Search found 20 matches

by zyc
Wed Feb 20, 2019 1:17 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 10427

Re: Driving synaptic event using vecStim

It works, thank you so much.
by zyc
Mon Feb 18, 2019 2:36 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 10427

Re: Driving synaptic event using vecStim

I tried to introduce "bbcore_write" and "bbcore_read" from netstim.mod into our vecstim.mod, but got some errors when compiling the mechanism file with CoreNEURON. The following shows modified code, did I do anything wrong? Thanks! NEURON { THREADSAFE ARTIFICIAL_CELL VecStim BBCOREPOINTER ptr } ASSI...
by zyc
Thu Jul 19, 2018 2:55 am
Forum: Anatomically detailed models
Topic: Use import3D_swc_read to read the morphology from swc file
Replies: 2
Views: 1296

Use import3D_swc_read to read the morphology from swc file

Dear all I have some problems while using import3D_swc_read() to read swc file. I notice that there are more than 9000 3D points in swc file, but when I load this swc file into NEURON, it shows that this model contains only 1974 segments. I guess some 3D points in swc are merged when I use import3D_...
by zyc
Thu Jun 14, 2018 3:43 am
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 1740

Re: Numerical methods in NEURON

Thank you so much!
by zyc
Mon Jun 11, 2018 12:41 am
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 1740

Re: Numerical methods in NEURON

Thank you, I'm more clear now. I see that in "nrn_fixed_step_thread" function, mainly three steps are done: 1) setup_tree_matrix 2) solve the tree matrix 3) update. So step 1) is to setup the matrix ( I - dt * f ( y (t+dt),t)), step 2) is to get the inverse of matrix, is that true? If it's true, why...
by zyc
Sun Jun 10, 2018 10:29 pm
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 1740

Re: Numerical methods in NEURON

Thank you for replying. I watched the source code of NEURON, and I found that when NEURON computes the ion channels (e.g. hh.c), there are two statements: NODERHS(_nd) -= _rhs; NODED(_nd) += _g; so I think the matrix represent the conductance and rhs represent current. When current is computed by i=...
by zyc
Sat Jun 09, 2018 2:24 am
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 1740

Numerical methods in NEURON

Dear all I am reading the NEURON book and try to understand the numerical methods in NEURON. In my understanding, when NEURON integrate one step, it first setup a matrix GV=I, where G is the Hines matrix representing the conductance, I is the current vector (including axial current, injected current...
by zyc
Tue Oct 17, 2017 1:55 am
Forum: Parallel NEURON
Topic: A multi-gpu version of CoreNEURON
Replies: 0
Views: 12732

A multi-gpu version of CoreNEURON

We have optimized the previous single GPU version of CoreNEURON and extended it to multi-GPU version, which can be downloaded at https://github.com/pkuzyc/Multi-GPU-CoreNeuron . The current version can work on single GPU server or GPU cluster. We have tested the sample model enclosed in the original...
by zyc
Thu May 04, 2017 4:11 am
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 24050

Re: How to build network model for coreNeuron 

Hello, is coreNeuron able to use two or more GPUs? I have tried to use two threads to run ringtest and it generate two network files after nrnbbcore_write(). However, when I use two threads to run this model by coreNeuron, only one GPU is used. Could you please tell me is coreNeuron able to use mult...
by zyc
Tue Apr 25, 2017 5:57 am
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 24050

Re: How to build network model for coreNeuron 

I built a stimulus model by NMODL and I want to run simulation on coreNeuron. It run well on CPU but cannot run on GPU. I found the reason is that I defined all the variables in PARAMETER block. After I move two variables into ASSIGNED block, it can run on GPU. Could you please tell me why it happen...
by zyc
Tue Apr 11, 2017 11:22 am
Forum: NEURON + Python
Topic: Some errors when I run ringtest.py
Replies: 5
Views: 9923

Re: Some errors when I run ringtest.py

The Neuron I use is downloaded from github, and the version is 7.5, not 7.4. I compile it from source. It shows the version information like that because the Neuron on github doesn't have the file "nrnversion.h", I copied nrnversion.h from an already installed neuron.
by zyc
Tue Apr 11, 2017 3:43 am
Forum: NEURON + Python
Topic: Some errors when I run ringtest.py
Replies: 5
Views: 9923

Some errors when I run ringtest.py

I installed the neruon from github, the python version is 2.7.12. When I tried to run ringtest.py, there arised some errors. When import neuron, it prints: .libs/libnrnmech.so: undefined symbol: hoc_register_dparam_semantics When I run "python ringtest.py", it prints: AttributeError 'hoc.HocObject' ...
by zyc
Fri Mar 24, 2017 8:53 am
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 24050

Re: How to build network model for coreNeuron 

Thank you!
by zyc
Thu Mar 23, 2017 10:44 am
Forum: Parallel NEURON
Topic: How to build network model for coreNeuron 
Replies: 24
Views: 24050

Re: How to build network model for coreNeuron 

Thank you so much, I can successfully use coreNeuron on my machine with your patient help. I have another question. Could you please tell me how can I set the stim for a cell when I do simulation on coreNeuron?