[yt-users] SciPy installation problem
Caroline Van Borm
borm at astro.rug.nl
Thu Jan 22 03:00:34 PST 2015
Hi Nathan,
I reran the install script from scratch every time, just to be safe. I
think I actually may have it working now, after setting
NUMPY_ARGS="--fcompiler=g77". I've tried to load and use several SciPy
functions and no errors so far. Hoping it stays that way!
Thanks again!
Cheers,
Caroline
On 01/20/2015 02:38 AM, Nathan Goldbaum wrote:
> 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
> <mailto: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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>>
>>
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