[Numpy-discussion] numpy + MKL problems

[Glen Jenness]

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

[Francesc Alted]

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

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[Glen Jenness]

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

--

[Francesc Alted]

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?

[Glen Jenness]

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.