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Loading mechanisms without a gui?
Posted: Mon Mar 19, 2007 7:24 pm
by mctavish
Hey all,
I am wanting to run neuron without a gui. I can launch via
However, this does not seem to find or load my NMODL files and I get "undefined function" errors from functions that are in these NMODL files.
If I call
, then these additional mechanisms are automatically loaded.
The reason I am wanting to run without the GUI when I have the GUI installed is that I am preparing simulations to run on a parallel computer without a GUI....
Thanks,
Tom
Posted: Wed Mar 21, 2007 7:49 am
by hines
In a non-parallel environment, launch the
<cpu_name>/special script instead of
nrniv. (or look at that script and when you
launch nrniv, use the proper -dll argument.
On a parallel computer, you will indeed
launch <installpath>/<cpu_name>/bin/nrniv
under mpiexec or mpirun and you will
give nrniv the -mpi argument. In that case
it will automatically load the shared library
containing the compiled mod files.
Posted: Wed Mar 21, 2007 12:12 pm
by mctavish
Perfect answer, Ted. Thanks!
Posted: Thu Mar 22, 2007 9:42 am
by ted
That should read "Perfect answer, Michael . . . "
Re: Loading mechanisms without a gui?
Posted: Thu Nov 12, 2009 10:18 pm
by eschombu
Where is this "<cpu_name>/special" script located? I don't know what folder <cpu_name> refers to. I'm now encountering this problem as well, so if there's newer documentation on how to do this could you point me there?
Thanks!
Erik
Re: Loading mechanisms without a gui?
Posted: Fri Nov 13, 2009 2:12 pm
by ted
Specific example on an Intel-based machine with a 32 bit OS:
Suppose ~/myhoc/mcproject contains na.mod
Code: Select all
$ cd ~/myhoc/mcproject
$ ls
na.mod
$ nrnivmodl
. . . a bunch of msgs ending with the following:
Successfully created i686/special
$ ls
i686 na.mod
$ ls i686/
libnrnmech.la mod_func.c mod_func.lo na.c na.lo na.mod special
Capisce?
Re: Loading mechanisms without a gui?
Posted: Mon Nov 16, 2009 6:07 pm
by eschombu
Thanks for the location. What can and cannot be done with this "special" script? I tried running my hoc code, which works through nrngui, but hit a syntax error when cvode.re_init() was called. It works with cvode statements all commented out. Also, one reason I wanted to run without the gui was to get rid of all the "first instance of [variable name]" output, but they are still there. Is there a way to suppress those? Not a big deal if not, though.
Thanks again,
Erik
Re: Loading mechanisms without a gui?
Posted: Mon Nov 16, 2009 7:22 pm
by ted
eschombu wrote:What can and cannot be done with this "special" script?
Whatever doesn't need the GUI. And, if you simply include
load_file("nrngui.hoc")
in your hoc file, you can also do whatever needs the GUI.
I tried running my hoc code, which works through nrngui, but hit a syntax error when cvode.re_init() was called. It works with cvode statements all commented out.
That's news to me. Maybe you uncovered a bug. What's the minimal code that is required to elicit the error msg?
Also, one reason I wanted to run without the gui was to get rid of all the "first instance of [variable name]" output, but they are still there. Is there a way to suppress those?
Try wrapping offending code blocks in paired curly brackets
{
like this
}