Problem installing devel version on Canopy

[Russ Poldrack]

hi all - I'm hitting a snag trying to use the latest version (from git) under Enthought's Canopy python distro.  The build and install works with no apparent errors, but I get this when I try to import:

In [2]: import nipype

---------------------------------------------------------------------------

ImportError                               Traceback (most recent call last)

<ipython-input-2-feb2fc727b0b> in <module>()

----> 1 import nipype

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipype/__init__.py in <module>()

     16 from .fixes.numpy.testing import nosetester

     17 

---> 18 from pipeline import Node, MapNode, Workflow

     19 from interfaces import (fsl, spm, freesurfer, afni, ants, slicer, dipy, nipy,

     20                         mrtrix, camino, DataGrabber, DataSink,

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipype/pipeline/__init__.py in <module>()

      6 """

      7 __docformat__ = 'restructuredtext'

----> 8 from engine import Node, MapNode, Workflow

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipype/pipeline/engine.py in <module>()

     37 from .. import config, logging

     38 logger = logging.getLogger('workflow')

---> 39 from ..interfaces.base import (traits, InputMultiPath, CommandLine,

     40                                Undefined, TraitedSpec, DynamicTraitedSpec,

     41                                Bunch, InterfaceResult, md5, Interface,

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipype/interfaces/__init__.py in <module>()

     10 from io import DataGrabber, DataSink

     11 from utility import IdentityInterface, Rename, Function, Select, Merge

---> 12 import fsl, spm, freesurfer, afni, ants, slicer, dipy, nipy, mrtrix, camino

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipype/interfaces/nipy/__init__.py in <module>()

----> 1 from .model import FitGLM, EstimateContrast

      2 from .preprocess import ComputeMask, FmriRealign4d

      3 from .utils import Similarity

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipype/interfaces/nipy/model.py in <module>()

     21 else:

     22     import nipy.modalities.fmri.design_matrix as dm

---> 23     import nipy.labs.glm as GLM

     24 

     25 if have_nipy:

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipy/labs/glm/__init__.py in <module>()

      1 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-

      2 # vi: set ft=python sts=4 ts=4 sw=4 et:

----> 3 from .glm import models, contrast, ols, load

      4 

      5 from nipy.testing import Tester

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipy/labs/glm/glm.py in <module>()

      5 

      6 from . import kalman

----> 7 from ..utils import mahalanobis

      8 from nipy.algorithms.statistics.utils import z_score as zscore

      9 

/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipy/labs/utils/__init__.py in <module>()

      1 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-

      2 # vi: set ft=python sts=4 ts=4 sw=4 et:

----> 3 from .routines import (quantile, median, mahalanobis, svd, permutations,

      4                        combinations, gamln, psi)

      5 from .zscore import zscore

ImportError: dlopen(/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipy/labs/utils/routines.so, 2): Symbol not found: _ATL_cGetNB

  Referenced from: /Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipy/labs/utils/routines.so

  Expected in: flat namespace

 in /Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/nipy/labs/utils/routines.so

I have the same problem under both nipy 0.3.0 and 0.4.0dev.  I have no problem running nipype 0.8.0.  Any suggestions?

cheers

russ

[Gael Varoquaux]

On Sun, Jul 21, 2013 at 01:33:14PM -0700, Russ Poldrack wrote:
> ImportError: dlopen(/Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/

> python2.7/site-packages/nipy/labs/utils/routines.so, 2): Symbol not found:
> _ATL_cGetNB
> Referenced from: /Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/
> python2.7/site-packages/nipy/labs/utils/routines.so
> Expected in: flat namespace
> in /Users/poldrack/Library/Enthought/Canopy_64bit/User/lib/python2.7/
> site-packages/nipy/labs/utils/routines.so

cGetNB: looks like an atlas problem. I can guess that the problem comes
from the fact that Canopy is using MKL, while nipy was compiled with an
Atlas. However, I don't know at all how to solve it.

One thing that you can try is to create a 'site.cfg' file in the nipy
source directory and add the following lines:

"""
[DEFAULT]
library_dirs = /usr/lib/atlas-base/atlas:/usr/lib:/usr/local/lib
include_dirs = /usr/include/atlas:/usr/include:/usr/local/include
"""

Where you make sure make that in the paths above there is the path of the
local atlas install.

Hope this helps,

Ga�l

[Ariel Rokem]

Hi Russ, 

I am not sure what this is, but just thought I would check this: did you build/install nipy with the system python or with Canopy's python? 

Cheers, 

Ariel 

Gaël

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[Ariel Rokem]

Hi again, 

On Sun, Jul 21, 2013 at 2:37 PM, Ariel Rokem <aro...@gmail.com> wrote:

Hi Russ, 

I am not sure what this is, but just thought I would check this: did you build/install nipy with the system python or with Canopy's python? 

On (rather short) further thought: what I just said doesn't make much sense. Please disregard and apologies for the noise. 

Ariel