Search found 1686 matches
- Wed Aug 30, 2023 8:02 pm
- Forum: Reaction-diffusion in NEURON
- Topic: MultiCompartmentReaction across sections
- Replies: 6
- Views: 13387
Re: MultiCompartmentReaction across sections
I've run the address sanitizer several times and upon ^C have always ended up at nrn-enable-sanitizer --preload python3 -i test.py ... Adding flux to exc. synapse 500/500 in spine 2/2: prend seg = spine[1](0.5), postnd seg = dend[65](0.5) Starting simulation ^CAddressSanitizer:DEADLYSIGNAL =========...
- Wed Aug 30, 2023 4:35 pm
- Forum: MSWin
- Topic: MSWin11 + Anaconda, Neuron 8.2.2
- Replies: 6
- Views: 15942
Re: MSWin11 + Anaconda, Neuron 8.2.2
Perhaps this is now somewhat stale. But if your windows11 computer is available, I would be happy to have a zoom meeting where you could share your screen and we might work through the issue. If you wish to proceed, contact me at michael dot hines at yale dot edu. The first thing to diagnose is the ...
- Wed Aug 30, 2023 2:23 pm
- Forum: Other questions
- Topic: Analyzing pointers
- Replies: 1
- Views: 11414
Re: Analyzing pointers
I'm sorry to say that in NEURON version 8 and before , the interpreters do not store the information used to determine the address. And in the internal implementation the only way to know what a pointer was pointing to was to search all internal data structures. This, of course, made it very inconve...
- Wed Aug 30, 2023 1:37 pm
- Forum: Reaction-diffusion in NEURON
- Topic: MultiCompartmentReaction across sections
- Replies: 6
- Views: 13387
Re: MultiCompartmentReaction across sections
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python3 mycode.py 2 10
I also built the master using the address sanitizer and there were no substantive complaints (only some memory leaks), so there is a possibility that the bug was fixed after 8.1.0.
- Wed Aug 09, 2023 8:13 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: NMODL code no longer works in version 8.2
- Replies: 7
- Views: 14504
Re: NMODL code no longer works in version 8.2
scoplib_ansi.h was removed from the system back in Jan 2022. I expect you need a clean folder where you type nrnivmodl. Just remove all the *.o, *.c, *.cpp, *.dll files from your folder. (and remove the x86_64 folder if it exists in your folder)
- Wed Aug 09, 2023 4:11 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: NMODL code no longer works in version 8.2
- Replies: 7
- Views: 14504
Re: NMODL code no longer works in version 8.2
No warnings?successful compilation
I would prefer accurate use of types. I.e.
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nrnran123_State*
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void*
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uint32_t
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int
- Mon Aug 07, 2023 8:11 pm
- Forum: Adding new mechanisms and functions to NEURON
- Topic: NMODL code no longer works in version 8.2
- Replies: 7
- Views: 14504
Re: NMODL code no longer works in version 8.2
try replacing the three lines #define VOIDCAST void** vp = (void**)(&(_p_ptr)) extern void * nrnran123_newstream(int,int); extern void nrnran123_deletestream(void *); with the single line #define VOIDCAST nrnran123_State** vp = (nrnran123_State**)(&(_p_ptr)) and also *vp = nrnran123_newstrea...
- Fri Jun 02, 2023 6:42 am
- Forum: UNIX/Linux
- Topic: configuring neuron on a cluster with a local install of python - and getting it to use that python with nrniv -python
- Replies: 3
- Views: 31269
Re: configuring neuron on a cluster with a local install of python - and getting it to use that python with nrniv -pytho
Perhaps this is beside the point since the configuration mentioned nothing about what in cmake is -DNRN_ENABLE_PYTHON_DYNAMIC=ON I mention it because usually it is in that context that multiple python installations allow the wrong choice at runtime for libpython..so If runtime dynamic loading is NOT...
