[SciPy-User] Problem with SciPy 0.17.1 integrate package

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[SciPy-User] Problem with SciPy 0.17.1 integrate package

Fausto Arinos de A. Barbuto

Hello,

I have just upgraded from SciPy 0.13.3 to 0.17.1 and Python scripts that used
to work don't work any more. The problem appears when I try to use the odeint
function. When I try this:

>>> from scipy.integrate import odeint

I get those following error messages:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/scipy/integrate/__init__.py", line 56, in <module>
    from .odepack import *
  File "/usr/local/lib/python2.7/dist-packages/scipy/integrate/odepack.py", line 6, in <module>
    from . import _odepack
ImportError: /usr/local/lib/python2.7/dist-packages/scipy/integrate/_odepack.so: undefined symbol: lsoda_


The command above always worked fine with SciPy 0.13.3. Is this error somehow
related to Numpy or Lapack (sorry if this question makes no sense, but I'm
really lost)? Is there any test I could do?

Despite this error the whole SciPy module/package seems to import OK:

>>> import scipy
>>> print scipy.__version__
0.17.1
>>>


I'm running Ubuntu 14.04 64-bits with Python 2.7.6, gcc 4.8.4 and Numpy 1.11.0.

Thanks in advance for any help you provide.

Fausto


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Re: Problem with SciPy 0.17.1 integrate package

Fausto Arinos de A. Barbuto
On 26-06-2016 01:15, Fausto Arinos de A. Barbuto wrote:

>
> Hello,
>
> I have just upgraded from SciPy 0.13.3 to 0.17.1 and Python scripts that used
> to work don't work any more. The problem appears when I try to use the odeint
> function. When I try this:
>
> *>>> from scipy.integrate import odeint*
>
> I get those following error messages:
>
> *Traceback (most recent call last):
>    File "<stdin>", line 1, in <module>
>    File "/usr/local/lib/python2.7/dist-packages/scipy/integrate/__init__.py", line 56, in <module>
>      from .odepack import *
>    File "/usr/local/lib/python2.7/dist-packages/scipy/integrate/odepack.py", line 6, in <module>
>      from . import _odepack
> ImportError: /usr/local/lib/python2.7/dist-packages/scipy/integrate/_odepack.so: undefined
> symbol: lsoda_*
>
> The command above always worked fine with SciPy 0.13.3. Is this error somehow
> related to Numpy or Lapack (sorry if this question makes no sense, but I'm
> really lost)? Is there any test I could do?
>
> Despite this error the whole SciPy module/package seems to import OK:
>
> *>>> import scipy
>  >>> print scipy.__version__
> 0.17.1
>  >>>*
>
> I'm running Ubuntu 14.04 64-bits with Python 2.7.6, gcc 4.8.4 and Numpy 1.11.0.
>
> Thanks in advance for any help you provide.
>
> Fausto
>
>
>
> _______________________________________________
> SciPy-User mailing list
> [hidden email]
> https://mail.scipy.org/mailman/listinfo/scipy-user
>

I found out what the problem was. Setup installs Scipy on
/usr/local/lib/python2.7/dist-packages/scipy by default, whereas Ubuntu puts the packages on
/usr/lib/python2.7/dist-packages/scipy,
and that was causing a conflict. I deleted the former and got 0.13.3 (which had never been
overwritten) back. I might have used "sudo python setup.py install --prefix=/usr/lib/..." but
SciPy's installation instructions do not recommend that. I guess I will have to wait for the
point release of 16.04 LTS to finally have 0.17.1.

Fausto



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Re: Problem with SciPy 0.17.1 integrate package

Evgeni Burovski
On Sun, Jun 26, 2016 at 6:43 AM, Fausto Arinos de A. Barbuto
<[hidden email]> wrote:

> On 26-06-2016 01:15, Fausto Arinos de A. Barbuto wrote:
>>
>>
>> Hello,
>>
>> I have just upgraded from SciPy 0.13.3 to 0.17.1 and Python scripts that
>> used
>> to work don't work any more. The problem appears when I try to use the
>> odeint
>> function. When I try this:
>>
>> *>>> from scipy.integrate import odeint*
>>
>> I get those following error messages:
>>
>> *Traceback (most recent call last):
>>    File "<stdin>", line 1, in <module>
>>    File
>> "/usr/local/lib/python2.7/dist-packages/scipy/integrate/__init__.py", line
>> 56, in <module>
>>      from .odepack import *
>>    File
>> "/usr/local/lib/python2.7/dist-packages/scipy/integrate/odepack.py", line 6,
>> in <module>
>>      from . import _odepack
>> ImportError:
>> /usr/local/lib/python2.7/dist-packages/scipy/integrate/_odepack.so:
>> undefined
>> symbol: lsoda_*
>>
>> The command above always worked fine with SciPy 0.13.3. Is this error
>> somehow
>> related to Numpy or Lapack (sorry if this question makes no sense, but I'm
>> really lost)? Is there any test I could do?
>>
>> Despite this error the whole SciPy module/package seems to import OK:
>>
>> *>>> import scipy
>>  >>> print scipy.__version__
>> 0.17.1
>>  >>>*
>>
>> I'm running Ubuntu 14.04 64-bits with Python 2.7.6, gcc 4.8.4 and Numpy
>> 1.11.0.
>>
>> Thanks in advance for any help you provide.
>>
>> Fausto
>>
>>
>>
>> _______________________________________________
>> SciPy-User mailing list
>> [hidden email]
>> https://mail.scipy.org/mailman/listinfo/scipy-user
>>
>
> I found out what the problem was. Setup installs Scipy on
> /usr/local/lib/python2.7/dist-packages/scipy by default, whereas Ubuntu puts
> the packages on /usr/lib/python2.7/dist-packages/scipy,
> and that was causing a conflict. I deleted the former and got 0.13.3 (which
> had never been
> overwritten) back. I might have used "sudo python setup.py install
> --prefix=/usr/lib/..." but
> SciPy's installation instructions do not recommend that. I guess I will have
> to wait for the
> point release of 16.04 LTS to finally have 0.17.1.
>
> Fausto


You might want to start using virtualenvs. This is precisely what they are for.
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