Opened 10 years ago

Closed 10 years ago

#14617 closed enhancement (fixed)

Update scipy to 0.12

Reported by: Jean-Pierre Flori Owned by: Jeroen Demeyer
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 10 years ago by Jean-Pierre Flori

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: https://github.com/scipy/scipy/pull/386

comment:2 Changed 10 years ago by Jean-Pierre Flori

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

comment:3 Changed 10 years ago by Volker Braun

Description: modified (diff)

Added a trial spkg

comment:4 Changed 10 years ago by Jean-Pierre Flori

There is one here as well:

Testing it right now :)

Last edited 10 years ago by Jean-Pierre Flori (previous) (diff)

comment:5 Changed 10 years ago by Volker Braun

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 10 years ago by Jean-Pierre Flori

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 10 years ago by Jean-Pierre Flori

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

comment:8 Changed 10 years ago by Jean-Pierre Flori

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 10 years ago by Volker Braun

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

comment:10 Changed 10 years ago by Jean-Pierre Flori

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

comment:11 Changed 10 years ago by Volker Braun

Authors: Jean-Pierre Flori
Reviewers: Volker Braun
Status: newneeds_review

comment:12 Changed 10 years ago by Volker Braun

Status: needs_reviewpositive_review

comment:13 Changed 10 years ago by Jeroen Demeyer

On hawk, importing scipy fails with

sage -t --long devel/sage/sage/plot/plot3d/list_plot3d.py
**********************************************************************
File "devel/sage/sage/plot/plot3d/list_plot3d.py", 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/forker.py", 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/forker.py", 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/list_plot3d.py", 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/list_plot3d.py", 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/__init__.py", 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/ndgriddata.py", line 10, in <module>
        from .interpnd import LinearNDInterpolator, NDInterpolatorBase, \
    ImportError: ld.so.1: 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/interpnd.so: 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 10 years ago by Jean-Pierre Flori

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 10 years ago by Jeroen Demeyer

Merged in: sage-5.10.beta5
Resolution: fixed
Status: positive_reviewclosed
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