[Mne_analysis] python-MNE installation
raij at nmr.mgh.harvard.edu
raij at nmr.mgh.harvard.edu
Tue Sep 30 21:42:59 EDT 2014
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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