Aug 9 22:50 libmkl_scalapack_lp64.so > -r--r--r-- 1 root root 9958444 Aug 9 22:07 libmkl_sequential.a > -r-xr-xr-x 1 root root 5926347 Aug 9 22:48 libmkl_sequential.so > -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_ilp64.a > -r--r--r-- 1 root root 1048 Aug 9 16:50 > libmkl_solver_ilp64_sequential.a > -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_lp64.a > -r--r--r-- 1 root root 1048 Aug 9 16:50 > libmkl_solver_lp64_sequential.a > -r-xr-xr-x 1 root root 6711968 Aug 9 22:48 libmkl_vml_avx.so > -r-xr-xr-x 1 root root 2795928 Aug 9 22:47 libmkl_vml_def.so > -r-xr-xr-x 1 root root 5476786 Aug 9 22:48 libmkl_vml_mc2.so > -r-xr-xr-x 1 root root 5778052 Aug 9 22:48 libmkl_vml_mc3.so > -r-xr-xr-x 1 root root 5382511 Aug 9 22:48 libmkl_vml_mc.so > -r-xr-xr-x 1 root root 4235841 Aug 9 22:48 libmkl_vml_p4n.so > drwxr-xr-x 3 root root 4096 Aug 18 11:43 locale > Y > > > you can reach the person managing the list at > numpy-discussion-ow...@scipy.org > > > Message: 1 > Date: Tue, 13 Sep 2011 09:58:27 -0400 > From: Olivier Delalleau > Subject: Re: [Numpy-discussion] Numpy - MKL - build error > To: Discussion of Numerical Python > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > > Sorry if it sounds li
Re: [Numpy-discussion] Numpy - MKL - build error
Yes, they all are present in that directory. Also, I tried with root as login. -r-xr-xr-x 1 root root 26342559 Aug 9 22:19 libmkl_avx.so -r--r--r-- 1 root root 1190224 Aug 9 22:26 libmkl_blacs_ilp64.a -r--r--r-- 1 root root 1191496 Aug 9 22:25 libmkl_blacs_intelmpi_ilp64.a -r-xr-xr-x 1 root root 497597 Aug 9 22:25 libmkl_blacs_intelmpi_ilp64.so -r--r--r-- 1 root root 676206 Aug 9 22:21 libmkl_blacs_intelmpi_lp64.a -r-xr-xr-x 1 root root 267010 Aug 9 22:21 libmkl_blacs_intelmpi_lp64.so -r--r--r-- 1 root root 674926 Aug 9 22:22 libmkl_blacs_lp64.a -r--r--r-- 1 root root 1218290 Aug 9 22:28 libmkl_blacs_openmpi_ilp64.a -r--r--r-- 1 root root 703042 Aug 9 22:23 libmkl_blacs_openmpi_lp64.a -r--r--r-- 1 root root 1191152 Aug 9 22:29 libmkl_blacs_sgimpt_ilp64.a -r--r--r-- 1 root root 675854 Aug 9 22:23 libmkl_blacs_sgimpt_lp64.a -r--r--r-- 1 root root 425802 Aug 9 20:44 libmkl_blas95_ilp64.a -r--r--r-- 1 root root 421410 Aug 9 20:44 libmkl_blas95_lp64.a -r--r--r-- 1 root root 144354 Aug 9 22:29 libmkl_cdft_core.a -r-xr-xr-x 1 root root 115588 Aug 9 22:29 libmkl_cdft_core.so -r--r--r-- 1 root root 231886824 Aug 9 22:07 libmkl_core.a -r-xr-xr-x 1 root root 16730033 Aug 9 22:18 libmkl_core.so -r-xr-xr-x 1 root root 21474555 Aug 9 22:18 libmkl_def.so -r--r--r-- 1 root root 14974574 Aug 9 22:06 libmkl_gf_ilp64.a -r-xr-xr-x 1 root root 7008828 Aug 9 22:48 libmkl_gf_ilp64.so -r--r--r-- 1 root root 15140998 Aug 9 22:06 libmkl_gf_lp64.a -r-xr-xr-x 1 root root 7055304 Aug 9 22:48 libmkl_gf_lp64.so -r--r--r-- 1 root root 16435120 Aug 9 22:07 libmkl_gnu_thread.a -r-xr-xr-x 1 root root 9816940 Aug 9 22:49 libmkl_gnu_thread.so -r--r--r-- 1 root root 14968130 Aug 9 22:06 libmkl_intel_ilp64.a -r-xr-xr-x 1 root root 7008368 Aug 9 22:48 libmkl_intel_ilp64.so -r--r--r-- 1 root root 15134406 Aug 9 22:06 