[yt-users] SciPy installation problem

[Nathan Goldbaum]

Hi Caroline,

Have you tried deleting the scipy installation and retrying from scratch?
You should be able to clean up most of the old scipy installations by
repeatedly running "pip uninstall scipy".  If you're patient, you can also
try the nuclear option of rerunning the install script from scratch.

-Nathan

On Mon, Jan 19, 2015 at 8:51 AM, Caroline Van Borm <borm at astro.rug.nl>
wrote:

>  Hi all,
>
> Thank you all for your suggestions! It turns out that iraf is installed on
> my work desktop and it somehow changes the F77 environment variable. After
> changing it back to /usr/bin/f77 I was able to install SciPy. However, when
> I now try to do 'from scipy.integrate import odeint' for example, I get the
> following error message:
>
> In [2]: from scipy.interpolate import odeint
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
> /data/users/borm/YT/yt-x86_64/src/yt-hg/scripts/iyt in <module>()
> ----> 1 from scipy.interpolate import odeint
>
> /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/__init__.py
> in <module>()
>     148 from __future__ import division, print_function, absolute_import
>     149
> --> 150 from .interpolate import *
>     151 from .fitpack import *
>     152
>
> /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/interpolate/interpolate.py
> in <module>()
>      10                   dot, poly1d, asarray, intp
>      11 import numpy as np
> ---> 12 import scipy.special as spec
>      13 import math
>      14
>
> /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/__init__.py
> in <module>()
>     527 from __future__ import division, print_function, absolute_import
>     528
> --> 529 from ._ufuncs import *
>     530 from ._ufuncs_cxx import *
>     531
>
> ImportError:
> /data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/scipy/special/_ufuncs.so:
> undefined symbol: s_stop
>
>
> It seems this is again related to the compiler, but I'm not sure what to
> do about it. I have tried once more to set the NUMPY_ARGS to the different
> options in the install script, and also to install yt without SciPy and
> then install it using 'pip install scipy', but every time I get the same
> error. My OS is Scientific Linux 6, by the way.
>
> Cheers,
> Caroline
>
>
>
>
> On 01/14/2015 05:32 PM, Peter Teuben wrote:
>
> I suspect this is a side-effect of the iraf virus.  I too have often run
> into the f77 trojan that comes to light
> in some (all?) iraf installations, and configure doesn't deal with it very
> well.
>
>
> On 01/13/2015 12:10 PM, Caroline Van Borm wrote:
>
> Dear yt users,
>
> I'm having some trouble installing SciPy. I can install yt just fine using
> the install script, but if I turn the option for installing SciPy on, I get
> the following error:
>
> creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack
> compile options:
> '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include
> -c'
> f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f
> Cannot open file dsint.f
> gcc: dsint.c: No such file or directory
> gcc: no input files
> Cannot open file dsint.f
> gcc: dsint.c: No such file or directory
> gcc: no input files
> error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form
> -fno-second-underscore -fPIC -O3 -funroll-loops
> -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include
> -c -c scipy/fftpack/src/dfftpack/dsint.f -o
> build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with
> exit status 1
>
> I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in
> the script, but none of that seems to work.
> I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps.
>
> Any ideas on how to fix this? Thanks!
>
> Cheers,
> Caroline
>
>
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