Scripting multiple simulations about hnn HOT 6 CLOSED

I couldn't get this to work on our Linux server, so I ended up going with hnn-core. That works well on the Linux server. Thanks!

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You might be interested in https://github.com/jonescompneurolab/hnn-core

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@tbardouille Here's the workaround for HNN right now. It's a workaround until hnn-core is integrated with HNN. Hence, the lack of documentation. Note that if you use hnn-core right now, each simulation trial will only run on a single core.

1. Generate individual parameter files for each parameter combination. Additionally, change the sim_prefix parameter to be unique for each file.

2. Script running HNN's run.py over the different files. The number of trials can be specified in the .param file or on the command line via ntrial 3.

mpiexec -np 16 nrniv -mpi -python -nobanner run.py param/default.param

3. Terminal output will be similar to the simulation log in the GUI. Results will be saved in ~/hnn_out/data/[sim prefix]/

4. View results in the GUI with the 'Set Parameters from File' button and choosing the appropriate parameter file in ~/hnn_out/param/[sim prefix]/

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Thanks for the advice. I installed Open-MPI on my Mac (v 4.0.4) so that I can run mpiexec. This installed fine, and I made a copy of AlphaAndBeta.param to test with. However, I have a problem when I run run.py, as follows (with standard output shown).

Any advice would be appreciated. Thanks.

$ mpiexec -np 4 nrniv -mpi -python -nobanner run.py param/AlphaAndBeta_testScript.param
numprocs=4
making dout: /Users/tbardouille/hnn_out/data/AlphaAndBeta
Traceback (most recent call last):
File "run.py", line 254, in
net = network.NetworkOnNode(p) # create node-specific network
File "/Users/tbardouille/GitHub/hnn/network.py", line 92, in init
self.__create_all_src()
File "/Users/tbardouille/GitHub/hnn/network.py", line 296, in __create_all_src
self.cells.append(L2Basket(gid, pos))
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 22, in init
self.__biophysics()
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 32, in __biophysics
self.soma.insert('hh2')
ValueError: argument not a density mechanism name.

Traceback (most recent call last):
File "run.py", line 254, in
net = network.NetworkOnNode(p) # create node-specific network
File "/Users/tbardouille/GitHub/hnn/network.py", line 92, in init
self.__create_all_src()
File "/Users/tbardouille/GitHub/hnn/network.py", line 296, in __create_all_src
self.cells.append(L2Basket(gid, pos))
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 22, in init
self.__biophysics()
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 32, in __biophysics
self.soma.insert('hh2')
ValueError: argument not a density mechanism name.

Traceback (most recent call last):
File "run.py", line 254, in
net = network.NetworkOnNode(p) # create node-specific network
File "/Users/tbardouille/GitHub/hnn/network.py", line 92, in init
self.__create_all_src()
File "/Users/tbardouille/GitHub/hnn/network.py", line 296, in __create_all_src
self.cells.append(L2Basket(gid, pos))
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 22, in init
self.__biophysics()
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 32, in __biophysics
self.soma.insert('hh2')
ValueError: argument not a density mechanism name.

Traceback (most recent call last):
File "run.py", line 254, in
net = network.NetworkOnNode(p) # create node-specific network
File "/Users/tbardouille/GitHub/hnn/network.py", line 92, in init
self.__create_all_src()
File "/Users/tbardouille/GitHub/hnn/network.py", line 296, in __create_all_src
self.cells.append(L2Basket(gid, pos))
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 22, in init
self.__biophysics()
File "/Users/tbardouille/GitHub/hnn/L2_basket.py", line 32, in __biophysics
self.soma.insert('hh2')
ValueError: argument not a density mechanism name.

from hnn.

@tbardouille I suspect this is from the NEURON .mod files not getting compiled. After typing make on a mac/linux in the hnn directory, there should be a folder x86_64. Is that the case?

You may have already seen these instructions, but in case they are of help, here's the link:
https://jonescompneurolab.github.io/hnn/installer/mac/native_install.html

from hnn.

Please let us know if you are still having this issue. Closing for now.

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