- Fri Jun 02, 2023 6:16 am
- Forum: Parallel NEURON
- Topic: Thread-safe non-voltage POINTER variables
- Replies: 4
- Views: 12935
Re: Thread-safe non-voltage POINTER variables
Multisplit will not provide a complete parallel solution as it is limited to voltage as the coupling variable between compartments. However it does suffice for the stiff (very small time constants can be a source of numerical instability and voltage coupling between small compartments is very large)...
- Thu Jun 01, 2023 12:23 pm
- Forum: Parallel NEURON
- Topic: Thread-safe non-voltage POINTER variables
- Replies: 4
- Views: 12935
Re: Thread-safe non-voltage POINTER variables
I'm afraid the model that coelesced in my mind after reading your post is unlikely to be the same as your existing (working serial?) model. I'm imagining a few states per compartment of a cell that are coupled to the corresponding states of adjacent compartments of the same cell via fluxes that are ...
- Tue Dec 20, 2022 8:39 pm
- Forum: Parallel NEURON
- Topic: NEURON: The total number of cells, 1, is different than the number of user partition cells, 0
- Replies: 2
- Views: 6901
Re: NEURON: The total number of cells, 1, is different than the number of user partition cells, 0
parcom.hoc is only for load balancing an already existing network model (or large cell). To make your 4 line fragment work , the 4 lines must be moved after cell = Section() However, I believe your purpose can be better achieved with pc = h.ParallelContext() pc.nthread(16) # assuming you have 16 cor...
- Tue Nov 15, 2022 7:39 am
- Forum: UNIX/Linux
- Topic: [SOLVED] Unable to run nrniv -python with NEURON 8.0.0 installed via pip
- Replies: 6
- Views: 14504
Re: Unable to run nrniv -python with NEURON 8.0.0 installed via pip
The problem is that nrnpyenv.sh cannot figure out the location of the shared python library. (I can't remember how the neuron wheel was configured but assume it was with NRN_ENABLE_DYNAMIC_PYTHON=ON. Please check with nrniv nrnversion(6) ) If that really is the case, then a correct value for the NRN...
- Tue Nov 15, 2022 2:48 am
- Forum: UNIX/Linux
- Topic: [SOLVED] Unable to run nrniv -python with NEURON 8.0.0 installed via pip
- Replies: 6
- Views: 14504
Re: Unable to run nrniv -python with NEURON 8.0.0 installed via pip
If you are happy with launching python instead of nrniv, then fine and we can consider the issue closed. If you do wish to resolve the nrniv -python issue then I'm happy to help lead you through the diagnosis and hopefully a solution. To start, I'll need to know the complete output of the above comm...
- Sat Sep 17, 2022 3:26 pm
- Forum: OS X
- Topic: nrngui not opening main menu GUI on startup on M1 Mac
- Replies: 13
- Views: 22503
Re: nrngui not opening main menu GUI on startup on M1 Mac
Hmmm. Maybe anaconda does now have an M1 version.
https://www.anaconda.com/blog/new-relea ... porting-m1
But it is surprising that the filename of the download is Anaconda3-2022.05-MacOSX-x86_64.pkg. so I guess I'm skeptical that that is a universal2 installer.
https://www.anaconda.com/blog/new-relea ... porting-m1
But it is surprising that the filename of the download is Anaconda3-2022.05-MacOSX-x86_64.pkg. so I guess I'm skeptical that that is a universal2 installer.
- Sat Sep 17, 2022 3:18 pm
- Forum: OS X
- Topic: nrngui not opening main menu GUI on startup on M1 Mac
- Replies: 13
- Views: 22503
Re: nrngui not opening main menu GUI on startup on M1 Mac
Please see https://nrn.readthedocs.io/en/latest/install/install_instructions.html#mac-os with special attention to the information that begins Universal2 installers generally “just work” on either an x86_64 or arm64 architecture. Your problem is that nrniv is a universal program that starts up by de...