Opened 8 years ago

Closed 8 years ago

#14617 closed enhancement (fixed)

Update scipy to 0.12

Reported by: jpflori Owned by: jdemeyer
Priority: major Milestone: sage-5.10
Component: packages: standard Keywords: scipy spkg
Cc: Merged in: sage-5.10.beta5
Authors: Jean-Pierre Flori Reviewers: Volker Braun
Report Upstream: N/A Work issues:
Branch: Commit:
Dependencies: Stopgaps:

Status badges

Change History (15)

comment:1 Changed 8 years ago by jpflori

  • Description modified (diff)

This won't fix the problem with updated ATLAS as ARPACK-NG is not in 0.12 unfortunately, but in the git repo only:

comment:2 Changed 8 years ago by jpflori

My, bad, it is. I read the wrong README in the tarball and got a wrong feeling.

comment:3 Changed 8 years ago by vbraun

  • Description modified (diff)

Added a trial spkg

comment:4 Changed 8 years ago by jpflori

There is one here as well:

Testing it right now :)

Last edited 8 years ago by jpflori (previous) (diff)

comment:5 Changed 8 years ago by vbraun

The way I read it, scipy's arpack has been renamed to arpack-ng. Nothing has been replaced, but there are a bunch of bugfixes to arpack in the new release.

comment:6 Changed 8 years ago by jpflori

Hum, anyway arpack-ng is just a fork of arpack, so would basically fit with "rename and fix bugs" because upstream was not active anymore. See:

comment:7 Changed 8 years ago by jpflori

And my scipy spkg failed on top of 5.10.beta3 plus #10508.

comment:8 Changed 8 years ago by jpflori

  • Description modified (diff)

I've reposted an spkg which now compiles (the only patch we used was now upstream). I've not tested Volker's one, whence the change in the ticket description, but if anyone (including Volker :)) feels it is better, feel free to change it back.

comment:9 Changed 8 years ago by vbraun

I had removed the upsteamed patch, too. Doctests pass for me.

comment:10 Changed 8 years ago by jpflori

Great, so I'll have a look at your spkg and give it positive review when my tests finish.

comment:11 Changed 8 years ago by vbraun

  • Authors set to Jean-Pierre Flori
  • Reviewers set to Volker Braun
  • Status changed from new to needs_review

comment:12 Changed 8 years ago by vbraun

  • Status changed from needs_review to positive_review

comment:13 Changed 8 years ago by jdemeyer

On hawk, importing scipy fails with

sage -t --long devel/sage/sage/plot/plot3d/
File "devel/sage/sage/plot/plot3d/", line 87, in sage.plot.plot3d.list_plot3d.list_plot3d
Failed example:
    list_plot3d(m, texture='yellow', interpolation_type='nn',frame_aspect_ratio=[1,1,1/3])
Exception raised:
    Traceback (most recent call last):
      File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/doctest/", line 466, in _run
        self.execute(example, compiled, test.globs)
      File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/doctest/", line 825, in execute
        exec compiled in globs
      File "<doctest sage.plot.plot3d.list_plot3d.list_plot3d[5]>", line 1, in <module>
        list_plot3d(m, texture='yellow', interpolation_type='nn',frame_aspect_ratio=[Integer(1),Integer(1),Integer(1)/Integer(3)])
      File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/plot/plot3d/", line 174, in list_plot3d
        return list_plot3d_tuples(l,interpolation_type,texture,**kwds)
      File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/sage/plot/plot3d/", line 356, in list_plot3d_tuples
        from scipy import interpolate
      File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/scipy/interpolate/", line 160, in <module>
        from .ndgriddata import *
      File "/export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/scipy/interpolate/", line 10, in <module>
        from .interpnd import LinearNDInterpolator, NDInterpolatorBase, \
    ImportError: python2.7: fatal: relocation error: file /export/home/buildbot/build/sage/hawk-1/hawk_full/build/sage-5.10.beta5/local/lib/python2.7/site-packages/scipy/interpolate/ symbol __sync_fetch_and_add_4: referenced symbol not found

This seems to come from GCC, so I'll try again with Sage's GCC (the error above was with GCC-4.4.3)

comment:14 Changed 8 years ago by jpflori

Indeed. Some pointers:

and a bunch of similar ones on other systems alos closed as invalid, or

For GCC 4.4.x you should explicitely pass -march=something-that-works to get that function, whereas for more recent GCCs it seems to be implied automatically from the value of target.

comment:15 Changed 8 years ago by jdemeyer

  • Merged in set to sage-5.10.beta5
  • Resolution set to fixed
  • Status changed from positive_review to closed
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