Search found 19 matches

by vgoudar
Thu Dec 08, 2016 1:29 pm
Forum: Parallel NEURON
Topic: netcon enhancement
Replies: 5
Views: 6070

Re: netcon enhancement

Hi Ted, This is brilliant, thanks for that. Getting the "half-way" solution working seems straightforward with some refactoring of the python and mod code for synaptic transmission. I will try that first. To address the problem flexibly for long-term, I will need to apply the full solution you descr...
by vgoudar
Tue Dec 06, 2016 1:33 pm
Forum: Parallel NEURON
Topic: netcon enhancement
Replies: 5
Views: 6070

Re: netcon enhancement

Hi Ted, Thanks for that detailed response. I should have described our setup more clearly, I apologize for not doing that. Here goes: We are using the standard Tsodyks-Markram formulation of short-term synaptic plasticity, similar to the 2nd link you responded with. As you surmised, these dynamics a...
by vgoudar
Fri Dec 02, 2016 7:40 pm
Forum: Parallel NEURON
Topic: netcon enhancement
Replies: 5
Views: 6070

netcon enhancement

Hello, Im updating some old neuron code to speed it up by parallelizing it. The code simulates a network of IAF neurons and uses pointers to pass variables pertaining to synaptic state between neurons. While porting the code, I've had to do away with the pointers and move to the netcon/NET_RECEIVE f...
by vgoudar
Tue Apr 12, 2016 11:59 am
Forum: NEURON + Python
Topic: Problem with setdata on NEURON+Python
Replies: 3
Views: 5629

Re: Problem with setdata on NEURON+Python

Hi Ted,

Yes, you're absolutely right. FYI, IAF has a single compartment.

Thanks.
by vgoudar
Fri Apr 08, 2016 2:30 pm
Forum: NEURON + Python
Topic: Problem with setdata on NEURON+Python
Replies: 3
Views: 5629

Problem with setdata on NEURON+Python

Hi, Im trying to instantiate a distributed mechanism that continuously injects random noise into an IAF cell. To generate a random sample for the noise, Im passing in a random object from python. In the mod file for the noise mechanism, this is handled identically to the random variable in netstim.m...
by vgoudar
Mon Mar 28, 2016 12:31 pm
Forum: NEURON + Python
Topic: Netcon source in NEURON+Python
Replies: 4
Views: 5967

Re: Netcon source in NEURON+Python

Hi Ted,

Yup, certainly a bit "dense" of me to mix up density mechanisms with point processes. Thanks for walking me through that.

Best,
Vishwa
by vgoudar
Sun Mar 27, 2016 12:51 am
Forum: NEURON + Python
Topic: Netcon source in NEURON+Python
Replies: 4
Views: 5967

Re: Netcon source in NEURON+Python

Hi Ted, I see my problem. I should have done nc = h.NetCon(pre(0.5)._ref_spike_IAF,ss). But, since IAF is a distributed mechanism, I didn't see the point in saying pre(0.5)._ref_spike_IAF. Although I didn't mention it in my earlier post, I had tried nc = h.NetCon(pre._ref_spike_IAF,ss) and got an er...
by vgoudar
Fri Mar 25, 2016 5:24 pm
Forum: NEURON + Python
Topic: Netcon source in NEURON+Python
Replies: 4
Views: 5967

Netcon source in NEURON+Python

Hello, I'm trying to do something pretty basic: I'd like the NetCon source to be a variable from a distributed mechanism in the presynaptic cell rather than its voltage, as is usually the case. Python doesnt pass references around, and HOC appears to complain about the variable not being a reference...
by vgoudar
Fri Apr 18, 2014 3:28 am
Forum: Modeling networks
Topic: Error inserting model into soma
Replies: 1
Views: 6353

Error inserting model into soma

Hello, Im having some trouble inserting a custom model (that Ive tested and it works) into the soma, and Id appreciate some help. Here it the definition of my cell template. The big change has been that Im now dynamically determining the type of synapse I want used (see synapses() definition). After...
by vgoudar
Tue Feb 15, 2011 10:15 pm
Forum: UNIX/Linux
Topic: Installing neuron (nrn 7.1) with openmpi
Replies: 3
Views: 5359

Re: Installing neuron (nrn 7.1) with openmpi

Hi Dr. Hines, Thanks for the input. I did go back to the cluster admin and get their help installing it. Apparently, the modules werent loaded correctly. Im now running into a different problem while running on multiple processors with MPI on the cluster. Scripts run properly up until pc.runworker()...
by vgoudar
Wed Feb 09, 2011 9:45 pm
Forum: UNIX/Linux
Topic: Installing neuron (nrn 7.1) with openmpi
Replies: 3
Views: 5359

Installing neuron (nrn 7.1) with openmpi

Hi, Im unable to configure neuron on a cluster running openmpi. I face similar issues on my multicore server. The installation goes fine with mpich2 on the server. This is the command I used on the cluser running openmpi: ./configure --prefix=`pwd` --without-iv --with-paranrn --with-mpi The output t...
by vgoudar
Mon Jan 24, 2011 7:33 pm
Forum: UNIX/Linux
Topic: Installation errors on FreeBSD 8.1 port
Replies: 1
Views: 2682

Installation errors on FreeBSD 8.1 port

Hi, While compiling from source, I get the following errors while running make: termio.c:100:63: error: sgtty.h: No such file or directory termio.c:105: error: variable 'ntchars' has initializer but incomplete type termio.c:105: warning: excess elements in struct initializer termio.c:105: warning: (...
by vgoudar
Sat Jan 08, 2011 3:57 am
Forum: Parallel NEURON
Topic: net_move with C-N fixed step and NetCon between two pps
Replies: 2
Views: 2450

Re: net_move with C-N fixed step and NetCon between two pps

Great! Your solution to my second issue also fixed the problem seen with the first one. Thanks!
by vgoudar
Mon Dec 13, 2010 11:24 pm
Forum: Parallel NEURON
Topic: net_move with C-N fixed step and NetCon between two pps
Replies: 2
Views: 2450

net_move with C-N fixed step and NetCon between two pps

Hi, 1. Im seeing a difference in behavior when I run the following code, based on thether I use implicit fixed step or C-N fixed step in the numerical method selection: NET_RECEIVE(weight, release, dead) { LOCAL q INITIAL { release = 0 dead = 0 } if (flag == 0) { net_send(Delay,1) } else { q = (t - ...
by vgoudar
Mon Dec 13, 2010 11:03 pm
Forum: Parallel NEURON
Topic: Mutex locking and unlocking with nmodl
Replies: 3
Views: 1949

Re: Mutex locking and unlocking with nmodl

Yes, you make a good point about ordering of the events. So, assuming I limit my model to global time, why wouldnt pointers be thread safe if they share the process's address space? I guess it doesnt make a difference if I use mutexes because, even if I run with a single thread the events may still ...