[Mne_analysis] python-MNE installation

Christopher Bailey bailey.cj at gmail.com
Wed Oct 1 03:14:10 EDT 2014
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Hi Tommi,

Strange. But your CentOS certainly has a system python by default: many aspects of Linux OS management are built on it. 

I'm also on the anaconda wagon these days, but had a go at EPD a while back. There are a bunch of environment variables that need to be set correctly in order for it to work (to prevent it from borking the system python). To debug this, would you please provide the output of 

echo $SHELL # CentOS defaults to bash according to docs, have you spawned tcsh in a bash shell?
cat ~/.cshrc

also cat any other csh-scripts (like ~/.cshrc_epd?) that you run prior to issuing the ipython-command.

/Chris

On Oct 1, 2014, at 3:42 AM, raij at nmr.mgh.harvard.edu wrote:

> 
> Hi Alex,
> 
> I am not sure the diagnosis is entirely correct.
> 
> I first checked that (to my knowledge) I have not installed any other
> pythons than Canopy (unless CentOS 6.5 includes a version by default).
> 
> Then, I checked that both "which python" and "which pip" already point to
> Canopy (I did not do anything to the system yet). Specifically:
> which python
> /usr/pubsw/packages/python/System/bin/python
> which pip
> /usr/pubsw/packages/python/System/bin/pip
> 
> (Note that when installing Canopy I set it to reside in
> /usr/pubsw/packages/python/)
> 
> Next, I re-installed (as root) the python mne package just to make sure it
> is there:
> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
> 
> However, the errors for
> ipython --pylab gt
> and
> ipython -> import mne
> 
> remain exactly the same as before.
> 
> If you still believe I need to uninstall the pip I installed with yum, I
> would greatly appreciate if you could let me know which command I should
> use for uninstallation (I found a ton of different ways, and some of these
> will likely mess up the system in more than one way).
> 
> Thank you!
> 
> Tommi
> 
> 
>> hi Tommi,
>> 
>> the problem is that you have 2 python systems installed:
>> - the system one that uses yum for installs + updates
>> - canopy
>> 
>> when you did "yum install -y python-pip" you installed pip
>> for the system and not for canopy. I suspect canopy already
>> comes with pip installed.
>> 
>> I recommend you uninstall pip with yum and any other python
>> packages you installed with yum and then make sure you use canopy.
>> 
>> to check this use:
>> 
>> which python
>> 
>> it should point to the canopy folder. If it's the case do the same with
>> pip
>> 
>> which pip
>> 
>> if it points to canopy then you can safely do:
>> 
>> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
>> 
>> let us know how it goes.
>> 
>> Alex
>> 
>> 
>> 
>> 
>> On Mon, Sep 29, 2014 at 11:50 PM,  <raij at nmr.mgh.harvard.edu> wrote:
>>> 
>>> Hi,
>>> 
>>> New python (and longtime MNE) user here, hello to all.
>>> 
>>> I am having trouble installing MNE-python on a linux box outside
>>> Martinos
>>> Center. The machine (Dell Precision T7500)) runs CentOS 6.5 and has
>>> Freesurfer (5.3), MNE suite (developmental), and MATLAB installed -
>>> these
>>> are running no prob.
>>> 
>>> I am doing installation as root on a csh terminal.
>>> 
>>> I have tried to follow the instructions at
>>> http://martinos.org/mne/stable/getting_started.html as follows:
>>> 
>>> 1. Install Canopy python. When launcing for the first time, I set up the
>>> environment to point to /usr/pubsw/packages/python/, then make Canopy as
>>> the default python. Version: canopy-1.4.1-full-rh5-64.sh
>>> 
>>> 2. Install pip (this did not exist on my system):
>>> yum install -y python-pip
>>> 
>>> 3. Install developmental MNE-python suite
>>> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
>>> 
>>> Then I open a new csh terminal as a regular user, and
>>> 4. Add the following line to my user-level ~/.cshrc:
>>> setenv PATH /usr/pubsw/packages/python/User/bin:${PATH}
>>> 
>>> Next, I launch a fresh csh terminal, and launch ipython. This appears
>>> (?)
>>> to work OK:
>>> 
>>> tmsh:raij[55] ipython
>>> 
>>> Python 2.7.6 | 64-bit | (default, Jun  4 2014, 16:32:15)
>>> Type "copyright", "credits" or "license" for more information.
>>> 
>>> IPython 2.1.0 -- An enhanced Interactive Python.
>>> ?         -> Introduction and overview of IPython's features.
>>> %quickref -> Quick reference.
>>> help      -> Python's own help system.
>>> object?   -> Details about 'object', use 'object??' for extra details.
>>> 
>>> In [1]:
>>> 
>>> 
>>> 
>>> 
>>> However, trying to follow the instructions:
>>> 
>>> ipython --pylab qt
>>> 
>>> produces a long list of errors suggesting that matplotlib (that I did
>>> not
>>> see mentioned in the MNE-python guide - is it needed and how is it best
>>> installed to avoid breaking dependencies?) may not be installed.
>>> 
>>> Moreover, regardless of if I launch ipython alone or with --pylab qt,
