Search found 26 matches

by bll5z6
Wed Mar 06, 2019 2:50 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

Well I tried your installation commands and it worked! I'm not sure if installing in /oasis/scratch/ instead of $HOME was the cure or something else. Thanks so much!
by bll5z6
Wed Mar 06, 2019 10:17 am
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

I don't think the Anaconda installation is available to others, it is just in my home directory. It is the install available here (I just accepted all the defaults): wget https://repo.anaconda.com/archive/Anaconda2-2018.12-Linux-x86_64.sh bash Anaconda2-2018.12-Linux-x86_64.sh Here's this: $ ldd /ho...
by bll5z6
Tue Mar 05, 2019 6:29 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

The .so file in /home/latimerb/utils/nrn/lib/python/neuron/ is hoc.so. Yes, which python is anaconda and yes pwd was /home/latimerb/utils/nrn $ which python ~/anaconda2/bin/python In config.status, it says: S["NRNPYTHON_LIBS"]="-lnrnpython -L/home/latimerb/anaconda2/lib -lpython2.7 -lpthread -ldl -l...
by bll5z6
Tue Mar 05, 2019 6:05 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

The file in <prefix>lib/python/neuron is called hoc.so. Sorry, I pasted the wrong error using a different configuration. This is the error when I do the config like this: $ ./configure --prefix=`pwd` --without-iv --with-nrnpython=`which python` --with-paranrn $ make $ make install $ export PYTHONPAT...
by bll5z6
Tue Mar 05, 2019 5:13 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

As I progressed I realized it would be easier to just download Anaconda 2.7 to my home directory and use this as my python distribution since it automatically installs other packages I need. So I deleted everything and installed Anaconda 2.7 (https://repo.anaconda.com/archive/Anaconda2-2018.12-Linux...
by bll5z6
Tue Mar 05, 2019 3:44 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

Using Python 2.7 (module load python) seems to have fixed the issue. Now I don't need to use any extra configuration parameters. Here are the installation commands for (mostly my own) future reference: module load python mkdir utils cd utils wget https://neuron.yale.edu/ftp/neuron/versions/v7.6/7.6....
by bll5z6
Fri Mar 01, 2019 3:27 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Re: Errors importing neuron

Thanks Michael. I tried your suggestions but still face the same issue. Here are the commands I used for installation: wget https://neuron.yale.edu/ftp/neuron/versions/v7.6/7.6.5/nrn-7.6.5.tar.gz tar xzf nrn-7.6.5.tar.gz rm nrn-7.6.5.tar.gz mv nrn-7.6 nrn cd nrn ./configure --prefix=`pwd` --without-...
by bll5z6
Tue Feb 26, 2019 3:43 pm
Forum: NEURON + Python
Topic: Errors importing neuron
Replies: 17
Views: 2767

Errors importing neuron

Hi all, I have installed NEURON + Python on many different systems but for some reason am hitting a wall while trying to do "import neuron" on the Comet supercomputer (CentOS 6.10). I followed the instructions at https://neuron.yale.edu/neuron/download/compile_linux and am downloading NEURON 7.6.5. ...
by bll5z6
Mon Feb 11, 2019 2:21 pm
Forum: NEURON + Python
Topic: Optimizing single cells programmatically
Replies: 3
Views: 916

Re: Optimizing single cells programmatically

Hi Ted, I believe you may be right.. I had assumed they were using the GUI because they have multiple .ses files here: https://github.com/AllenInstitute/biophys_optimize/tree/master/biophys_optimize/passive But upon closer inspection, it looks like they do create some reference to h.MulRunFitter() h...
by bll5z6
Thu Feb 07, 2019 1:24 pm
Forum: NEURON + Python
Topic: Optimizing single cells programmatically
Replies: 3
Views: 916

Optimizing single cells programmatically

Hi all, I'm trying to adopt the Allen Institute's single-cell model creation workflow: https://www.nature.com/articles/s41467-017-02718-3 However, during the "passive fitting" stage of the process (i.e. determining the optimal capacitance and leak conductance for the model), they use NEURON's Multip...
by bll5z6
Fri Aug 17, 2018 11:17 am
Forum: Adding new mechanisms and functions to NEURON
Topic: HOC kernel for Jupyter
Replies: 3
Views: 1611

Re: HOC kernel for Jupyter

This is awesome, thanks for the reply!
by bll5z6
Tue Jun 19, 2018 3:15 pm
Forum: Parallel NEURON
Topic: want_all_spikes recording from axon
Replies: 2
Views: 1022

Re: want_all_spikes recording from axon

Awesome, thank you!
by bll5z6
Tue Jun 19, 2018 1:57 pm
Forum: Parallel NEURON
Topic: want_all_spikes recording from axon
Replies: 2
Views: 1022

want_all_spikes recording from axon

Hi all, I have a model that includes axo-axonic cells that cause pyramidal cells to fire APs in the axon that do not backpropagate to the soma. I want to use the ParallelNetManager's want_all_spikes() because it's easy but it seems to only record spikes at the soma. Is there a simple way to force it...
by bll5z6
Thu May 03, 2018 3:03 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: HOC kernel for Jupyter
Replies: 3
Views: 1611

HOC kernel for Jupyter

Hey all,

Would there be any interest in making a HOC kernel so that HOC code can be interpreted in a Jupyter notebook/ the new Jupyter Lab? I'm using it beautifully with NEURON as a Python module but it would be cool to do HOC as well (mainly for teaching). Just thought I'd throw it out there!

Ben
by bll5z6
Wed Jul 12, 2017 4:26 pm
Forum: MSWin
Topic: Application unable to start correctly (0xc0000142)
Replies: 1
Views: 9047

Application unable to start correctly (0xc0000142)

Hey all, We are running a comp. neuroscience workshop using NEURON and I had a participant with a strange issue. Every time he double clicks a .hoc file, he gets this error: http://i64.tinypic.com/259zf5z.jpg However, I can run the code manually i.e. by typing "nrniv script.hoc" in bash and it works...