NEURON-7.2 installation on MAC OS 10.7: error and summary

Post Reply
AGBX2
Posts: 14
Joined: Thu Jun 16, 2011 11:12 am

NEURON-7.2 installation on MAC OS 10.7: error and summary

Post by AGBX2 » Tue Sep 25, 2012 8:38 am

Hi,

When installing NEURON-7.2 with the dmg I always face these error messages:
Sep 25 13:51:48 MyLaptop.local nrniv[27518] <Error>: kCGErrorInvalidConnection: CGSGetWindowTags: Invalid connection
Sep 25 13:51:48 MyLaptop.local nrniv[27518] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged.

This becomes a real problem when I try to use the GUI to build even small networks because after numerous error messages the interface freeze (my Mac runs OS 10.7.4 and XCode 4.4.1 is installed with the latest command line tool). Since the .dmg is very easy to use and install, my question: is how can this problem be solved ? :)

To overcome this problem I decided to compile NEURON and IV from the sources (IV: http://www.neuron.yale.edu/ftp/neuron/v ... -17.tar.gz and NEURON: http://www.neuron.yale.edu/ftp/neuron/v ... 7.2.tar.gz). I added here a minimalist installation script which seems to work perfectly at least on my laptop configuration (which is quite a common one):

Code: Select all

IDIR=/Applications/NEURON-7.2
cd iv-17
./configure --prefix=$IDIR/iv
make
make install
cd ../nrn-7.2
./configure --prefix=$IDIR/nrn --with-iv=$IDIR/iv/x86_64
make
make install
make after_install
Then to avoid a comon error message nrniv: unable to open font *Arial*bold*--12*", using "fixed" just modify the /Application/NEURON-7.2/nrn/share/nrn/lib/nrn.defaults and to comment the line

Code: Select all

*font: *Arial*bold*--12*

Finaly in the /Users/UserName/.bash_profile hidden file add

Code: Select all

export PATH=/Applications/NEURON-7.2/nrn/x86_64/bin/:$PATH
This is a simple synthesis of what is suggested in the NEURON site and on the forum and I hope it can help :)

ted
Site Admin
Posts: 5218
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: NEURON-7.2 installation on MAC OS 10.7: error and summar

Post by ted » Tue Sep 25, 2012 10:47 am

Thanks for reporting how you got NEURON 7.2 working. If you have another Mac with Lion or Mountain Lion, or if you just want to try the most recent alpha version of NEURON (full of improvements and bug fixes), you might want to get
http://www.neuron.yale.edu/ftp/neuron/v ... 10.7.4.dmg

Anyone else who reads this thread will need to know the following:

1. Lion and Mountain Lion both need the latest version of the command line developer tools--without them, you won't be able to compile mod files. Go to http://developer.apple.com/opensource and click on the "Download command line developer tools . . . " link. You'll have to sign in with your Apple ID and password.

2. If you are interested in using parallel hardware to handle large models or speed up your simulations (who isn't?), you will want to install OpenMPI. Download http://www.open-mpi.org/software/ompi/v ... 1.6.tar.gz, then

Code: Select all

tar xzf openmpi-1.6.tar.gz
cd openmpi-1.6
./configure
make
make install
With the 7.3 dmg there should be no need to do anything to environment variables--NEURON, Python, MPI etc. should be able to find each other automatically.

Post Reply