Incomplete directory tree within NEURON

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neuromau
Posts: 97
Joined: Mon Apr 20, 2009 7:02 pm

Incomplete directory tree within NEURON

Post by neuromau »

Hello, this may be a Cygwin issue and not a NEURON issue; I'm not sure. I'm on a 64-bit Windows 8 Machine using the NEURON 7.3 GUI.

I have a main folder where I keep all my NEURON models; each model is in its own subdirectory. Lately when I open the NEURON 7.3 GUI and use the commands under the File menu (load hoc file, change working directory), I can get into the main folder, but then it only shows one of the model subdirectories within the main folder, even though there are many folders there. I don't know why all of the folders are not shown. At the command line, I can tell NEURON to load any file from the invisible folders (giving the relative path to the file in the load_file command) and NEURON loads it just fine. NEURON just won't display some of the folders in its folder-picker or file-picker.

I don't think that I had this problem a few months ago. I noticed a lot of problems with NEURON and Cygwin right after I installed the Java JDK (in preparation for downloading NeuroConstruct), so I uninstalled the Java JDK, did a system restore, and reinstalled NEURON. Most of the problems disappeared, but this issue I just described was not resolved. It could be a coincidence that the problems started at the time of the JDK installation, but I am not aware of any other changes made at that time.
hines
Site Admin
Posts: 1600
Joined: Wed May 18, 2005 3:32 pm

Re: Incomplete directory tree within NEURON

Post by hines »

I only have a windows 7 virtual box on my mac for the next several weeks. (traveling) But if you tell me the name of the
nrn*setup*.exe file you used to install, I'll see if I can reproduce the problem.
neuromau
Posts: 97
Joined: Mon Apr 20, 2009 7:02 pm

Re: Incomplete directory tree within NEURON

Post by neuromau »

I used nrn-7.3.i686-pc-cygwin-setup

However, I've just realized that this problem is definitely broader than NEURON. Within MATLAB, path completion only works if I use the Windows path form (C:\...). If I use the Cygwin form of /cygdrive/c/..., then only one model subdirectory is available (the same one available in the NEURON GUI). MATLAB refuses to load a file from one of the "invisible" folders even if the path is specified in Cygwin form.

I think this is an underlying Cygwin problem. I can't find any difference between the subdirectory that shows and the invisible ones, in terms of permissions or anything, so I will try reinstalling Cygwin another time and then post in a Cygwin forum.
neuromau
Posts: 97
Joined: Mon Apr 20, 2009 7:02 pm

Re: Incomplete directory tree within NEURON

Post by neuromau »

So somehow an actual "cygdrive" folder got created in my C: drive, and it partially replicated the directory tree under my C: drive. The NEURON GUI would only look into that cygdrive folder, and couldn't look higher than its level. But it is fixed now.

There was a newer version of Cygwin available. I updated Cygwin and reinstalled the same NEURON version and was not able to reproduce the problem but still deleted the cygdrive folder. Thanks!
hines
Site Admin
Posts: 1600
Joined: Wed May 18, 2005 3:32 pm

Re: Incomplete directory tree within NEURON

Post by hines »

/cygdrive should not be a real dos folder but is the syntax cygwin uses to specify the drive letter. ie.
/cygdrive/c/... or /cygdrive/d/... etc.
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