www.neuron.yale.edu

Posted: **Fri Jun 16, 2023 3:26 am**

Dear Neuron Comunity,

I'm trying to run my model on a high performance computer (HPC). On my local computer everything runs fine, but if I run it on the HPC I get the following error:

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axon.insert('ks')
ValueError: argument not a density mechanism name.

I installed the latest version of Neuron 8.2.2
I use Python 3.10.4

I put all mod files in the same folder as the python code and recompiled the nrnmech.dll in this folder on the HPC. There were no errors.
I also used the remote desktop connection to the HPC, opened a console and run this short code snippet:

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from neuron import h

soma = h.Section(name='soma')

soma.insert('ks')

soma.psection()

This worked fine, no errors.
But when I try to run even this small example as a batch job I get the above mentioned error.

Does anyone know what could be the problem?

Best regards,
Anna

Posted: **Thu Jun 22, 2023 3:13 pm**

cd to the directory that contains your .py files. In that directory execute the command
nrniv

What is the message that NEURON prints to the terminal (that would be stdout on the HPC machine)?

That message should include a line that looks like this

Additional mechanisms from files

followed by a list of file names inside double quotes, for example

"foo.mod", "bah.mod" . . .

One, and only one, of those files should have a NEURON block that contains the statement

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SUFFIX ks

Is that indeed the case?

Posted: **Wed Jul 05, 2023 5:53 am**

Hello,

thank you for your reply. Unfortunatly, I can't run nrniv. I alwas get "command not found".

Best,
Anna

www.neuron.yale.edu

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