install latest nrn7 + Python does not work

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

Moderator: hines

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arb
Posts: 19
Joined: Mon Jul 02, 2007 6:18 am
Location: Humboldt-University, Berlin

install latest nrn7 + Python does not work

Post by arb » Thu Sep 25, 2008 11:59 am

As there is this to_python() bug in the neuron 6.2. version I need to install the latest alpha version..
But when I try to install this I get the following

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./configure --with-nrnpython
make
sudo make install
... works fine,
but installing the python package

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cd src/nrnpython
sudo python setup.py install
gives the following error:

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running install
running build
running build_py
error: package directory '../.././share/lib/python/neuron/tests' does not exist
and when I start python and Neuron I get

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bahl@opt2:~$ python
Python 2.5.2 (r252:60911, Jul 31 2008, 17:31:22) 
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import neuron
NEURON -- VERSION 7.0 (163:293f207e00dc) 2008-09-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/neuron/__init__.py", line 175, in <module>
    class Vector(Wrapper):
  File "/usr/lib/python2.5/site-packages/neuron/__init__.py", line 202, in Vector
    if not hoc.test_numpy()==None:
AttributeError: 'module' object has no attribute 'test_numpy'
I really need this to work, because I need to use variable time steps and record a lot of data in my cells that need to be copied to python...

Thank you for help,
Armin

ted
Site Admin
Posts: 5566
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: install latest nrn7 + Python does not work

Post by ted » Thu Sep 25, 2008 1:12 pm

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tar xzf nrn-7.0...tar.gz
cd nrn-7.0
./configure --prefix=where_you_want_it --with-iv=path_to_iv --with-nrnpython=path_to_python
make
make install
In my case,
path_to_python is /usr/bin/python

arb
Posts: 19
Joined: Mon Jul 02, 2007 6:18 am
Location: Humboldt-University, Berlin

Re: install latest nrn7 + Python does not work

Post by arb » Mon Oct 13, 2008 10:30 am

The installation of the latest neuron version still does not work. I have downloaded the latested alhpa version and I tries to install it on two different computers. I did the same as usual

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./configure --prefix=/home/me/nrn7 --with-nrnpython --with-paranrn
make
make install
this works
but when I try to intstall the python inferface I get:

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python setup.py install --prefix=/home/me/nrn7

running install
running build
running build_py
error: package directory '../.././share/lib/python/neuron/tests' does not exist
the installer scripts does not find a test package, which really does not exist in the python/neuron folder..

Thanks
Armin

hines
Site Admin
Posts: 1575
Joined: Wed May 18, 2005 3:32 pm

Re: install latest nrn7 + Python does not work

Post by hines » Tue Oct 14, 2008 4:10 pm

I forgot to add those to the distribution files. You can get them from the mercurial repository at
http://www.neuron.yale.edu/hg/neuron/nr ... ron/tests/
I also just fixed a related problem when running setup.py when the build directory is not
the source directory.

arb
Posts: 19
Joined: Mon Jul 02, 2007 6:18 am
Location: Humboldt-University, Berlin

Re: install latest nrn7 + Python does not work

Post by arb » Wed Oct 15, 2008 8:51 am

thank you for the help...
adding these files to the directory solves the problem..
however, python installation still does not work, when I compile everything with the -with-mpi option

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bahl@colamn:~/install/nrn-7.0/src/nrnpython> python setup.py install
running install
running build
running build_py
running build_ext
building 'neuron.hoc' extension
mpicc -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/bahl/include/python2.4 -c inithoc.cpp -o build/temp.linux-x86_64-2.4/inithoc.o
mpicxx -pthread -shared build/temp.linux-x86_64-2.4/inithoc.o -L/home/bahl/x86_64/lib -L/home/bahl/x86_64/lib -lnrnpython -lnrnoc -loc -lnrniv -livoc -lmemacs -lmeschach -lneuron_gnu -lnrnmpi -lscopmath -lsparse13 -lsundials -lIVhines -lreadline -o build/lib.linux-x86_64-2.4/neuron/hoc.so -Wl,-R/home/bahl/x86_64/lib -Wl,-R/home/bahl/x86_64/lib
g++: build/temp.linux-x86_64-2.4/inithoc.o: No such file or directory
error: command 'mpicxx' failed with exit status 1
the directory build/temp.linux-x86_64-2.4/ exists but is empty..
Are there still missing files??

Thank you,
Armin

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