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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...

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...

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...

Hi Ted,

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

Thanks.

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...

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

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...

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...

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...

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()...

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...

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: (...

Great! Your solution to my second issue also fixed the problem seen with the first one. Thanks!

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 - ...

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 ...