www.neuron.yale.edu

I'm building from source, so I'm all set. Thanks!

How do I get access to the i_cap variable from the Python interpreter?

I tried and but neither work. The equivalent statements with "cm" work fine.

Thanks!!! The following works: ./configure --prefix=$IDIR/nrn --with-iv=$IDIR/iv --with-nrnpython=$ENTHOUGHT_HOME/bin/python PYLIB="-L$ENTHOUGHT_HOME/lib -lpython2.7" PYLIBLINK="-L$ENTHOUGHT_HOME/lib -lpython2.7" PYINCDIR="$ENTHOUGHT_HOME/include/python2.7" PYLIBDIR=&qu...

Neat! It works.

Ok... It looks like NEURON is using the preinstalled python instead of the enthought python distribution. I am compiling with ./configure --prefix=$IDIR/nrn --with-iv=$IDIR/iv --with-nrnpython PYLIB='-framework Python' PYLIBLINK='-framework Python' --build=x86_64-apple-darwin11.2.0 --with-paranrn Sh...

The menu bar appears, but the problem is that python exits at the end of the script instead of remaining open for user interaction.

Thanks for the fast response!

I'm trying to use Enthought's python distribution to have scipy accessible when using NEURON. I am compiling NEURON from the latest source checked out with mercurial. When I use the command nrngui -python I can import numpy, but not scipy (it says the module does not exist). When using just python, ...

Is there a way to keep the gui open for user interaction when importing neuron in a python script using similar to how it stays open when using nrngui -python?

I think I did it! I found http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0 and removed -lutil from the file mpic++-wrapper-data.txt now I can import neuron: Python 2.7.1 (r271:86882M, Nov 30 2010, 09:39:13) [GCC 4.0.1 (Apple Inc. build 5494)] on darwin Type "help"...

running env ARCHFLAGS='-arch i386' python setup.py install gives output: running install running build running build_py creating build/lib.macosx-10.3-i386-2.7 creating build/lib.macosx-10.3-i386-2.7/neuron copying /Applications/NEURON-7.2-test/nrn/share/nrn/lib/python/neuron/__init__.py -> build/li...

before removing -arch ppc: LDCXXSHARED : c++ -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g -bundle -undefined dynamic_lookup BLDSHARED : gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -isysroot /Developer/SDKs/MacO...

so once you have the variables from sysconfig.get_config_vars(), how do you actually override them with the new values? presumably sysconfig.get_config_vars() is returning a copy of the variable dictionary? edit: I wrote a little script to see if I could edit the dictionary returned by sysconfig.get...

Where would that go? in setup.py? import sysconfig import re new_config_vars = {} for k, v in sysconfig.get_config_vars().items(): if type(v) is str and '-arch ppc' in v: new_config_vars[k] = v.replace('-arch ppc', '').replace(' ', ' ') for k, v in new_config_vars.items(): print k + ' : ' + v Is thi...

Notice that NEURON-7.2 guesses i386, others guess i686: Macintosh-4% cd ~/NEURON/iv-17 Macintosh-4% ./config.guess i686-apple-darwin9.8.0 Macintosh-4% cd ../nrn-7.1 Macintosh-4% ./config.guess i686-apple-darwin9.8.0 Macintosh-4% cd ../nrn-7.2 Macintosh-4% ./config.guess i386-apple-darwin9.8.0 Config...

ok... I think one problem was that I set DYLD_LIBRARY_PATH to open mpi's library, and I wasn't supposed to. that fixed the nrn_load_dll not available problem. setup.py still gives the error: ldld: library not found for -lutil : library not found for -lutil collect2: ld returned 1 exit status collect...