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precompiled Atlas - cannot import name flapack

asked 2011-02-06 11:26:13 -0600

Emil Widmann gravatar image

updated 2015-01-13 13:55:48 -0600

FrédéricC gravatar image

I tried to get sage to run on a windows Laptop using "andLinux" - this is Ubuntu on a Colinux kernel. Atlas refused to build, so I installed atlas using synaptic and followed advice from here (steps from John Palmieri): (http://ask.sagemath.org/question/107/...)

it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:

  • ImportError: /mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv
  • ImportError: cannot import name
    flapack

I have the full testlog at (http://sage.math.washington.edu/home/...)

Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.

Any pointers appreciated!

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This is an update, also reminder to myself. I researched a little and it seems that the root of the problem is burried in the clapack_sgesv not found (probably clapack not found at all). The second error message probably stems form a fallback mechanism, if clapack is not found it is tried to call flapack. google shows a lot for this specific error message and mostly this are incombatible atlas/lapack/blas packages. I have to examine my install and two useful commands probably are ldd /PATH_TO/clapack.so and nm /PATH_TO/liblapack.so | grep clapack_sgesv

Emil Widmann gravatar imageEmil Widmann ( 2011-02-08 02:18:32 -0600 )edit

OK, a short progress report: clapack.so was there, but I noticed that clapack.h was just an empty file, so probably that was the reason - I make distclean and try again, double check that all header files are "nonempty".

Emil Widmann gravatar imageEmil Widmann ( 2011-02-09 10:13:28 -0600 )edit

Thanks for the updates -- I wonder if some of what you learn is relevant to the Cygwin port of sage. Here's the list of open tickets: http://trac.sagemath.org/sage_trac/wiki/CygwinPort. Scanning the list, nothing is seeming obviously related . . . maybe you can tell better.

niles gravatar imageniles ( 2011-02-09 10:50:52 -0600 )edit

Well, after the last discussions on sage devel I had a look at the related threads, but I thought I have no experience with some of the main problems there (rebasing). Instead I stumbled on a project named andLinux, wich offers an exe installer of a colinux based Ubuntu, i.e you run Ubuntu under the windows desktop environment. So far this is just an experiment, but I got an "almost" working prototype build of sage,and the only major missing piece is a working clapack library. See a first screenshot [http://sage.math.washington.edu/home/emil/doc/SageWin/screensh17.JPG]

Emil Widmann gravatar imageEmil Widmann ( 2011-02-09 23:09:18 -0600 )edit

wow -- this is great! Unfortunately I don't have any useful suggestions, but keep working :)

niles gravatar imageniles ( 2011-02-10 00:10:24 -0600 )edit

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answered 2011-02-10 19:58:09 -0600

Emil Widmann gravatar image

I got a solution to the problem I had, but if fails to be a solution to "use a precompiled Atlas". After some unsuccessful tries to copy in the required libraries and headers (it compiled ok, but there was an incompatibility somewhere and I always got these failing clapack dependency - very annoying) I found a possible solution to my original problem: the inability to compile atlas.

It seems that the build procedure for Atlas was rewritten recently by Volker Braun to address exactly such problems. It already has a positive review and will be in the next sage releases. Track-ticket with new atlas spkg download. I just needed to replace the old atlas spkg with the new one, Atlas built successfully.

With the old Atlas Package it stopped with: CageEdge detection failed, unable to build Atlas

I am sure with the right combination of precompiled libraries and headers also my first approch would work: (http://ask.sagemath.org/question/107/building-atlas), but I stick with the new Atlas package :-)

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this is great!

niles gravatar imageniles ( 2011-02-10 22:48:23 -0600 )edit

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Asked: 2011-02-06 11:26:13 -0600

Seen: 1,116 times

Last updated: Feb 10 '11