Search found 20 matches

by lneisenman
Tue Apr 22, 2014 11:08 am
Forum: NEURON + Python
Topic: NEURON does not compile with Python 3.4
Replies: 2
Views: 1822

Re: NEURON does not compile with Python 3.4

That did the trick, thanks.

Larry
by lneisenman
Mon Apr 21, 2014 10:48 am
Forum: NEURON + Python
Topic: NEURON does not compile with Python 3.4
Replies: 2
Views: 1822

NEURON does not compile with Python 3.4

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...
by lneisenman
Fri Jan 10, 2014 10:18 am
Forum: NEURON + Python
Topic: possible memory leak with random in python3
Replies: 5
Views: 2495

Re: possible memory leak with random in python3

That did the trick, thanks.

Larry
by lneisenman
Wed Jan 08, 2014 2:43 pm
Forum: NEURON + Python
Topic: possible memory leak with random in python3
Replies: 5
Views: 2495

Re: possible memory leak with random in python3

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 "license" for more information. >...
by lneisenman
Fri Dec 20, 2013 9:48 am
Forum: NEURON + Python
Topic: possible memory leak with random in python3
Replies: 5
Views: 2495

Re: possible memory leak with random in python3

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
by lneisenman
Fri Nov 22, 2013 10:43 am
Forum: NEURON + Python
Topic: possible memory leak with random in python3
Replies: 5
Views: 2495

possible memory leak with random in python3

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...
by lneisenman
Wed May 15, 2013 9:32 am
Forum: NEURON + Python
Topic: NEURON does not compile with python3.3
Replies: 2
Views: 1768

Re: NEURON does not compile with python3.3

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

Larry
by lneisenman
Wed May 08, 2013 2:39 pm
Forum: NEURON + Python
Topic: NEURON does not compile with python3.3
Replies: 2
Views: 1768

NEURON does not compile with python3.3

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....
by lneisenman
Fri Apr 12, 2013 10:40 am
Forum: NEURON + Python
Topic: import neuron crash in ipython console
Replies: 22
Views: 11495

Re: import neuron crash in ipython console

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...
by lneisenman
Tue Apr 09, 2013 9:58 am
Forum: NEURON + Python
Topic: import neuron crash in ipython console
Replies: 22
Views: 11495

Re: import neuron crash in ipython console

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...
by lneisenman
Tue Apr 09, 2013 9:39 am
Forum: UNIX/Linux
Topic: problem building NEURON 7.3 with python3 on Ubuntu 12.04
Replies: 3
Views: 6862

Re: problem building NEURON 7.3 with python3 on Ubuntu 12.04

That did the trick. Thanks.

Larry
by lneisenman
Wed Apr 03, 2013 10:27 am
Forum: UNIX/Linux
Topic: problem building NEURON 7.3 with python3 on Ubuntu 12.04
Replies: 3
Views: 6862

problem building NEURON 7.3 with python3 on Ubuntu 12.04

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...
by lneisenman
Wed Nov 16, 2011 10:18 am
Forum: UNIX/Linux
Topic: Neuron with Python on Ubuntu 11.10 32 bit
Replies: 1
Views: 3296

Neuron with Python on Ubuntu 11.10 32 bit

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 extras t...
by lneisenman
Fri Aug 05, 2011 5:24 pm
Forum: Specific models
Topic: NEURON implementation of Vogels & Abbott model
Replies: 4
Views: 13335

Re: NEURON implementation of Vogels & Abbott model

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

Larry