NEURON installation was fine, now somewhat broken [resolved]

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neuromau
Posts: 95
Joined: Mon Apr 20, 2009 7:02 pm

NEURON installation was fine, now somewhat broken [resolved]

Post by neuromau » Sat Sep 07, 2013 2:27 pm

Hello, I have the 32-bit Cygwin installation on my Windows 8 machine. It's been working fine for months. Then, yesterday it began exhibiting problems. I think the only thing I did yesterday was install Java JDK and NeuroConstruct, and alter the NeuroConstruct settings so that it could find and work with NEURON. Not sure if that is related or not, but now when I try to use NEURON, I have these troubles:

1. At the Cygwin command line, enter:

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nrniv /cygdrive/c/nrn73/lib/hoc/nrngui.hoc
Then it displays the banner message and shows the NEURON menubar, but if I click on the menubar, NEURON hangs and never responds, graying it out. The command prompt still works though.

2. At the Cygwin command line, enter:

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nrniv
Then it displays the banner message and seems to work okay.

3. In the Start menu, choose NEURON 7.3>nrngui:
Then the following message appears:
Can't load NEURON resources from C:\nrn73\bin/lib/nrn.def[aults]
NEURON -- Release 7.3 (849:5be3d097b917) 2013-04-11
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

nrniv: Couldn't find: stdgui.hoc
in /cygdrive/c/nrn73/lib/hoc/nrngui.hoc near line 1
{load_file("stdgui.hoc")}
^
nrniv: nrnmainmenu undefined function
in /cygdrive/c/nrn73/lib/hoc/nrngui.hoc near line 2
nrnmainmenu()
^
nrnmainmenu( )
oc>
The menubar is not loaded but NEURON seems to work fine at the command prompt. I checked and stdgui.hoc is located in the same directory as nrngui.hoc, so I don't know why it can't find it (seems to be some issue with slashes both directions in the path).

4. From MATLAB, execute a system call for nrniv

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system('nrniv')
Displays the banner message plus an error message:
Can't load NEURON resources from C:\nrn73\bin/lib/nrn.def[aults]
I'm not sure why executing nrniv as a system call in MATLAB is now producing different behavior than #2 above, executing nrniv from a Cygwin window.

I tried restoring my system to a time before installation of neuroConstruct and Java SDK, as well as restarting my computer, and uninstalling and reinstalling NEURON. I've also tried various combinations of values for my environmental variables, appending any one of the following to the path and setting NEURONHOME to one of them:

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C:\nrn73

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C:\nrn73\bin

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/cygdrive/c/nrn73

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/cygdrive/c/nrn73/bin
I realize I must have done something that broke the installation, I just can't recall what... and since the problem is still there after the NEURON reinstall, I don't know how to fix it. I appreciate your assistance.
Last edited by neuromau on Sat Sep 07, 2013 3:39 pm, edited 2 times in total.

neuromau
Posts: 95
Joined: Mon Apr 20, 2009 7:02 pm

Re: NEURON installation was fine, now somewhat broken

Post by neuromau » Sat Sep 07, 2013 3:38 pm

Also, I saw this in ivocmain.cpp:

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#if defined(CYGWIN)
                        sprintf(nrn_props, "%s/%s", neuron_home, "lib/nrn.def");
#else
                        sprintf(nrn_props, "%s\\%s", neuron_home, "lib\\nrn.def");
#endif
So I tried removing my CYGWIN environmental variable and now the NEURON installation works again for numbers 2, 3, and 4 above. So I guess the problem lies in that Cygwin has somehow stopped converting paths to its preferred POSIX equivalent, so now NEURON is dealing with a nrn_props that has both forward and backslashes in it, and is getting confused (?)

Anyway, I uninstalled CYGWIN and reinstalled CYGWIN and now NEURON works just fine again. I'll leave this thread up in case anyone else finds themselves in a situation where NEURON is trying to read a path that includes both forward slash / and backslash \. Still not sure of the root cause of this issue though.

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