libmkl_intel_lp64.a -r-xr-xr-x 1 root root 7053588 Aug 9 22:48 libmkl_intel_lp64.so -r--r--r-- 1 root root 2472940 Aug 9 22:07 libmkl_intel_sp2dp.a -r-xr-xr-x 1 root root 1191479 Aug 9 22:20 libmkl_intel_sp2dp.so -r--r--r-- 1 root root 27642508 Aug 9 22:07 libmkl_intel_thread.a -r-xr-xr-x 1 root root 17516608 Aug 9 22:49 libmkl_intel_thread.so -r--r--r-- 1 root root 5350948 Aug 9 20:44 libmkl_lapack95_ilp64.a -r--r--r-- 1 root root 5413476 Aug 9 20:44 libmkl_lapack95_lp64.a -r-xr-xr-x 1 root root 29543829 Aug 9 22:19 libmkl_mc3.so -r-xr-xr-x 1 root root 25428037 Aug 9 22:19 libmkl_mc.so -r-xr-xr-x 1 root root 22888659 Aug 9 22:18 libmkl_p4n.so -r--r--r-- 1 root root 19232716 Aug 9 22:07 libmkl_pgi_thread.a -r-xr-xr-x 1 root root 12243062 Aug 9 22:49 libmkl_pgi_thread.so -r-xr-xr-x 1 root root 4984870 Aug 9 22:49 libmkl_rt.so -r--r--r-- 1 root root 10367758 Aug 9 22:49 libmkl_scalapack_ilp64.a -r-xr-xr-x 1 root root 6574928 Aug 9 22:50 libmkl_scalapack_ilp64.so -r--r--r-- 1 root root 10292432 Aug 9 22:49 libmkl_scalapack_lp64.a -r-xr-xr-x 1 root root 6452627 Aug 9 22:50 libmkl_scalapack_lp64.so -r--r--r-- 1 root root 9958444 Aug 9 22:07 libmkl_sequential.a -r-xr-xr-x 1 root root 5926347 Aug 9 22:48 libmkl_sequential.so -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_ilp64.a -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_ilp64_sequential.a -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_lp64.a -r--r--r-- 1 root root 1048 Aug 9 16:50 libmkl_solver_lp64_sequential.a -r-xr-xr-x 1 root root 6711968 Aug 9 22:48 libmkl_vml_avx.so -r-xr-xr-x 1 root root 2795928 Aug 9 22:47 libmkl_vml_def.so -r-xr-xr-x 1 root root 5476786 Aug 9 22:48 libmkl_vml_mc2.so -r-xr-xr-x 1 root root 5778052 Aug 9 22:48 libmkl_vml_mc3.so -r-xr-xr-x 1 root root 5382511 Aug 9 22:48 libmkl_vml_mc.so -r-xr-xr-x 1 root root 4235841 Aug 9 22:48 libmkl_vml_p4n.so drwxr-xr-x 3 root root 4096 Aug 18 11:43 locale Y you can reach the person managing the list at numpy-discussion-ow...@scipy.org Message: 1 Date: Tue, 13 Sep 2011 09:58:27 -0400 From: Olivier Delalleau Subject: Re: [Numpy-discussion] Numpy - MKL - build error To: Discussion of Numerical Python Message-ID: Content-Type: text/plain; charset="iso-8859-1" Sorry if it sounds like a stupid question, but are the files listed in the error message present in that directory? If yes, maybe try running the command with sudo, just in case it would be some weird permission issue. -=- Olivier 2011/9/13 Igor Ying > Hi, > > I am very new to Numpy and trying to build Numpy 1.6.1 with Intel MKL > 10.3.6 and getting the following errors. > > $python setup.py config --compiler=intel build_clib --compiler=intel > build_ext --compiler=intel install > > Running from numpy source directory.F2PY Version 2 > blas_opt_info: > blas_mkl_info: > libraries mkl_def,mkl_intel_lp64,mkl_intel_thread,mkl_core,iomp5md not > found in /opt/intel/composer_xe_2011_sp1/mkl/lib/intel64 >
Re: [Numpy-discussion] Numpy - MKL - build error
Sorry if it sounds like a stupid question, but are the files listed in the
error message present in that directory?
