undefined symbol: nrnmpi_myid

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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aeronlaffere
Posts: 6
Joined: Thu Apr 19, 2018 10:53 am

undefined symbol: nrnmpi_myid

Post by aeronlaffere » Tue Sep 18, 2018 12:34 pm

When trying to import compiled mechanisms into a NEURON model in the Python environment I get this error.

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loading membrane mechanisms from x86_64/.libs/libnrnmech.so
dlopen failed - 
x86_64/.libs/libnrnmech.so: undefined symbol: nrnmpi_myid
This error does not appear when starting NEURON with nrniv or nrngui. However, I still come across the following error when attempting to load from my model file.

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NEURON: syntax error
 in reduced_model.hoc near line 49
 	insert ih
          ^
        xopen("reduced_mo...")
      execute1("{xopen("re...")
    load_file("reduced_mo...")
This happens in Python and NEURON. I think it has to do with the failure to load indicated by the initial error message in both cases. I know others have brought up the undefined symbol: nrnmpi_myid error before but none of the answers given so far seemed relevant.

ted
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Location: Yale University School of Medicine
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Re: undefined symbol: nrnmpi_myid

Post by ted » Tue Sep 18, 2018 2:12 pm

Open a terminal and execute the command
neurondemo
Do you see a message in the terminal that looks something like

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loading membrane mechanisms from /home/ted/bin/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
 cabpump.mod cachan1.mod . . .
and do you also see a bunch of NEURON-related windows such as the NEURON Main Menu toolbar, a RunControl panel etc.?

aeronlaffere
Posts: 6
Joined: Thu Apr 19, 2018 10:53 am

Re: undefined symbol: nrnmpi_myid

Post by aeronlaffere » Tue Sep 18, 2018 4:20 pm

Thanks for the quick reply. Yes, the following appears along with NEURON Demonstrations, RunControl, and VariableTimeStep windows.

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NEURON -- VERSION 7.5 master (6b4c19f) 2017-09-25
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2016
See http://neuron.yale.edu/neuron/credits

loading membrane mechanisms from /usr/local/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
 cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod

ted
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Re: undefined symbol: nrnmpi_myid

Post by ted » Tue Sep 18, 2018 4:30 pm

Aha. Uninstall your current version of NEURON, and install the latest version for your particular operating system, which plays much more nicely with Python and shouldn't generate the error message you were getting. You will have to delete any old x86_64 directories and their contents, and recompile mod files.

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