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Re: Installation problem Neuron
Posted: Sun Nov 18, 2018 12:38 pm
by AGBX2
Thanks for the answer, I am going to try this now. Does this mean that we cannot use the binaries and that NEURON has to be compiled to be installed with OSX ?
Best,
AGBX2
bschneiders wrote: ↑Thu Nov 15, 2018 5:42 pm
I ended up getting mine to work. I did the following:
-added the same 3 flags mentioned by aaronmil to my bash_profile
-deleted Neuron again and built it from source code
-used the configure option --with-readline=no
-did the following step after "make after_install" to make sure python and neuron could talk to each other:
Code: Select all
cd src/nrnpython
python setup.py install
I did not try the alpha version - I think that is why mine was not working when I tried the first time (before using source code).
Re: Installation problem Neuron
Posted: Sun Nov 18, 2018 1:16 pm
by AGBX2
Impossible to compile, too many errors generated during the compilation process even if I precisely followed the indications. I will wait for a binary version compatible with Mojave.
AGBX2
Re: Installation problem Neuron
Posted: Sat Dec 01, 2018 5:49 am
by AGBX2
Hello :)
Thanks a lot, the last binary version of NEURON I tried this morning works fine with OSX-Mojave
https://neuron.yale.edu/ftp/neuron/vers ... 64-osx.pkg
Best Regards,
AG.
Re: Installation problem Neuron
Posted: Fri Apr 05, 2019 12:26 pm
by stephanmg
Greetings!
Will it be necessary to apply the patch you posted below to the source?
Or will be the --with-readline=no option enough to get rid of the error
?
Kind Regards,
SG
hines wrote: ↑Sat Sep 29, 2018 2:39 am
If installing from sources, use the configure option --with-readline=no
Also a library I used for the icon launch mechanism has been deprecated out of existence. That can be temporarily worked around by
modifying nrn/src/mac/Makefile.am to comment out a single line. ie.
Code: Select all
diff --git a/src/mac/Makefile.am b/src/mac/Makefile.am
index a612653..241f45a 100755
--- a/src/mac/Makefile.am
+++ b/src/mac/Makefile.am
@@ -23,7 +23,7 @@ if UniversalMacBinary
$(CC) -arch i386 -o aouti386 -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon
lipo aouti386 aoutppc -create -output a.out
else
- gcc -g -arch i386 -Dncpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon
+# gcc -g -arch i386 -Dncpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon
endif
carbon=$(carbon) sh $(srcdir)/launch_inst.sh "$(host_cpu)" "$(DESTDIR)$(prefix)" "$(srcdir)"
If you install from a package file, let me know and I can upload to the alpha folder.
Re: Installation problem Neuron
Posted: Fri Apr 05, 2019 1:05 pm
by ted
stephanmg: that post is more than half a year old. Chances are that the "library deprecated out of existence" issue has been resolved. You could try to confirm that by searching the commits at
https://github.com/neuronsimulator/nrn/commits/master, or just get the most recent source code and see what happens when you compile with the --with-readline=no option
Re: Installation problem Neuron
Posted: Fri Apr 05, 2019 1:07 pm
by stephanmg
Thank you very much.
I'll forward this to my colleagues who try to build it - I presume they still have the old source code and did not update it.
Kind Regards,
SG
ted wrote: ↑Fri Apr 05, 2019 1:05 pm
stephanmg: that post is more than half a year old. Chances are that the "library deprecated out of existence" issue has been resolved. You could try to confirm that by searching the commits at
https://github.com/neuronsimulator/nrn/commits/master, or just get the most recent source code and see what happens when you compile with the --with-readline=no option
Re: Installation problem Neuron
Posted: Tue Aug 20, 2019 8:13 am
by wvangeit
mhines, we're still running into this issue.
Providing --with-readline=no makes neuron compile, but it makes bluepyopt crash during tests (and it's difficult to see what exactly happens).
What would be the effect of disabling readline ?