Search found 19 matches

by arb
Tue Dec 01, 2009 7:18 am
Forum: Other questions
Topic: Different Levels of Access?
Replies: 1
Views: 1019

Different Levels of Access?

Hi, I am using the latest NEURON 7.1 on my MacBook Pro.. I was just wondering what the difference between the two pieces of code are: create soma soma { objref test test = new IClamp(0.5) } producing an error: /Applications/NEURON/nrn/i686/bin/nrniv: syntax error in test.hoc near line 5 test = new I...
by arb
Mon Nov 03, 2008 10:08 am
Forum: Other questions
Topic: changed dt
Replies: 1
Views: 1373

changed dt

I am running a simulation on many parallel machines and each of them calculates a voltage trace with a variable time step..
During this simulation my screen is filled with hundreds of "changed dt"..
Is there a way to get rid of that output??
Thank you,
Armin
by arb
Wed Oct 15, 2008 8:51 am
Forum: NEURON + Python
Topic: install latest nrn7 + Python does not work
Replies: 4
Views: 2785

Re: install latest nrn7 + Python does not work

thank you for the help... adding these files to the directory solves the problem.. however, python installation still does not work, when I compile everything with the -with-mpi option bahl@colamn:~/install/nrn-7.0/src/nrnpython> python setup.py install running install running build running build_py...
by arb
Mon Oct 13, 2008 10:30 am
Forum: NEURON + Python
Topic: install latest nrn7 + Python does not work
Replies: 4
Views: 2785

Re: install latest nrn7 + Python does not work

The installation of the latest neuron version still does not work. I have downloaded the latested alhpa version and I tries to install it on two different computers. I did the same as usual ./configure --prefix=/home/me/nrn7 --with-nrnpython --with-paranrn make make install this works but when I try...
by arb
Thu Sep 25, 2008 11:59 am
Forum: NEURON + Python
Topic: install latest nrn7 + Python does not work
Replies: 4
Views: 2785

install latest nrn7 + Python does not work

As there is this to_python() bug in the neuron 6.2. version I need to install the latest alpha version.. But when I try to install this I get the following ./configure --with-nrnpython make sudo make install ... works fine, but installing the python package cd src/nrnpython sudo python setup.py inst...
by arb
Wed Sep 17, 2008 5:59 pm
Forum: NEURON + Python
Topic: ParallelPython and Neuron
Replies: 3
Views: 2766

Re: ParallelPython and Neuron

Thank you -- a system based on mpi seems to be the better way to do for the future.. I will give ipython a try.. However I have been able to use parallel python with neuron.. The nice thing is that you could use it on every computer where you can install normal neuron and python (even within www). N...
by arb
Wed Sep 17, 2008 5:43 pm
Forum: NEURON + Python
Topic: to_python() causes big memory problems
Replies: 8
Views: 5231

to_python() causes big memory problems

Since the new version (6.2.3) came out I am using the to_python function to copy neuron vectors to python arrays.. The function to_python seems to allocate new memory that it never gives free again.. I wrote a simple example to illustrate this problem. (Points are spaces below) Example 1: 16GB Memor...
by arb
Sat Sep 06, 2008 6:33 pm
Forum: NEURON + Python
Topic: Install nrnpython when Python is in home
Replies: 2
Views: 2351

Re: Install nrnpython when Python is in home

Hi Michael, Unfortunately, all combination of pylib and pyinc, etc... yield the same effect when I try to configure python. I am trying to install neuron on a beowulf cluster -- and on a single 64bit machine.. Beowulf has Suse Linux 10 installed and the single 64bit machine debian, the messages are ...
by arb
Sat Sep 06, 2008 9:45 am
Forum: NEURON + Python
Topic: Install nrnpython when Python is in home
Replies: 2
Views: 2351

Install nrnpython when Python is in home

Hi, I am using a server where python is not installed and I cannot install python as root. So I have installed python locally in my home directory and it works without any problems. When I want to install neuron, it finds my python version, but it seems to have problems with other standard libraries...
by arb
Wed Aug 20, 2008 12:28 pm
Forum: NEURON + Python
Topic: Two instances of Neuron in a Python script
Replies: 1
Views: 1389

Two instances of Neuron in a Python script

I tried to create a python class, that should create an instance of neuron: Here a very simple example: class neuron(): def __init__(self, tstop): import neuron self.h = neuron.h self.h("tstop = %d"%tstop) n1 = neuron(100) n2 = neuron(500) print n1.h.tstop print n2.h.tstop I expected that once a new...
by arb
Wed Aug 20, 2008 6:51 am
Forum: NEURON + Python
Topic: ParallelPython and Neuron
Replies: 3
Views: 2766

Re: ParallelPython and Neuron

On the parallelpython webpage they suggest to do something like this for external programmes to solve the problem with output from different processes, : def test(): from subprocess import Popen, PIPE p = Popen(['ls', '-l'], stdout=PIPE, stderr=PIPE) return p.stdout.read() this gives me indeed the l...
by arb
Wed Aug 20, 2008 6:32 am
Forum: NEURON + Python
Topic: ParallelPython and Neuron
Replies: 3
Views: 2766

ParallelPython and Neuron

Does anyone has experience with ParallelPython and Neuron? Im very much using the python interface for neuron and I want now to start some huge calculation now for which I need parallel computing ... For python there is a wonderful package that provides parallel computing in a very simple way (http:...
by arb
Wed Aug 20, 2008 6:11 am
Forum: NEURON + Python
Topic: New nrnpython compiling problem
Replies: 4
Views: 2128

Re: New nrnpython compiling problem

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
by arb
Thu Aug 14, 2008 12:00 pm
Forum: NEURON + Python
Topic: New nrnpython compiling problem
Replies: 4
Views: 2128

New nrnpython compiling problem

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 f...
by arb
Fri Jul 20, 2007 6:03 pm
Forum: NEURON + Python
Topic: Compling Problem
Replies: 21
Views: 16847

no module named hoc

installation works fine this way. ... but which problems do I get not compiling it with numpy? after make install I switched to the src/nrnpython dir and typed python setup.py install in super user mode: ..... sudo python setup.py install getting: Warning: NEURON was build without support for numpy....