Run neuron.exe from mpi programs

[zerostar07]

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.

[ted]

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

[zerostar07]

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?

[ted]

[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.

[ted]

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]

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.

[zerostar07]

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.