NEURON-nightly and compiling mod files

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jared
Posts: 1
Joined: Tue May 21, 2024 4:02 pm

NEURON-nightly and compiling mod files

Post by jared »

Hi, all. I'm relatively new to NEURON. I am currently using NEURON version 8.2.4, but am interested in upgrading to the current nightly version, as it offers 3D diameter plotting in matplotlib and plotly (viewtopic.php?t=4677).

However, after upgrading (pip install NEURON-nightly), my mechanisms are not recognized. So, with an attempt to recompile my mod files, errors are thrown, even though they compile fine in 8.2.4.
Also, It is unique to individual mod files. Removing the ones reported in the errors, reveals a few that compile properly.

Here's the output from nrnivmodl:
cfiles =
Mod files: "kLT_VCN2003.mod" "khurana_ih.mod" "khurana_klva.mod" "krl_scott_KLVA.mod" "krl_scott_ih.mod" "leak.mod" "mathewsIH.mod" "mathews_KLT.mod" "mathews_KLT2.mod" "mathews_KLVA.mod" "mathews_NA.mod"

MODOBJS= ./kLT_VCN2003.o ./khurana_ih.o ./khurana_klva.o ./krl_scott_KLVA.o ./krl_scott_ih.o ./leak.o ./mathewsIH.o ./mathews_KLT.o ./mathews_KLT2.o ./mathews_KLVA.o ./mathews_NA.o
-> Compiling mod_func.cpp
-> NMODL ../khurana_ih.mod
-> NMODL ../kLT_VCN2003.mod
-> NMODL ../khurana_klva.mod
Translating khurana_klva.mod into /Users/.../x86_64/khurana_klva.cpp
Translating kLT_VCN2003.mod into /Users/.../x86_64/kLT_VCN2003.cpp
Translating khurana_ih.mod into /Users/.../x86_64/khurana_ih.cpp
Notice: VERBATIM blocks are not thread safe
Error: r_inf used as both variable and function in file khurana_ih.mod
Notice: This mechanism cannot be used with CVODE
Error: tau_z used as both variable and function in file khurana_klva.mod
Warning: Default 22 of PARAMETER celsius will be ignored and set by NEURON.
Warning: Default -70 of PARAMETER ek will be ignored and set by NEURON.
make: *** [khurana_ih.cpp] Error 1
make: *** Waiting for unfinished jobs....
make: *** [khurana_klva.cpp] Error 1
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.12/bin/nrnivmodl", line 115, in <module>
subprocess.check_call([exe, *sys.argv[1:]])
File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/neuron/.data/bin/nrnivmodl']' returned non-zero exit status 2.

If this is an intentional change in how mod files are handled and the only solution is to rewrite/reformat them, then I'll begin learning NMODL. Just trying to see how best to proceed.
ted
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Re: NEURON-nightly and compiling mod files

Post by ted »

Interesting. Needs to be brought to the attention of the NEURON development team. Regarding what you should do, if your goal is to do science, decide what's most important to you--cosmetics, or results; spending time trying to work around problems in development code, or addressing scientific problems that will gain credit for you and your colleagues--and then proceed accordingly. If your goal is to be a software developer, then join the NEURON development team, work to fix the problems that you encountered, and get the credit for that.
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