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. Any advice would be appreciated! Dr. Glen Jenness Schmidt Group Department of Chemistry University of Wisconsin - Madison
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
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 <francesc@continuum.io>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
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
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 <francesc@continuum.io>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
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