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I have been trying to install Neuron 7.3 on a Bluegene/P machine using the two step process that I had earlier used for the compilation of Neuron on a Cray XE6 machine. The specific steps are: ./configure --prefix=`pwd` --enable-bluegeneP --with-nmodl-only followed by make, make install and ./config...

Thanks a bunch, this is indeed very helpful.

Thanks Ted. What I meant was: I use connect axon(0), soma(1) which is basically a ball and stick model, similar to your toy example. So in summary (using your toy example), the path resistance at the connection between soma and dend is between soma(1) and dend(0) and not between soma(0.5) and dend(0...

With some help I have been able to tackle the mod file. The question that I now have is: say that a soma (nseg=1) is connected to an axon (nseg=3), does ri at axon position 0 mean that the path resistance is calculated between soma(position = 1) and axon(position = 0) or is it between soma(position=...

I wanted to compute the time course of axial currents as a function of space and time in multi-compartment models. To this effect Mike had proposed that I write a mod file whereby the axial current is implemented as a density mechanism. I cooked up the following mod file to achieve this (note that p...

Thanks Ted. My code presently runs on Crays, although I and Michael had to go through a tenuous iterative process to get it working. The aspect that I would really like to avoid is passing 20s of parameters in a compound statement -- what I had in my mind was something like a XML file that can be pi...

I am using a PBS script to initiate Montecarlo runs on 100s of processors. Can anyone please suggest me the best way to pass arguments to a hoc file in a PBS script i.e., instead of executing: aprun -n 320 x86_64/special -mpi foo which works well, I would like to execute something like the following...

Yes, I realized that after posting my query in the BB. The reason step 3 had failed previously was due to the fact that I used cc and CC, the compiler wrappers provided on XE6 instead of the standard gcc and g++. Even after successfully finishing step 3, the next hurdle to cross is static linking . ...

I have been trying to install Neuron 7.3 on our Cray XE6. Are there any specific make rules that needs to be followed to get a working NEURON installation? I have even tried to follow the instructions by Michael in http://www.neuron.yale.edu/phpBB/viewtopic.php?f=6&t=2277&p=8800&hilit=cr...

Thanks Ted for your speedy reply and the link to the reference! Could you let me know of a reference that studies which of the ions is the major intracellular charge carrier?

Hi Ted/Michael, I seek your advice in modelling a two compartment model (a sphere and a cylinder) with their respective Na/K currents. Both soma and the dendrite have a Na/K pump of the form ipumpsoma[t] = gpump*(3*(vsoma[t]- revpot[nain[t], naout[t]]) - 2*(vsoma[t] - revpot[kin[t], kout[t]])- EATPs...