neuron 7.5 crashes on cygwin 2.9.0

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alexandrapierri
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Joined: Wed Jun 17, 2015 5:31 pm

neuron 7.5 crashes on cygwin 2.9.0

Post by alexandrapierri » Wed Dec 20, 2017 10:15 pm

Hello NEURON team,

1. On my Windows 10 machine NEURON 7.5 crashes on cygwin 2.9.0 after successful installation of cygwin.
I have tried to install first NEURON and then cygwin or reverse the order of installation and the problem persists.

The extra packages I have installed with cygwin are:
1. procps
2. openssl
3. openssh
4. devel
6. rsync

In addition to modifying my environment variables on Windows I have also configured my bashrc files as follows:

export NEURONHOME=/cygdrive/c/nrn
export N=/cygdrive/c/nrn
export PYTHONHOME=/cygdrive/c/nrn
export PYTHONPATH=/cygdrive/c/nrn/lib
export PATH=/cygdrive/c/nrn/bin:$PATH
export PATH=/cygdrive/c/cygwin/bin:$PATH

2. On a separate note the directory "\nrn\usr\share\termininfo" which is supposed to be generated with NEURON installation does not appear on my machine. I need this directory to share termininfo with cygwin by typing: "cp -r C:\cygwin\usr\share\terminfo\* C:\nrn73\usr\share\terminfo"

any help with these two issues (mainly the first one) would be much appreciated.

thank you,
Alexandra

ted
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Re: neuron 7.5 crashes on cygwin 2.9.0

Post by ted » Thu Dec 21, 2017 12:58 pm

You're probably the only person on the planet who is trying to run NEURON 7.5 under Cygwin. The latest NEURON installer for MSWin should produce a working installation of NEURON, and it does not need Cygwin at all. Unless you absolutely must have Cygwin for some other reason (what would that be?), suggest you uninstall both NEURON _AND_ Cygwin--make absolutely sure to eliminate any shred of both of them--and then do a clean install of NEURON.

alexandrapierri
Posts: 6
Joined: Wed Jun 17, 2015 5:31 pm

Re: neuron 7.5 crashes on cygwin 2.9.0

Post by alexandrapierri » Thu Dec 21, 2017 1:26 pm

Hi Ted

thanks so much for your prompt response.
I need cygwin for SimTracker (by Marianne Bezaire) and I assumed that the latest version of NEURON is what I should install.

Would you suggest that I install a previous version of NEURON to use with cygwin on Sim Tracker?

thank you again,
Alexandra

ted
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Re: neuron 7.5 crashes on cygwin 2.9.0

Post by ted » Sun Dec 24, 2017 2:13 pm

You definitely want to use a recent version of NEURON. There have been many performance improvements and bug fixes, and some new features, since the last time an installer for NEURON with cygwin was released.
alexandrapierri wrote:
Thu Dec 21, 2017 1:26 pm
I need cygwin for SimTracker (by Marianne Bezaire)
If cygwin is required to use SimTracker, one might think that the instructions for installing and configuring SimTracker would say something about it, and how to work around problems that might arise. Or maybe I'm missing the point--is there something specific about your particular situation that requires you to use cygwin?

alexandrapierri
Posts: 6
Joined: Wed Jun 17, 2015 5:31 pm

Re: neuron 7.5 crashes on cygwin 2.9.0

Post by alexandrapierri » Sat Dec 30, 2017 11:35 am

Thanks again Ted

Based on SimTracker instructions Cygwin is required on Windows operating systems to enable certain Linux commands used by the SimTracker.
http://mariannebezaire.com/simtracker/

For instance based on the instructions the packages below are required:
• openssh
• procps
• rsync

Unfortunately the instructions refer to installation of NEURON 7.3 therefore they are likely outdated for NEURON 7.5.
I guess the straightforward thing to do would be to install SimTracker on linux at this moment (to avoid cygwin issues) until the configuration details for MSwin are updated, unless you have another suggestion.

ted
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Re: neuron 7.5 crashes on cygwin 2.9.0

Post by ted » Sun Dec 31, 2017 12:26 pm

I'm generally in favor of using Linux rather than MSWin, but the plain truth is that half or more of the people who use NEURON are using MSWin. You might contact Marianne about the issue. I wonder if Python might provide a workaround (yes, that would require installing Python, but that's not as bad as having to switch to an unfamiliar OS).

alexandrapierri
Posts: 6
Joined: Wed Jun 17, 2015 5:31 pm

Re: neuron 7.5 crashes on cygwin 2.9.0

Post by alexandrapierri » Mon Jan 01, 2018 11:41 pm

I will keep that in mind about finding a workaround with Python ( I do have Python installed) but will switch to linux for now.

thanks a lot for all help Ted!

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