Search found 1516 matches

by hines
Fri Oct 12, 2018 1:58 pm
Forum: Other questions
Topic: Conflict between CVode.maxstep, NetCon instances, and extracellular
Replies: 1
Views: 94

Re: Conflict between CVode.maxstep, NetCon instances, and extracellular

That is an oversight. cvode wraps ida and the former is persistent while the latter is destroyed/created whenever the model topology, or if the model requires a differential algebraic solver, changes. Extacellular requires ida. I forgot to make all the ida calls to reflect the existing cvode style f...
by hines
Wed Oct 10, 2018 10:39 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 21
Views: 942

Re: Installation problem Neuron

Ok. so there is no problem with command line tools and readline. I think the next diagnostic test is to install a distributed pkg file for NEURON and see if that works with your python3.7. Please try https://neuron.yale.edu/ftp/neuron/versions/alpha/nrn-7.6.2-18-gcfe5f00.x86_64-osx-py-37-36-27.pkg J...
by hines
Fri Oct 05, 2018 6:41 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 21
Views: 942

Re: Installation problem Neuron

-with-readline=no
I assume that is just a typo and you used --with-readline=no
Anyway, have you updated the command line tools. And perhaps you can reinstall python3.7.
I build the distribution with python3.7 and do not see this issue.
by hines
Wed Oct 03, 2018 7:02 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 21
Views: 942

Re: Installation problem Neuron

The icon launch mechanism is fixed with nrn-7.6.2-18-gcfe5f00.x86_64-osx-py-37-36-27.pkg in the alpha download folder. So all functionality on high sierra 10.13 exists with Mojave 10.14. Note that the first launch of an icon may pop up a system request for your permission. Mojave has increased the s...
by hines
Tue Oct 02, 2018 2:48 pm
Forum: NEURON hacks
Topic: Compile models from hoc code.. need an updated hack
Replies: 1
Views: 256

Re: Compile models from hoc code.. need an updated hack

you are missing a declaration of s
objref s
by hines
Sun Sep 30, 2018 3:13 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 21
Views: 942

Re: Installation problem Neuron

Please try
nrn-7.6.2-15-gbdf78f2+.x86_64-osx-py-37-36-27.pkg
from
https://neuron.yale.edu/ftp/neuron/versions/alpha/

The icons are non-functional in this version due to the missing launcher program. So you will have to use a terminal window for
nrnivmodl
nrngui
etc.
by hines
Sat Sep 29, 2018 2:39 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 21
Views: 942

Re: Installation problem Neuron

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. diff --git a/src/mac/Makefile...
by hines
Thu Sep 20, 2018 12:15 pm
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Well, good. However I am truly astonished by this requirement. What specific anaconda version is this?
by hines
Thu Sep 20, 2018 7:54 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Ok. So the issue is related to anaconda python. turns out there are a number of google error references for vtable for std::__cxx11:: basic_stringbuf and I notice on that may be relevant. As it turns out,e GCC 5 introduced new implementations of std::string and std::list. You can try the workaround ...
by hines
Wed Sep 19, 2018 8:06 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I'm traveling and have a Mac powerbook with a virtual box guest ubuntu 16.4 with gcc 5.4.0. Are you using a tar.gz or the GitHub repository files? I would try the latter git clone http://github.com/neuronsimulator/nrn cd nrn sh build.sh ./configure ... etc. It may be worth while to focus on a stripp...
by hines
Tue Sep 18, 2018 10:12 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

Shall I try installing NEURON again? I don't see much chance of success unless something substantive changes on your system. This is not a problem I have ever encountered. https://debian-administration.org/article/176/Reinstalling_packages_to_fix_problems What I would do next. is base="build-essent...
by hines
Tue Sep 18, 2018 8:23 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

The openmpi is working. But I missed the fact in your earlier message that the problem has nothing to do with mpi as linking fails even in the absence of --with-paranrn. That makes me wonder if you have an incomplete g++ development environment or one that has inconsistent libraries. The build envir...
by hines
Mon Sep 17, 2018 2:51 pm
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

I found out that I had already openmpi.
Nothing wrong with that in principle. So for nrn
make distclean
./configure ... # just like you did before
make -j install

and does that succeed?
by hines
Mon Sep 17, 2018 10:18 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

It is easier to see the relationship between stderr and stdout by making available the interleaved output in a single file via make >& temp But no need to do that in this case as it is undoubtedly similar to your first message. We already suspect that the problem is related to your mpich installatio...
by hines
Fri Sep 14, 2018 11:44 am
Forum: UNIX/Linux
Topic: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)
Replies: 25
Views: 1793

Re: Problems with 'make' when trying to install NEURON with MPI+Python (Ubuntu 16.04)

do which mpicc which mpic++ which mpicxx which mpiexe all seem to come from the same place? The interviews installation seemed to work. But can you verify by launching $HOME/neuron/iv/x86_64/bin/idraw I'm going to guess that the mpich installation has a problem. Do things compile with make dist_clea...