Unix/linux installation failure

Post Reply
RBJ
Posts: 54
Joined: Sun Aug 02, 2015 4:28 am

Unix/linux installation failure

Post by RBJ » Mon Aug 10, 2015 7:58 am

Hello All, I am trying to install NEURON on my University "mainframe" computer, just as a user, I have no root privileges. It runs both UNIX and LINUX, so I am trying with the linux (REDHAT) version. This is how far I have gotten:
1 Downloaded and unzipped the packages nrn and iv (nrn7.4/iv19). Apparent success.
2 Renamed everything as suggested (neuron\nrn neuron\iv).
3 Entered neuron\iv and ran configure with the pwd prefix option set.
Warnings emerged and I think something has already gone wrong.
4 Then gone through all the stated steps to end-up with the warning that nrn can't find iv where it expects it and ultimately, nrndemo does not run.

So rather than just start at the end with the "can't find iv error" (yes, i definitely told configure where to find it) I thought I would point out the very first sign I get that all is not well....
When I run (neuron/iv) ./configure --prefix=`pwd`
At the end of the stream of feedback I get:
config.status: creating Makefile
config.status: WARNING: 'Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/Makefile
config.status: WARNING: 'src/Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/bin/Makefile
config.status: WARNING: 'src/bin/Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/bin/idemo/Makefile
config.status: WARNING: 'src/bin/idemo/Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/bin/idraw/Makefile
config.status: WARNING: 'src/bin/idraw/Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/bin/iclass/Makefile
config.status: WARNING: 'src/bin/iclass/Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/include/Makefile
config.status: WARNING: 'src/include/Makefile.in' seems to ignore the --datarootdir setting
config.status: creating src/lib/Makefile
config.status: WARNING: 'src/lib/Makefile.in' seems to ignore the --datarootdir setting
Is that OK? It's just a warning.

If I press on and..."make"... the first error I can see says:
"../include/IV-X11/Xext.h:44:33: error: X11/extensions/Xext.h: No such file or directory
../include/IV-X11/Xext.h:45:34: error: X11/extensions/shape.h: No such file or directory"
Now that sounds bad....
Following make install...
Nothing at all appears in the neuron/iv/x86_64/lib directory; which seems like a bad sign.
/usr/include/X11/extensions does include various *.h files, but NOT the two listed above. I am not sure how to handle that.
Is anyone able to help me? I have been through all the previous posts and been fighting with this for a few days now.
Kindest Regards
Richard

RBJ
Posts: 54
Joined: Sun Aug 02, 2015 4:28 am

Re: Unix/linux installation failure

Post by RBJ » Mon Aug 10, 2015 9:48 am

...update... I changed the include file to include the obscure location in which shape.h resides on our system....
(having first done a system-wise file search)...
and Neurondemo now works. I have left this post here in case of use to anyone. Hope I didn't waste anyone else's time too...
Thanks for reading

Javier_PalmaEspinosa
Posts: 12
Joined: Tue Nov 10, 2015 5:01 pm

Re: Unix/linux installation failure

Post by Javier_PalmaEspinosa » Wed Mar 16, 2016 4:49 pm

Hello RBJ
I am having the EXACT problem, but running on OS X El Capitán.
Could you please, post exactly what you did in order to solve the issue?

do you know what those obscure headers do? (Xext.h and shape.h)

ted
Site Admin
Posts: 5623
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Unix/linux installation failure

Post by ted » Wed Mar 16, 2016 5:57 pm

Delete whatever was installed and follow these instructions instead:
https://www.neuron.yale.edu/ftp/neuron/ ... nstall.pdf

Post Reply