www.neuron.yale.edu

Hello,

I am trying to run a package for parameter fitting that needs to run neuron remotely on a windows mpich-based cluster. There is an executable program that runs in parallel and calls system() to run neuron on a number of machines. This system call runs a batch file that runs neuron.exe with the model file.

The problem is that neuron.exe seems to get stuck when it starts up through mpi. Unfortunately, i do not get any output either. I suppose the problem has to do with incorrect initialization of nrniv.

What is a full windows shell command line that i can use to run nrniv.exe? do i need to run neuron.exe with some special parameter?

Please note that I am not referring running neuron in parallel through mpi, but initiate neuron.exe locally in each machine through mpi.

Any help would be appreciated. Thanks.

c:\nrnnn filename.hoc
where nn is NEURON's version number (assuming that's the directory you installed it in)
should start NEURON and make it read filename.hoc

thanks for your reply. However, on my setup, running nrniv.exe sth.hoc does nothing.

also running neuron.exe from within another program ends up with a rxvt.exe.stackdump (which i suppose is a cygwin core dump).

Is this normal?

[quote="ted"]c:\nrnnn filename.hoc[/quopte]
How sloppy. I meant to type
c:\nrnnn\bin\nrniv.exe filename.hoc
but was too hasty to get it right. My apologies.

Under Win2K on my PC, I just started an MSWin "command interpreter
window," cd'd to a directory that contained a hoc file, and executed
c:\nrn61\bin\nrniv.exe filename.hoc
NEURON started, read the specified file and recreated some GUI windows,
but then froze and had to be killed via the MSWin task manager.

However, if I tried this from within the cygwin rxvt window, the program executed correctly.

This
http://www.linuxquestions.org/questions ... in-594988/
suggests that an MSWin batch file with contents something like this might work:
c:\nrnnn\bin\bash c:\nrnnn\bin\nrniv.exe filename.hoc
If you add c:\nrn\bin to the Windows PATH, it may be possible to use a simpler command line
in the batch file:
bash nrniv.exe filename.hoc

ted wrote:This
http://www.linuxquestions.org/questions ... in-594988/
suggests that an MSWin batch file with contents something like this might work:
c:\nrnnn\bin\bash c:\nrnnn\bin\nrniv.exe filename.hoc

But it doesn't work.

On my WinXP laptop, executing this command
c:\nrnnn\bin\neuron.exe filename.hoc
in an MSWin "Command Prompt" window works.
This command string also works when contained in an MSWin batch file.

I just saw your posts. Thanks for your help. I tried all sorts of combinations, via bash, sh etc. It still doesn't work the way i want it to, so i guess i 'll give up on my windows cluster and try setting up a linux cluster instead.