www.neuron.yale.edu

That did the trick, thanks.

Larry

When trying to compile NEURON ( either the standard distribution or cloned today from the repository) with python3.4 on Ubuntu 14.04 64 bit I get the following error: ($HOME/neuron/nrn/configure --prefix=`pwd` --with-iv --with-nrnpython=python3 --srcdir=$HOME/neuron/nrn) Larry make[4]: Entering dire...

That did the trick, thanks.

Larry

Sorry it took so long to respond. The memory leak appears to be fixed. However, I now get errors from trying to use references to record time in a vector. Larry Python 3.3.3 (default, Dec 27 2013, 19:27:19) [GCC 4.6.3] on linux Type "help", "copyright", "credits" or &qu...

Replacing MCellRan4 with Random123 does not eliminate the leak so it is likely something related to the python3 interface (e.g. http://www.neuron.yale.edu/phpBB/viewto ... 818#p11360) rather than MCellRan4.

Larry

In debugging a batch simulation, I ran into what looks like a memory leak in python3 with the randomstream object from Brette 2007. Attached is a simple example to illustrate the issue. The leak does not seem to be present in python2. I'm using Ubuntu 12.04 64bit running in virtualbox on a Win7 64 b...

That did the trick. Thanks for the heads up on the potential memory leak.

Larry

When trying to compile NEURON with python3.3.1 on Ubuntu 13.04 64 bit I get the following error: (./configure --prefix=`pwd` --with-iv --with-nrnpython=python3) make[4]: Entering directory `/home/larry/neuron/nrn/src/nrnpython' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I....

Thanks for the fix. It works for me with python3 on Ubuntu 12.04 64 bit. One interesting behavior I noted is that when using neuron from a qtconsole or notebook, the message about neuron that prints when executing 'from neuron import h' does not display in the qtconsole or notebook, but rather in th...

I'm seeing the same issue using python3 in ubuntu 12.04 64 bit. to install in ubuntu for python2 (probably should 'sudo apt-get remove ipython' first if apt-get was used to install ipython): sudo apt-get install build-essential sudo apt-get install python-dev sudo apt-get install libqt4-dev # Qt nee...

That did the trick. Thanks.

Larry

I ran into an issue trying to build NEURON 7.3 on Ubuntu 12.04 64bit with python3 using the following configure command ./configure --prefix=`pwd` --with-iv --with-nrnpython=python3 I got the following error: Python binary found (/usr/bin/python3) checking nrnpython configuration... get_python_versi...

FWIW, Bill Lytton implemented a version of this model in NEURON.

https://senselab.med.yale.edu/modeldb/S ... odel=35358

Larry

I had to set up Neuron on a new install of 32 bit Ubuntu 11.10 running in Virtualbox. Based on some recent posts about dependencies ( viewtopic.php?f=6&t=2387#p9420 and viewtopic.php?f=6&t=1772#p9596 ) and some trial and error, I came up with the following script. It obviously includes some ...

Thanks for the rapid clarification. I was worried about re-using code I wasn't sure I understood.

Larry