Search found 18 matches

by phendric
Mon Mar 28, 2016 7:11 pm
Forum: MSWin
Topic: Runtime error (R6034)
Replies: 2
Views: 9294

Re: Runtime error (R6034)

Almost - turns out that the student already had Anaconda/Python 3.5 installed on his machine when the project was assigned...and reverting to 2.7 didn't move all the libraries it should have moved, apparently. Seems like Python 3 is becoming more and more the de facto version of Python people are le...
by phendric
Mon Mar 28, 2016 5:01 pm
Forum: MSWin
Topic: Runtime error (R6034)
Replies: 2
Views: 9294

Runtime error (R6034)

Guys, One of my students is trying to get NEURON + Anaconda (Python 2.7) installed on Windows 10 (x86_64). They want Anaconda because it gives them access to NumPy, SciPy, Pylab, etc. But after installing Anaconda and the latest version of MinGW NEURON, they get the following error when trying to im...
by phendric
Tue Feb 12, 2013 2:19 pm
Forum: NEURON Announcements
Topic: Webcast tutorial: Introduction to the Neuroscience Gateway
Replies: 2
Views: 12421

Re: Webcast tutorial: Introduction to the Neuroscience Gate

The XSEDE website you link to:

https://www.xsede.org/web/xup/course-ca ... /class/109

says that the course is an in-person course (they make that quite clear, with large, bolded text). But your announcement says it's a webcast?
by phendric
Tue Feb 12, 2013 2:07 pm
Forum: NEURON + Python
Topic: NEURON 7.2 + Python + cPickle on Fedora 17- hoc module error
Replies: 3
Views: 2783

Re: NEURON 7.2 + Python + cPickle on Fedora 17- hoc module e

Ted, well, it's not quite as simple as you make it out to be - when what you want to "move" is a small part of a much larger model implementation (ie, only a few cells of a much larger network), you can't just copy and paste the source code and data files. That's the route I ended up going...but it ...
by phendric
Fri Feb 08, 2013 8:08 pm
Forum: NEURON + Python
Topic: NEURON 7.2 + Python + cPickle on Fedora 17- hoc module error
Replies: 3
Views: 2783

NEURON 7.2 + Python + cPickle on Fedora 17- hoc module error

Guys, I'm trying to do something that may seem a little odd - I want to serialize a NEURON cell and write it to disk so that I can move it to another computer (and easily load the cell again). The cell is implemented using a combination of HOC and Python code, and I'm using the cPickle module to try...
by phendric
Tue Mar 20, 2012 2:54 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 6964

Re: Using ions in multiple mechanisms

Will the revised code find its way into ModelDB? Future users would find that to be a great benefit. Absolutely! My time investment, especially in the time taken for documentation, is really only worth it if I share the product with others. I've gotten through most of the code, rewriting, comparing...
by phendric
Tue May 03, 2011 8:32 pm
Forum: Anatomically detailed models
Topic: Import3D in batch-process mode?
Replies: 11
Views: 10446

Import3D in batch-process mode?

Guys, As I outlined in another post earlier today (http://www.neuron.yale.edu/phpBB/viewtopic.php?f=13&t=2161#p8770), I'm using L-NEURON (http://krasnow.gmu.edu/cn3/L-Neuron/index.htm) to generate unique morphologies of cells within a certain morphological class. L-NEURON outputs these virtual cells...
by phendric
Tue May 03, 2011 8:24 pm
Forum: Anatomically detailed models
Topic: SWC files with a single "soma" point
Replies: 13
Views: 12554

Re: SWC files with a single "soma" point

If such swc files are common, I would expect Import3D to already have a policy for dealing with them. Have you such a file, and what did Import3D do? Yes, I downloaded the file from http://neuromorpho.org/neuroMorpho/dableFiles/amaral/CNG%20version/c10261.CNG.swc . The first two data lines of it lo...
by phendric
Mon Jun 28, 2010 1:56 am
Forum: NEURON + Python
Topic: NEURON + Python hands-on tutorial, San Diego 2010
Replies: 3
Views: 3350

Re: NEURON + Python hands-on tutorial, San Diego 2010

I'm interested in taking this course, especially with the bits about integrating Python's data analysis/visualization libraries into NEURON models.

Phillip
by phendric
Sat Oct 03, 2009 4:56 am
Forum: UNIX/Linux
Topic: NEURON can't find IV headers/libs
Replies: 7
Views: 3771

Re: NEURON can't find IV headers/libs

Keivan, Genius - the problem was, in fact, due to the Intel compiler. The cluster I'm on has another compiler available to use...so I'm using it: [phendric@hpc-login2 CA1Model]$ gcc --version gcc (GCC) 4.3.3 Copyright (C) 2008 Free Software Foundation, Inc. This is free software; see the source for ...
by phendric
Fri Oct 02, 2009 1:09 pm
Forum: UNIX/Linux
Topic: NEURON can't find IV headers/libs
Replies: 7
Views: 3771

Re: NEURON can't find IV headers/libs

Another update: I tried compiling NEURON without any graphical interface... ./configure --prefix=`pwd` --with-mpi --without-x When I came back an hour later, I found that the build process had failed with several errors. I'm including the last part of the output, but you can see that there are multi...
by phendric
Fri Oct 02, 2009 12:53 pm
Forum: UNIX/Linux
Topic: NEURON can't find IV headers/libs
Replies: 7
Views: 3771

Re: NEURON can't find IV headers/libs

Michael, Under /home/rcf-proj3/tb/phendric/nrn70/ I have two directories: iv & nrn. From within /home/rcf-proj3/tb/phendric/nrn70/iv I run ./configure --prefix=`pwd` make make install As far as I can tell from the output, the compilation process for Interviews completes successfully. I then navigate...
by phendric
Thu Oct 01, 2009 7:35 pm
Forum: UNIX/Linux
Topic: NEURON can't find IV headers/libs
Replies: 7
Views: 3771

NEURON can't find IV headers/libs

Hi all, I'm currently compiling NEURON to run on a CentOS-based cluster we recently set up. I followed the instructions to compile InterViews, which completed successfully. However, when I try to run ./configure on the NEURON source files, I eventually get the error: ... checking compilation with in...
by phendric
Mon Jul 06, 2009 2:47 pm
Forum: Getting started
Topic: Why does this variable temporarily disappear?
Replies: 1
Views: 1631

Why does this variable temporarily disappear?

Michael or Ted (or anyone else who would know the answer to this): I have a case of a missing variable when running a NEURON script. It's the Poirazi model I talked a little bit with both of you about at this year's NEURON course - I'm in the process of re-working the code so that I can make the ent...
by phendric
Tue Apr 21, 2009 11:01 pm
Forum: Getting started
Topic: Neuron 7 returns Segmentation violation
Replies: 11
Views: 9779

Re: Neuron 7 returns Segmentation violation

Doh!

Problem solved. I forgot to execute nrnivmodl in the /mechanism sub-directory. That created a directory named x86_64, and to finish, I went and edited all of the run_* files, changing "i686" to "x86_64".

Everything runs beautifully now. Thanks for the help.

Phillip