Search found 70 matches

by Krishna Chaitanya
Sat Aug 31, 2013 3:23 am
Forum: Parallel NEURON
Topic: Splitting on a single machine.
Replies: 4
Views: 2552

Re: Splitting on a single machine.

Dear Ted, Thank you very much for the answer. Another problem I have is with pc.gid2cell. I have gone through the reference you quoted and found that for pc.gid2cell to work, it needs connect2target function. If I don't have connect2target function in my cell template, it is giving me this error: 1 ...
by Krishna Chaitanya
Fri Aug 30, 2013 1:30 am
Forum: Parallel NEURON
Topic: Splitting on a single machine.
Replies: 4
Views: 2552

Splitting on a single machine.

Hi, I have a very basic question on splitting a group of cells over 'n' processes on a single machine. I have 4000 cells which were distributed over 3 processes. I have used the usual syntax "for (i=pc.id; i<$1; i+=pc.nhost)". And the gid is assigned with "pc.setgid2node(i, pc.id)" to that process. ...
by Krishna Chaitanya
Sat Dec 29, 2012 11:26 pm
Forum: Other questions
Topic: Accessing neuron variables in MATLAB
Replies: 1
Views: 1243

Accessing neuron variables in MATLAB

Hi, I wanted to run a neuron simulation from MATLAB, which I did with the command "!nrngui <file.hoc>". Later I wanted to calculate spikes with APCount procedure in NEURON and return it to MATLAB variable for further computation. One way is to create file, store value into it and open it in MATLAB. ...
by Krishna Chaitanya
Wed Oct 03, 2012 4:58 am
Forum: Parallel NEURON
Topic: Print values from slave nodes
Replies: 1
Views: 1473

Print values from slave nodes

Hi, Is there a way to know how many cells each node has received through print command? Though it distributes via round robin, I am interested in knowing through print command. And also when I try to print the positions of a large group of cells distributed through round robin, I am only able to see...
by Krishna Chaitanya
Sat Apr 21, 2012 2:49 am
Forum: UNIX/Linux
Topic: NEURON installation with Python and MPICH2
Replies: 7
Views: 5791

NEURON installation with Python and MPICH2

Hi, When I try to compile neuron source code (nrn-7.3 and iv-18) with the following options: ./configure --prefix=`pwd` --with-nrnpython=/usr/bin/python --with-iv=../iv --with-paranrn make It gives me the following errors: /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32 a...
by Krishna Chaitanya
Fri Apr 20, 2012 7:30 am
Forum: Modeling networks
Topic: Playing vector values to a section voltage.
Replies: 1
Views: 1690

Playing vector values to a section voltage.

Hi, I have a spikegenerator and a dummy section. I wanted to play spikegenerator values into dummy section voltage. Should it be done in the following way? vect.play(&dummy.v(0.5), tvec) where vect contains recorded values of spikegenerator run for 100 msec. tvec is the vector contains 't' value for...
by Krishna Chaitanya
Fri Apr 20, 2012 6:26 am
Forum: NEURON + Python
Topic: Section creation
Replies: 2
Views: 1863

Re: Section creation

Dear mctavish,

Thank you very much for your detailed explanation illustrated with examples. It helped me a lot in understanding the usage of "cell=self". Thank you once again.
by Krishna Chaitanya
Tue Apr 17, 2012 12:46 am
Forum: NEURON + Python
Topic: Section creation
Replies: 2
Views: 1863

Section creation

Hi,

If I use,

self.hillock = [h.Section(cell=self)]

In the above syntax, why should we use "cell=self"? What is the importance of that? Thank you.
by Krishna Chaitanya
Thu Apr 05, 2012 8:54 pm
Forum: Parallel NEURON
Topic: Splitbit value assignment
Replies: 2
Views: 2322

Re: Splitbit value assignment

Dear mctavish,

Thank you very much for the in detail explanation about splitbit assignment in your model.
by Krishna Chaitanya
Thu Apr 05, 2012 8:18 am
Forum: Parallel NEURON
Topic: Splitbit value assignment
Replies: 2
Views: 2322

Splitbit value assignment

Hi,

In https://senselab.med.yale.edu/modeldb/S ... \split.hoc, what does splitbit refer to? How is it calculated? I didn't understand on what basis they are assigning splitbit values.

Can anyone kindly let me know. Thank you.
by Krishna Chaitanya
Mon Apr 02, 2012 10:37 pm
Forum: Parallel NEURON
Topic: Network Multisplit Problem
Replies: 3
Views: 1923

Re: Network Multisplit Problem

Dear Ted,

Thank you very much for the reply. Please kindly let me know the corrections in the file. Thank you.
by Krishna Chaitanya
Sun Apr 01, 2012 6:24 am
Forum: Parallel NEURON
Topic: Network Multisplit Problem
Replies: 3
Views: 1923

Network Multisplit Problem

Hi, When I am trying to test a network with multisplit method described in Hines 2008 paper, the following error results. all not a public member of GrC 0 /mirror/neuron/nrn-7.3/x86_64/bin/nrniv: GrC all 0 in init1.hoc near line 95 0 model() ^ 0 CellBalanceInfo[0].msdiv(GrC[0], SectionRef[8], 100, P...
by Krishna Chaitanya
Wed Mar 28, 2012 10:39 pm
Forum: Parallel NEURON
Topic: Parallel Context Source Var and Target Var Usage
Replies: 2
Views: 1325

Re: Parallel Context Source Var and Target Var Usage

Dear Ted,

Thank you very much for your quick reply. I have gone through the examples which you posted here from modeldb which were very useful in understanding. Thank you.
by Krishna Chaitanya
Mon Mar 26, 2012 11:08 pm
Forum: Parallel NEURON
Topic: Parallel Context Source Var and Target Var Usage
Replies: 2
Views: 1325

Parallel Context Source Var and Target Var Usage

Hi, I have come across pc.source_var and pc.target_var functions which were meant to be used for synaptic communication and gap junctions. And if I wanted to use them for synaptic communication, how can I use them? Considering with an example, I have AMPA synapse connected to Multi Compatment Granul...
by Krishna Chaitanya
Thu Mar 15, 2012 9:46 am
Forum: Parallel NEURON
Topic: Synaptic input problem when run with mpi
Replies: 0
Views: 1157

Synaptic input problem when run with mpi

Hi, I recently tried to parallelize multi compartmental granule cell model (Diwakar, 2009). I followed similar approach described in "Translating network models to parallel hardware" and found that I couldn't get synaptic input to my model through spikegenerators. The model has AMPA, NMDA and GABA s...