Search found 89 matches

by pascal
Tue Nov 08, 2016 11:17 am
Forum: UNIX/Linux
Topic: Which version of mpich2 is recommended for NEURON 7.4?
Replies: 1
Views: 8857

Which version of mpich2 is recommended for NEURON 7.4?

I am attempting to install NEURON in Linux for the first time, and I need it to work with mpich2. I've searched the documentation, but I can't find which version is best for NEURON 7.4. Does it matter?
by pascal
Sat Oct 29, 2016 6:58 pm
Forum: UNIX/Linux
Topic: unable to execute 'mpicc': No such file or directory
Replies: 5
Views: 13839

Re: unable to execute 'mpicc': No such file or directory

Whoops...yes, I meant /usr/lib64/openmpi/lib was in LD_LIBRARY_PATH. Okay, I re-installed openmpi from source, putting it in /usr/local/openmpi. Then I installed interviews in ~/local/iv. No problem. Then I tried installing nrn in ~/local/nrn, so that I would not have to use sudo to install it. Unfo...
by pascal
Fri Oct 28, 2016 1:48 pm
Forum: UNIX/Linux
Topic: unable to execute 'mpicc': No such file or directory
Replies: 5
Views: 13839

Re: unable to execute 'mpicc': No such file or directory

I checked, and /usr/lib64/openmpi/bin is already included in LD_LIBRARY_PATH. To install openmpi, I simply executed the command yum install openmpi openmpi-devel, and it apparently installed it in /usr/lib64. Should I perhaps uninstall it and then re-install in /usr/local ?
by pascal
Thu Oct 27, 2016 6:16 pm
Forum: UNIX/Linux
Topic: unable to execute 'mpicc': No such file or directory
Replies: 5
Views: 13839

unable to execute 'mpicc': No such file or directory

I am trying to install NEURON on CentOS 7. I need it to have parallel capabilities and work with Python, so I am following these steps: 1. Clone InterViews and NEURON sources into the current directory: hg clone http://www.neuron.yale.edu/hg/neuron/iv hg clone http://www.neuron.yale.edu/hg/neuron/nr...
by pascal
Wed May 25, 2016 11:14 am
Forum: UNIX/Linux
Topic: Installing NEURON on ROCKS cluster
Replies: 4
Views: 10980

Re: Installing NEURON on ROCKS cluster

Thanks for all the help, Michael. Just so everyone else can benefit, the solution was to issue the following installation commands in the /share/apps directory (installing in this directory makes the program available to all compute nodes in Rocks): ./configure --prefix=/share/apps/neuron-73 --with-...
by pascal
Sun May 22, 2016 12:50 pm
Forum: UNIX/Linux
Topic: Installing NEURON on ROCKS cluster
Replies: 4
Views: 10980

Re: Installing NEURON on ROCKS cluster

It turns out I spoke too soon. I *thought* everything was working fine because my simulations seemed to start all right, but then they crashed with the error message ./special: line 13: 18039 Killed “${NRNIV}” –dll “/share_home/cgfink/Documents/hfo/base_code/mod/x86_64/.libs/libnrnmech.so” “$@” Base...
by pascal
Wed May 18, 2016 2:32 pm
Forum: UNIX/Linux
Topic: Installing NEURON on ROCKS cluster
Replies: 4
Views: 10980

Re: Installing NEURON on ROCKS cluster

I figured out a simple solution. I just deleted the installation from the /exports/apps directory, and re-installed in the /share/apps directory. Everything works fine now.
by pascal
Tue May 17, 2016 1:10 pm
Forum: UNIX/Linux
Topic: Installing NEURON on ROCKS cluster
Replies: 4
Views: 10980

Installing NEURON on ROCKS cluster

I recently installed NEURON 7.3 on our small ROCKS cluster (running CentOS). I can run simulations just fine on the head node, but I cannot get NEURON to work on any other nodes. I get the following error message: /export/apps/neuron-73/x86_64/bin/nrniv: No such file or directory I believe the issue...
by pascal
Wed Jan 15, 2014 9:56 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Setting the global index with Random123
Replies: 1
Views: 1224

Setting the global index with Random123

A few years ago I went to the NEURON tutorial in La Jolla and received help writing a mod file which stimulated noisy synaptic events to a cell. It uses Random123, but there are no hoc calls to Random123--everything is done within the mod file. Within the INITIAL section, the two "identifier" seeds ...
by pascal
Sun Apr 14, 2013 9:43 pm
Forum: Other questions
Topic: Trouble with NEURON 7.3
Replies: 3
Views: 1297

Re: Trouble with NEURON 7.3

Actually, your suggestion to delete the old nrnmech.dll file and compile a new one worked--thanks so much!
by pascal
Sun Mar 24, 2013 6:00 pm
Forum: Other questions
Topic: Trouble with NEURON 7.3
Replies: 3
Views: 1297

Trouble with NEURON 7.3

I've been using NEURON 7.3 for about a year now, and it worked quite well on my old computer. Unfortunately, that computer died, and on my new computer I can't get NEURON 7.3 to successfully run the same files that worked on my old computer. My new one is a Windows 7 machine, as was my old one. Toda...
by pascal
Mon Dec 10, 2012 11:42 am
Forum: Specific models
Topic: Running the Santhakumar/Morgan model
Replies: 1
Views: 10968

Running the Santhakumar/Morgan model

I recently downloaded the Santhakumar/Morgan dentate gyrus model from ModelDB (listed as Model Number 231, Accession Number 124513). Unfortunately, when I run 50knet.hoc on both my machine (Windows 7, NEURON 7.3) and a Linux machine (NEURON 7.3), I get the following error: nrniv: syntax error in 50k...
by pascal
Sat Sep 29, 2012 10:18 pm
Forum: Other questions
Topic: Implementing "Extracellular stimulation and recording"
Replies: 2
Views: 1523

Re: Implementing "Extracellular stimulation and recording"

Thanks, Ted, that is very helpful.
by pascal
Thu Sep 27, 2012 12:28 pm
Forum: Other questions
Topic: Implementing "Extracellular stimulation and recording"
Replies: 2
Views: 1523

Implementing "Extracellular stimulation and recording"

I have inherited some code that implements the "Extracellular stimulation and recording" code, and it is *almost* working perfectly, except for one glitch. The network simulation is composed of 5-compartment pyramidal cells and 1-compartment basket cells. Recording the contribution of each compartme...
by pascal
Wed Aug 29, 2012 4:39 pm
Forum: Modeling networks
Topic: Activating netcons
Replies: 1
Views: 2156

Activating netcons

I am working to revise some code I've been given, and I noticed a curious block: synR.uniform(5, 10) co = pnm.nclist for ltr(xo, co) { sprint(cmd, "%s", xo.postcell) if(strcmp(cmd, "NULLobject")!=0) { sprint( cmd, "%s.active(1)", xo ) cvode.event(synR.repick(), cmd) //makes NetCon[#] active at rando...