COMPILING HOC FILES FROM TERMINAL IN UBUNTU

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mazid
Posts: 6
Joined: Tue Feb 10, 2015 1:14 pm

COMPILING HOC FILES FROM TERMINAL IN UBUNTU

Post by mazid » Fri Dec 18, 2015 9:46 pm

HI,
I've been trying to re-run an old project made with NEURON7.3 on OSX, on Ubuntu with the 64 bit .deb linux version. The project was working fine under OSX but now i cant re-run and do some new experimentation on it.
I execute this command:

Code: Select all

nrngui CA1_Final_Geometry.hoc
And get this :
/usr/local/nrn/x86_64/bin/nrniv: Couldn't find: all_tau_vecs.hoc
in CA1_Final_Geometry.hoc near line 9
load_file("all_tau_vecs.hoc")
^
0
Which i don't understand because the all_tau_vecs.hoc is really present in the folder. So NEURON must have seen it.
Then in order to make some test i put that line in comments and try to run. Then I got this:
/usr/local/nrn/x86_64/bin/nrniv: table not specified in hoc_func_table
near line 1
run()
^
fadvance()
advance()
step()
continuerun(1e+06)
and others
This is the first line which is important. But i'vent define any hoc_func_table. Early guess is , this something relatable with the NEURON implementation.
I've been looking for similar problem but i couldn't find one, so i made this post. Thank you for your help.

ted
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Location: Yale University School of Medicine
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Re: COMPILING HOC FILES FROM TERMINAL IN UBUNTU

Post by ted » Fri Dec 18, 2015 11:18 pm

FYI hoc is not a compiled language. It is an interpreted language.

Now on to your problem.

First, is NEURON working properly on your Ubuntu machine? Test by executing
neurondemo
then click on "Release"
and finally click on "Init & Run" in the RunControl panel. That should launch a simulation that generates many plots.

Second, does your old model implementation involve any mod files? If yes, you'll have to recompile them. You may have already done this, but if not . . . delete any .dll file that you might have brought along from what was on the Mac. Also delete any .o or .c files, as well as any i686 or x86_64 directories and their contents. Then at the system prompt execute nrnivmodl to compile the mod files. Having done that, when you execute
nrngui
at the system prompt, NEURON will start and load the compiled mechanisms, and it will also print a message something like this:
loading membrane mechanisms from /home/foo/.../i686/.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

mazid
Posts: 6
Joined: Tue Feb 10, 2015 1:14 pm

Re: COMPILING HOC FILES FROM TERMINAL IN UBUNTU

Post by mazid » Sat Dec 19, 2015 4:50 pm

Thank you for the quick reply. I've test the neirondemo and yes it's working properly.
For the recompilation of the mod files i've already done that too...
And it's still not working

ted
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Location: Yale University School of Medicine
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Re: COMPILING HOC FILES FROM TERMINAL IN UBUNTU

Post by ted » Sat Dec 19, 2015 5:00 pm

In that case, I'll have to reproduce the problem on my own machine. If you zip up just the necessary source code (hoc, mod, ses files) and email them to
ted dot carnevale at yale dot edu
I'll let you know what I find out.

mazid
Posts: 6
Joined: Tue Feb 10, 2015 1:14 pm

Re: COMPILING HOC FILES FROM TERMINAL IN UBUNTU

Post by mazid » Sun Dec 20, 2015 4:09 pm

Ok Thank you. I send the link of the project in yoour mail.

ted
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Posts: 5566
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Re: COMPILING HOC FILES FROM TERMINAL IN UBUNTU

Post by ted » Sun Dec 20, 2015 11:10 pm

mazid wrote:I execute this command:

Code: Select all

nrngui CA1_Final_Geometry.hoc
And get this :

Code: Select all

/usr/local/nrn/x86_64/bin/nrniv: Couldn't find: all_tau_vecs.hoc
 in CA1_Final_Geometry.hoc near line 9
 load_file("all_tau_vecs.hoc")
                              ^
	0 
Which i don't understand because the all_tau_vecs.hoc is really present in the folder.
The files you sent didn't include any that had that name. However there was one file called
all_Tau_Vecs.hoc
Case may not matter to you, but it matters a lot to Linux and OS X. Fix that and I bet your program will load without error.

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