Hi,
I have installed NEURON v7.3 in my Macbook with OS X 10.7.5. And I have installed the Xcode v4.5 as well as the latest version of the command line developer tools to compile mod files as suggested.
The problem is, when I try to use terminal to run it, it shows "-bash: nrnivmodl: command not found".
I also tried to first double click the ion button and then drag the entire folder that contains the mod file into the terminal window, but after I enter the return button, the window disappeared with nothing changes in the file.
Could you please help me solve this problem? Many thanks.
Problems running NEURON
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Re: Problems running NEURON
Let me guess--you installed NEURON from the dmg, right?
Can you tell if NEURON is even on your path? In the terminal enter this command
echo $PATH
and tell me what you get.
Can you tell if NEURON is even on your path? In the terminal enter this command
echo $PATH
and tell me what you get.
Re: Problems running NEURON
Hi Ted,
Thanks for your reply! Your guess is exactly right, I installed NEURON from the dmg.
If I enter the command echo $PATH in the terminal, the following shows up,
applematoMacBook-Pro-3:~ apple$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/texbin
Thanks for your reply! Your guess is exactly right, I installed NEURON from the dmg.
If I enter the command echo $PATH in the terminal, the following shows up,
applematoMacBook-Pro-3:~ apple$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/texbin
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Re: Problems running NEURON
Since your PATH environment variable does not contain NEURON, you can only compile mod files by dragging and dropping the folder that contains the mod files onto the mknrndll icon. I suppose there's a way to change your PATH variable so you will be able to compile mod files and launch NEURON from a terminal, but I'll have to find out exactly what has to be added to the PATH and get back to you.
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Re: Problems running NEURON
OK, here's what to do. This assumes that you dragged NEURON into Applications.
First open a terminal and at the system prompt enter the commandThen in that terminal enter the commandNEURON should start up and the NEURON Main Menu toolbar should appear.
If that works, quit NEURON, and execute the commandLook for a file called .bashrc or .bash_profile.
Open that file with a plain text editor and insert the following linethen save the file.
Log out of OS X.
The next time you log in, you should be able to run nrngui, nrniv, and nrnivmodl (or mknrndll if that's what it's called in OS X) from the command line.
First open a terminal and at the system prompt enter the command
Code: Select all
export PATH=/Applications/NEURON-7.3/nrn/x86_64/bin
Code: Select all
nrngui
If that works, quit NEURON, and execute the command
Code: Select all
ls -a
Open that file with a plain text editor and insert the following line
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export PATH=/Applications/NEURON-7.3/nrn/x86_64/bin
Log out of OS X.
The next time you log in, you should be able to run nrngui, nrniv, and nrnivmodl (or mknrndll if that's what it's called in OS X) from the command line.
Re: Problems running NEURON
Hi Ted,
I try to follow your procedure, it's okay that I can run after enter the command
But when I try to use , the terminal returns command not found. It seems I cannot use any command after the export. Do you have any idea how to continue? Many thanks!
I try to follow your procedure, it's okay that I can run
Code: Select all
nrngui
Code: Select all
export PATH=/Applications/NEURON-7.3/nrn/x86_64/bin
Code: Select all
ls -a
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Re: Problems running NEURON
Oops, that should have been
If you can edit .bashrc or .bash_profile, whichever it was, and make this change, then log out and log back in, everything should be OK.
Code: Select all
export PATH=$PATH:/Applications/NEURON-7.3/nrn/x86_64/bin
Re: Problems running NEURON
Yes, it works now. Thanks a lot!
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Re: Problems running NEURON
Glad to hear that it works.