Cant run a program given by my supervisor
Cant run a program given by my supervisor
Hey guys,
I am new to NEURON
and I have two problems
1 is my supervisor has given me a program which i cant run on my comp
but it runs ok at his lab
hes using WinXP
and mine is 7
when I run the mosintsimple (which i assume to be the already compiled program starter)
it gives me this error
nrniv: Couldn't find: current.hoc
in /cygdrive/C/Users/John/Desktop/RGC_model/mosinitSimple.hoc near line 2
load_file("current.hoc")
so what is problem there?
and the second question is
my supervisor wants me to input different conductance
one is excitatory and the other is inhibitory
and there are many different values that he wants me to have a combination of these to see the effects
so the best way is to run a for loop
the thing is I dont know how to get inputs from a txt file
I read the tutorial and tried it but its not working
I got the sine wave data from the igor wave generator
which i want to insert to the neuron and run few times to get the action potential numbers average
and i cant now
really appreciate the help
thanks
I am new to NEURON
and I have two problems
1 is my supervisor has given me a program which i cant run on my comp
but it runs ok at his lab
hes using WinXP
and mine is 7
when I run the mosintsimple (which i assume to be the already compiled program starter)
it gives me this error
nrniv: Couldn't find: current.hoc
in /cygdrive/C/Users/John/Desktop/RGC_model/mosinitSimple.hoc near line 2
load_file("current.hoc")
so what is problem there?
and the second question is
my supervisor wants me to input different conductance
one is excitatory and the other is inhibitory
and there are many different values that he wants me to have a combination of these to see the effects
so the best way is to run a for loop
the thing is I dont know how to get inputs from a txt file
I read the tutorial and tried it but its not working
I got the sine wave data from the igor wave generator
which i want to insert to the neuron and run few times to get the action potential numbers average
and i cant now
really appreciate the help
thanks
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Re: Cant run a program given by my supervisor
The MSWin installation of NEURON runs under Cygwin. Cygwin reports paths as if the root directory is called /cygdrive. To discover the MSWin equivalent of a Cygwin path, replace the /cygdrive/C part with C:, and replace all of the forward slashes / with backward slashes.firejohnx wrote:nrniv: Couldn't find: current.hoc
in /cygdrive/C/Users/John/Desktop/RGC_model/mosinitSimple.hoc near line 2
load_file("current.hoc")
so what is problem there?
So the error message tells you three things:
1. there is a file called
mosinitSimple.hoc
in a directory called
C:\Users\John\Desktop\RGC_model
2. the file mosinitSimple.hoc contains the statement
load_file("current.hoc")
3. the statement load_file("current.hoc") fails because there is no file called current.hoc in the same directory as mosinitSimple.hoc
So look in
C:\Users\John\Desktop\RGC_model
and see what's there. Note: case matters. A file called foo.hoc is not the same as a file called Foo.hoc.
First things first. If you can't run the program, you can't do anything else.and the second question is
Re: Cant run a program given by my supervisor
I am 100% sure that the demo_gfluct.oc is within the same file
but its still not running
but its still not running
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Re: Cant run a program given by my supervisor
demo_gfluct.oc? Who said anything about demo_gfluct.oc?firejohnx wrote:I am 100% sure that the demo_gfluct.oc is within the same file
but its still not running
Re: Cant run a program given by my supervisor
oops
well I opened another one and that one is giving the same problem
(requireing demo_gfluct.oc)
and again the current.hoc is in the same file
well I opened another one and that one is giving the same problem
(requireing demo_gfluct.oc)
and again the current.hoc is in the same file
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Re: Cant run a program given by my supervisor
So you are quite sure that C:\Users\John\Desktop\RGC_model contains a file called current.hoc.
Please do the following:
1. In the NEURON Program Group click on rxvt.sh
This will bring up a window with the name
bash
in the drag bar.
2. In the bash window execute the command
pwd
Tell me what it prints in the bash window (just click and drag to select the output, then use ^v (Control-V) to paste it into your reply on the Forum).
3. Next, execute the command
4. Now execute
pwd
again, and tell me what it prints in the bash window.
5. Finally, type(that's LS in lower case) and tell me what it prints in the bash window.
Please do the following:
1. In the NEURON Program Group click on rxvt.sh
This will bring up a window with the name
bash
in the drag bar.
2. In the bash window execute the command
pwd
Tell me what it prints in the bash window (just click and drag to select the output, then use ^v (Control-V) to paste it into your reply on the Forum).
3. Next, execute the command
Code: Select all
cd /cygdrive/C/Users/John/Desktop/RGC_model
pwd
again, and tell me what it prints in the bash window.
5. Finally, type
Code: Select all
ls
Re: Cant run a program given by my supervisor
The first result is:
/cygdrive/c
The second one is:
/cygdrive/C/Users/John/Desktop/RGC_model
And the third is:
/cygdrive/c
The second one is:
/cygdrive/C/Users/John/Desktop/RGC_model
And the third is:
Code: Select all
Gex.mod IM.mod demo_gfluct.oc mosinit.hoc
Gex.o IM.o h.mod mosinitSimple.hoc
Gfluct.mod INa_traub_shifted.mod h.o nap.mod
Gfluct.o INa_traub_shifted.o hocload.tmp nap.o
Gin.mod V_m.ses lva.mod spike.mod
Gin.o capump.mod lva.o spike.o
IKd_traub.mod capump.o mod_func.c test.ses
IKd_traub.o current.hoc mod_func.o
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Re: Cant run a program given by my supervisor
How are you "running" mosinitsimple.hoc? Double click on mosinitsimple.hoc?when I run the mosintsimple
What happens if you double click on mosinit.hoc?
If this is from ModelDB, what is the accession number?
Re: Cant run a program given by my supervisor
I have to right click and open them with neuron.exe
They both give the cant find the file response
and what is the accession number?
They both give the cant find the file response
and what is the accession number?
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Re: Cant run a program given by my supervisor
Unimportant. There are more serious problems to deal with.what is the accession number?
The big question right now is whether any aspect of NEURON works properly on your PC.firejohnx wrote:I have to right click and open them with neuron.exe
What happens if you go to the NEURON program group (under the MSWin Start menu) and select the item called
neurondemo
?
Re: Cant run a program given by my supervisor
It opens up several panels
which include:
- NEURON main menu
- NEURON demonstration
- Temperature
- RunControl
- Variable Time Step
which include:
- NEURON main menu
- NEURON demonstration
- Temperature
- RunControl
- Variable Time Step
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Re: Cant run a program given by my supervisor
In the
NEURON Demonstrations
panel, click on the "Release" button.
A bunch of new windows should pop up.
After these new windows have appeared, in the RunControl panel click on the "Init & Run" button. This should make a bunch of colored traces appear in the graph windows (to the right of the RunControl panel).
Did all of this happen as described?
NEURON Demonstrations
panel, click on the "Release" button.
A bunch of new windows should pop up.
After these new windows have appeared, in the RunControl panel click on the "Init & Run" button. This should make a bunch of colored traces appear in the graph windows (to the right of the RunControl panel).
Did all of this happen as described?
Re: Cant run a program given by my supervisor
There is no graph shown
so pushing the init & run did nothing
does that mean there are some problems?
so pushing the init & run did nothing
does that mean there are some problems?
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Re: Cant run a program given by my supervisor
Exit NEURON, then start neurondemo again. What happens when you click on the Release button in the NEURON Demonstrations panel?