If yes, maybe try running the command with sudo, just in case it would be
some weird permission issue.
-=- Olivier
2011/9/13 Igor Ying
> Hi,
>
> I am very new to Numpy and trying to build Numpy 1.6.1 with Intel MKL
> 10.3.6 and getting the following errors.
>
> $python setup.py config --compiler=intel build_clib --compiler=intel
> build_ext --compiler=intel install
>
> Running from numpy source directory.F2PY Version 2
> blas_opt_info:
> blas_mkl_info:
> libraries mkl_def,mkl_intel_lp64,mkl_intel_thread,mkl_core,iomp5md not
> found in /opt/intel/composer_xe_2011_sp1/mkl/lib/intel64
> NOT AVAILABLE
>
> I have modified the site.cfg as below.
>
> [mkl]
> library_dirs = /opt/intel/composer_xe_2011_sp1/mkl/lib/intel64
> include_dirs = /opt/intel/composer_xe_2011_sp1/mkl/include
> mkl_libs = mkl_def,mkl_intel_lp64,mkl_intel_thread,mkl_core,iomp5md
> lapack_libs = mkl_lapack_lp64
>
>
> Environment variables are also set to point to mkl libraries.
>
> source /opt/intel/composer_xe_2011_sp1/bin/compilervars.sh intel64 lp64
>
> export OMP_NUM_THREADS=4
> LD_LIBRARY_PATH="/opt/intel/composer_xe_2011_sp1/mkl/lib/intel64:${LD_LIBRARY_PATH}";
>
> export LD_LIBRARY_PATH
> export
> LD_RUN_PATH=/opt/lib:/opt1/composer_xe_2011_sp1/lib/intel64:/opt/composer_xe_2011_sp1/mkl/lib/intel64
>
> Can anyone help me?
>
>
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Re: [Numpy-discussion] Numpy & MKL
On 7-Jan-10, at 8:13 PM, Xue (Sue) Yang wrote:
> This is what I had (when I built numpy, I chose gnu compilers
> instead of
> intel compilers),
>
numpy.show_config()
> lapack_opt_info:
>libraries = ['mkl_lapack', 'mkl', 'vml', 'guide', 'pthread']
>library_dirs = ['/usr/physics/intel/mkl/lib/32']
>define_macros = [('SCIPY_MKL_H', None)]
>include_dirs = ['/usr/physics/intel/mkl/include']
>
> blas_opt_info:
>libraries = ['mkl', 'vml', 'guide', 'pthread']
>library_dirs = ['/usr/physics/intel/mkl/lib/32']
>define_macros = [('SCIPY_MKL_H', None)]
>include_dirs = ['/usr/physics/intel/mkl/include']
>
> lapack_mkl_info:
>libraries = ['mkl_lapack', 'mkl', 'vml', 'guide', 'pthread']
>library_dirs = ['/usr/physics/intel/mkl/lib/32']
>define_macros = [('SCIPY_MKL_H', None)]
>include_dirs = ['/usr/physics/intel/mkl/include']
>
> blas_mkl_info:
>libraries = ['mkl', 'vml', 'guide', 'pthread']
>library_dirs = ['/usr/physics/intel/mkl/lib/32']
>define_macros = [('SCIPY_MKL_H', None)]
>include_dirs = ['/usr/physics/intel/mkl/include']
>
> mkl_info:
>libraries = ['mkl', 'vml', 'guide', 'pthread']
>library_dirs = ['/usr/physics/intel/mkl/lib/32']
>define_macros = [('SCIPY_MKL_H', None)]
>include_dirs = ['/usr/physics/intel/mkl/include']
That looks right to me... And you're sure you've set the environment
variable before Python is run and NumPy is loaded?
Try running:
import os; print os.environ['OMP_NUM_THREADS']
and verify it's the right number.
David
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Re: [Numpy-discussion] Numpy & MKL
On 7-Jan-10, at 6:58 PM, Xue (Sue) Yang wrote: > Do I need any specifications when I run numpy with intel MKL (MKL9.1)? > numpy developers would be able to answer this question? Are you sure you've compiled against MKL properly? What is printed by numpy.show_config()? David ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