>>> trying to "import mne" gives the error "No module named mne". See the
>>> end
>>> of message for the full error list.
>>> 
>>> Any suggestions would be much appreciated!
>>> 
>>> Best regards,
>>> 
>>> Tommi
>>> 
>>> 
>>> ---
>>> Tommi Raij, MD, PhD
>>> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
>>> Bldg 149, 13th St
>>> Charlestown, MA 02129
>>> U.S.A.
>>> 
>>> 
>>> ERROR OUTPUT FOR
>>> 
>>> ipython --pylab qt (from a csh terminal)
>>> 
>>> Python 2.7.6 | 64-bit | (default, Jun  4 2014, 16:32:15)
>>> Type "copyright", "credits" or "license" for more information.
>>> 
>>> IPython 2.1.0 -- An enhanced Interactive Python.
>>> ?         -> Introduction and overview of IPython's features.
>>> %quickref -> Quick reference.
>>> help      -> Python's own help system.
>>> object?   -> Details about 'object', use 'object??' for extra details.
>>> [TerminalIPythonApp] WARNING | Eventloop or matplotlib integration
>>> failed.
>>> Is matplotlib installed?
>>> ---------------------------------------------------------------------------
>>> ImportError                               Traceback (most recent call
>>> last)
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/shellapp.pyc
>>> in <lambda>(key)
>>>    231         shell = self.shell
>>>    232         if self.pylab:
>>> --> 233             enable = lambda key: shell.enable_pylab(key,
>>> import_all=self.pylab_import_all)
>>>    234             key = self.pylab
>>>    235         elif self.matplotlib:
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc
>>> in enable_pylab(self, gui, import_all, welcome_message)
>>>   2980         from IPython.core.pylabtools import import_pylab
>>>   2981
>>> -> 2982         gui, backend = self.enable_matplotlib(gui)
>>>   2983
>>>   2984         # We want to prevent the loading of pylab to pollute the
>>> user's
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc
>>> in enable_matplotlib(self, gui)
>>>   2941                 gui, backend =
>>> pt.find_gui_and_backend(self.pylab_gui_select)
>>>   2942
>>> -> 2943         pt.activate_matplotlib(backend)
>>>   2944         pt.configure_inline_support(self, backend)
>>>   2945
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/pylabtools.pyc
>>> in activate_matplotlib(backend)
>>>    285     matplotlib.rcParams['backend'] = backend
>>>    286
>>> --> 287     import matplotlib.pyplot
>>>    288     matplotlib.pyplot.switch_backend(backend)
>>>    289
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/pyplot.py
>>> in <module>()
>>>     22
>>>     23 import matplotlib
>>> ---> 24 import matplotlib.colorbar
>>>     25 from matplotlib import _pylab_helpers, interactive
>>>     26 from matplotlib.cbook import dedent, silent_list,
>>> is_string_like,
>>> is_numlike
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/colorbar.py
>>> in <module>()
>>>     27 import matplotlib.artist as martist
>>>     28 import matplotlib.cbook as cbook
>>> ---> 29 import matplotlib.collections as collections
>>>     30 import matplotlib.colors as colors
>>>     31 import matplotlib.contour as contour
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/collections.py
>>> in <module>()
>>>     21 import matplotlib.artist as artist
>>>     22 from matplotlib.artist import allow_rasterization
>>> ---> 23 import matplotlib.backend_bases as backend_bases
>>>     24 import matplotlib.path as mpath
>>>     25 from matplotlib import _path
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/backend_bases.py
>>> in <module>()
>>>     48
>>>     49 import matplotlib.tight_bbox as tight_bbox
>>> ---> 50 import matplotlib.textpath as textpath
>>>     51 from matplotlib.path import Path
>>>     52 from matplotlib.cbook import mplDeprecation
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/textpath.py
>>> in <module>()
>>>      9 from matplotlib.path import Path
>>>     10 from matplotlib import rcParams
>>> ---> 11 import matplotlib.font_manager as font_manager
>>>     12 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT,
>>> LOAD_NO_HINTING
>>>     13 from matplotlib.ft2font import LOAD_TARGET_LIGHT
>>> 
>>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/font_manager.py
>>> in <module>()
>>>     51 import matplotlib
>>>     52 from matplotlib import afm
>>> ---> 53 from matplotlib import ft2font
>>>     54 from matplotlib import rcParams, get_cachedir
>>>     55 from matplotlib.cbook import is_string_like
>>> 
>>> ImportError: libpng16.so.16: cannot open shared object file: No such
>>> file
>>> or directory
>>> 
>>> 
>>> 
>>> Inside python, the attempt to import MNE gives this error:
>>> 
>>> In [1]: import mne
>>> ---------------------------------------------------------------------------
>>> ImportError                               Traceback (most recent call
>>> last)
>>> <ipython-input-1-39fc8b1a8697> in <module>()
>>> ----> 1 import mne
>>> 
>>> ImportError: No module named mne
>>> 
>>> In [2]:
>>> 
>>> 
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