ASKSAGE: Sage Q&A Forum - Individual question feedhttp://ask.sagemath.org/questions/Q&A Forum for SageenCopyright Sage, 2010. Some rights reserved under creative commons license.Thu, 10 Feb 2011 22:48:23 -0600precompiled Atlas - cannot import name flapackhttp://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/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/building-atlas)
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/emil/doc/SageWin)
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!
Sun, 06 Feb 2011 11:26:13 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/Comment by Emil Widmann for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22142#post-id-22142Ok, currently building again. Just a note that the original failure of the Atlas build is*maybe* solved by track ticket #10226.Thu, 10 Feb 2011 06:49:08 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22142#post-id-22142Comment by Emil Widmann for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22149#post-id-22149Well, 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]Wed, 09 Feb 2011 23:09:18 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22149#post-id-22149Comment by niles for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22148#post-id-22148wow -- this is great! Unfortunately I don't have any useful suggestions, but keep working :)Thu, 10 Feb 2011 00:10:24 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22148#post-id-22148Comment by Emil Widmann for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22179#post-id-22179This 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_sgesvTue, 08 Feb 2011 02:18:32 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22179#post-id-22179Comment by Emil Widmann for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22156#post-id-22156OK, 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".Wed, 09 Feb 2011 10:13:28 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22156#post-id-22156Comment by niles for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22153#post-id-22153Thanks 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.Wed, 09 Feb 2011 10:50:52 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22153#post-id-22153Answer by Emil Widmann for <p>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):
(<a href="http://ask.sagemath.org/question/107/building-atlas">http://ask.sagemath.org/question/107/...</a>)</p>
<p>it compiled, but some doctest failed, mainly concerning linear algebra, there are errors like:</p>
<ul>
<li>ImportError:
/mnt/extend/sage-4.6.1/local/lib/python/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv </li>
<li>ImportError: cannot import name <br/>
flapack</li>
</ul>
<p>I have the full testlog at
(<a href="http://sage.math.washington.edu/home/emil/doc/SageWin">http://sage.math.washington.edu/home/...</a>)</p>
<p>Now, it almost works, would be cool if somebody could give some hints how to plug in those atlas/blas/lapack libraries correctly.</p>
<p>Any pointers appreciated!</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?answer=12010#post-id-12010I 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](http://trac.sagemath.org/sage_trac/ticket/10226).
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](http://)), but I stick with the new Atlas package :-)
Thu, 10 Feb 2011 19:58:09 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?answer=12010#post-id-12010Comment by niles for <p>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.</p>
<p>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. <a href="http://trac.sagemath.org/sage_trac/ticket/10226">Track-ticket with new atlas spkg download</a>.
I just needed to replace the old atlas spkg with the new one, Atlas built successfully.</p>
<p>With the old Atlas Package it stopped with:
<em>CageEdge detection failed, unable to build Atlas</em></p>
<p>I am sure with the right combination of precompiled libraries and headers also my first approch would work: (<a href="http://">http://ask.sagemath.org/question/107/building-atlas</a>), but I stick with the new Atlas package :-)</p>
http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22139#post-id-22139this is great!Thu, 10 Feb 2011 22:48:23 -0600http://ask.sagemath.org/question/7926/precompiled-atlas-cannot-import-name-flapack/?comment=22139#post-id-22139