"Point process not located in a section" error with v7.5 but not v7.4

tclose
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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Mon Nov 06, 2017 8:51 pm

Great, thanks! I will try check out the updated version tomorrow.

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Thu Nov 09, 2017 3:14 pm

Hi Mike,

Thanks, that's great. I reinstalled Neuron from that commit and the error has gone away. When is that commit likely to make it into a released version?

Tom

hines
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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by hines » Thu Nov 09, 2017 3:32 pm

https://neuron.yale.edu/ftp/neuron/versions/alpha/
contains a mac and windows installer that has that change (anything after Nov 6, 2017)

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Mon Nov 13, 2017 11:34 pm

Okay great. I assume it has also been merged into the master branch. If so, would it be possible to tag a release on the github repo so I can point my travis build at it?

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by hines » Tue Nov 14, 2017 9:44 am

Ok. The 1665alpha tag for f6c657c master contains the desired 9fc7197 changeset

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Tue Nov 14, 2017 7:39 pm

Thanks!

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Wed Nov 15, 2017 7:45 pm

Hi Mike,

The trouble with using a pre-release I realise, but just FYI the combination of that tag and PyNN's 0.9.1 built-in mod files throws a segfault, so I haven't been able to use it.

Cheers,

Tom

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by hines » Wed Nov 15, 2017 9:14 pm

I unchecked the 'prerelease' item so it is now a release. Does that fix the problem? I admit to knowing nothing about why things work the way
they do in this domain. Is there a simple explanation of why a prerelease would cause an error but a release does not in your situation?

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Thu Nov 16, 2017 6:27 pm

No sorry if my message was a little confusing, I was referring to it being a pitfall os using code that is deemed "prerelease" (i.e. not fully tested) rather than any difference between 'prerelease' and 'release' on GitHub (there shouldn't be any in my understanding).

I reverted my build to download the 9fc719735a2d0a9446f59065534d5326a6bd179d commit directly and the segfault has gone away so it must be due to some difference between 9fc7197 and the alpha-1665 tag. Are there many differences between these two commits (i.e. were the changes in 9fc7197 merged with other code to get to alpha-1665)?

Can you see if you can reproduce the error by installing pyNN 0.9.1 (i.e. pip install --upgrade pyNN ensuring that 'nrnivmodl' of the Neuron installation you want to test against is first on your PATH) and importing the pyNN.neuron module? It occurred both on my local macOS and on Ubuntu-14.04 (on Travis).

Thanks,

Tom

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Thu Nov 16, 2017 9:13 pm

Actually, scratch all that. It appears the segfault I am getting on travis is unrelated so I expect the problem I am having is caused by having multiple Neuron installations on my laptop and the PyNN extensions being built against the wrong one.

So probably all good now, sorry for the confusion.

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by hines » Fri Nov 17, 2017 7:52 am

I reverted my build to download the 9fc719735a2d0a9446f59065534d5326a6bd179d commit directly
I was wondering about that possibility when I made the tag but could not quickly find the answer. Since the hash can
be used there does not seem to be any real need for the tag and it can be deleted. Let me know if the tag is still useful
to you

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Re: "Point process not located in a section" error with v7.5 but not v7.4

Post by tclose » Mon Nov 27, 2017 2:05 am

Sorry for the delay in replying I only just saw your response. Yes, you could delete the tag now.

On the topic of tagging releases, I have noticed that the link to the latest version of neuron seems to be updated as you add bug fixes, is that right? If so, this causes issues for the Homebrew (https://brew.sh) neuron formula (https://github.com/Homebrew/homebrew-sc ... /neuron.rb), which checks the downloaded tar file against the saved SHA256 (as generated when the Homebrew formula was last updated) before running the installation procedure. So I was wondering whether it would be possible for you to tag point releases (either on Github or on your download page), e.g. 7.5.1, 7.5.2, etc... for these bug fixes, or at least tag the minor releases in GitHub so that these SHAs for these don't go out of date.

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