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Error using 2 different cells with network gui

Posted: Tue May 08, 2018 6:07 am
by guloncu

I'm using GUI of NEURON 7.5 on Windows 10. I want to test my cells in network but NEURON gives me error if I have 2 different cell builder pages opened.

I can see the different cells in network builder page, connect the synapses but as I hit the create button it gives me this error:

Code: Select all

section is unnamed
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and others
initcode failed with 1 left
I received this error when I loaded 2 different single cell .ses files. To test, I created 2 new single cell using build>network cell>from cell builder. Both of the trials gave me the same error. If I load 2 different single cells but include only 1 in the network, I still receive the same error. I do not get this error if I have only 1 cell builder page and build a network with that type using it multiple types.

I would appreciate any hints, comments and suggestions that can help me,

Re: Error using 2 different cells with network gui

Posted: Tue May 08, 2018 10:17 am
by ted
I haven't seen this happen before; will have to be able to reproduce the problem in order to find out what's wrong and how to fix it. If you zip up the files needed to reproduce it and email that file to
ted dot carnevale at yale dot edu
I'll tell you what I find out. I'll need the .ses files for the NetReadyCellGUIs ("Network Cell from CellBuilder" and "Network Cell Artificial Cell" tools) plus any .mod files that they need, and also the .ses file for the NetGUI (Network Builder).

Also, please tell me the first line that NEURON prints to its terminal when starts--should contain version numbers and a date, and will look something like this:
NEURON -- VERSION 7.5 master (5524b18) 2018-02-21
You should be able to just copy and paste it into your reply in the Forum.

Re: Error using 2 different cells with network gui

Posted: Thu May 10, 2018 2:23 pm
by guloncu
Hi Ted,
I sent you the .ses file. The first line of terminal is:

NEURON -- VERSION 7.5 master (6b4c19f) 2017-09-25

Thanks a lot

Re: Error using 2 different cells with network gui

Posted: Fri May 11, 2018 12:00 pm
by ted
The following note is for the benefit of others who may read this thread.

The problem may have been caused by the fact that the CellBuilders that belonged to the NetReadyCellGUI tools (which are used to set up biophysical model cell classes) were in "Continuous Create" mode. That led to many collisions in name space, since both cell classes had sections called soma, dend, axon etc., and NEURON's interpreter printed out a lot of warning messages of the form

"Previously existing <sectionname> points to a section which is being deleted"

I took the CellBuilders out of Continuous Create mode by clicking on their Continuous Create checkboxes, then closed them, and saved everything to a new ses file and exited NEURON. Next I restarted NEURON and had it load the new ses file. No more warning messages, and now everything worked properly.

I'm still not sure if that was the cause of the problem, or whether there is a bug in the particular version of NEURON that guloncu was using (I'm using a more recent version). However, if there is a bug, it must be very subtle, because the new ses file worked for guloncu too.