gilgamesh: importing scipy(python error)

[John Kitchin]

you need to use the python/python-2.6.5 module with the scipy module.

this is the set of modules I load to get my python environment:

module load blas-lapack-atlas-gcc
module load python/python-2.6.5
module load python/mypython
module load python/ipython-0.10
module load python/numpy-1.5.0b1-gcc
module load python/scipy-0.80-gcc
module load python/matplotlib-1.0.0
module load python/ScientificPython2.8
module load python/ase-svn-r1777
module load python/torque-r214
module load python/htp-r214
module load python/pygtk
module load vtk-5.6.0
module load wxpython

you can leave out several of these if you don't use them, liek the
ase, torque, htp modules.


or

module load python/python-environment-v1


John

-----------------------------------
John Kitchin
Assistant Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu




On Wed, Oct 13, 2010 at 9:04 AM, Craig Maloney <craigmaloney at cmu.edu> wrote:

> Hi Kamran.
>
> You need to make sure that the versions of scipy, numpy, and the python
> interpreter itself were all built in a consistent way.  The correct version
> of the Py_InitModule4_64 routine should be provided (I think) by the
> standard support libraries for the python interpreter and not the
> site-package (scipy/numpy).  But you must use the same version of the python
> interpreter for which the package (scipy) was built!
>
> This scipy (the one for python/scipy-0.80-gcc) was built for python2.6.
>  Maybe whoever in the Kitchin group (Spencer?/John?) set up
> the python/scipy-0.80-gcc module can help us find the appropriate python
> interpreter.
>
> --Craig
>
> On Oct 12, 2010, at 10:12 PM, Kamran Karimi wrote:
>
> Dear Gilgamesh users,
>
> I'm trying to use the sparse libraries in scipy installed on Gilgamesh.
>
> After typing "module load python/scipy-0.80-gcc \n python \n import
> scipy.sparse", I get the following error message:
>
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File
> "/opt/python/scipy/scipy-0.8.0-gcc/lib/python2.6/site-packages/scipy/sparse/__init__.py",
> line 6, in ?
>    from csr import *
>  File
> "/opt/python/scipy/scipy-0.8.0-gcc/lib/python2.6/site-packages/scipy/sparse/csr.py",
> line 12, in ?
>    from sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
>  File
> "/opt/python/scipy/scipy-0.8.0-gcc/lib/python2.6/site-packages/scipy/sparse/sparsetools/__init__.py",
> line 4, in ?
>    from csr import *
>  File
> "/opt/python/scipy/scipy-0.8.0-gcc/lib/python2.6/site-packages/scipy/sparse/sparsetools/csr.py",
> line 7, in ?
>    import _csr
> ImportError:
> /opt/python/scipy/scipy-0.8.0-gcc/lib/python2.6/site-packages/scipy/sparse/sparsetools/_csr.so:
> undefined symbol: Py_InitModule4_64
>
> Please help me.
>
> Regards,
> Kamran Karimi
> Graduate Student
> Mechanics, Materials and Computing
> Civil and Environmental Engineering
> Carnegie Mellon University
> Pittsburgh PA 15213
>
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> gilgamesh-users at lists.andrew.cmu.edu
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>
>
> -----------------------------------------------
> Contact info:
> http://www.ce.cmu.edu/People/faculty/maloney.html
>
>
>
>
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