New nrnpython compiling problem

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

New nrnpython compiling problem

Post by arb » Thu Aug 14, 2008 12:00 pm

I have just downloaded the new version of neuron 6.2. that promises significant improvements in the python interface.

But when I try to install it as usual:
./configure --prefix=/home/armin --with-iv=/home/armin --with-nrnpython --with-numpy

the configuration process stops and tells:

Python binary found (/home/armin/bin/python)
checking nrnpython configuration... get_python_version() '2.5'
get_python_inc(1) '/home/armin/include/python2.5'
get_config_var('LIBS') '-lpthread -ldl -lutil'
get_config_var('LINKFORSHARED') '-Xlinker -export-dynamic'
get_config_var('LIBDIR') '/home/armin/lib'
checking numpy availability... checking if python include files and libraries work... configure: error: could not run a test that used the python library.
Examine config.log to see error details. Something wrong with
PYLIB=-L/home/armin/lib -lpython2.5 -lpthread -ldl -lutil -Xlinker -export-dynamic -R/home/armin/lib
or
PYLIBDIR=/home/armin/lib
or
PYLIBLINK=-L/home/armin/lib -lpython2.5 -lpthread -ldl -lutil
or
PYINCDIR=/home/armin/include/python2.5

python is installed into /home/armin and works fine with numpy..

I have played around with the library path, but I have yet not been able to start compiling..
I think one should just tell it not to start this test (that seems to be the new part of this version)..

Thank you very much for your help,
Armin

ted
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Re: New nrnpython compiling problem

Post by ted » Fri Aug 15, 2008 9:16 am

Could you please describe your software environment--OS, distribution (if Linux), release, Python version(s) installed--just in case that has anything to do with the problem.

hines
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Re: New nrnpython compiling problem

Post by hines » Fri Aug 15, 2008 9:56 am

Try leaving out the --with-numpy option. That is still under development. Even without the option, you can
still import numpy and get good performance.

ted
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Re: New nrnpython compiling problem

Post by ted » Fri Aug 15, 2008 10:54 am

I just succeeded in compiling Release 6.2.1 (2189) 2008-08-01 with numpy.
Centos 5.2 Linux
Python 2.4.3
python-numpy-1.0.1-1.el5.rf
Latter two are the latest versions obtained from Centos 5's standard repositories.

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

Re: New nrnpython compiling problem

Post by arb » Wed Aug 20, 2008 6:11 am

After several days of installing and deinstalling neuron and python, I decided to fully reinstall our server. We have a new fresh ubuntu version now, with up to date python packages.. And Neuron installs without problems... (however still without numpy)
Thank you,
armin

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