Search found 1509 matches

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: 23
Views: 153

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: 23
Views: 153

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: 23
Views: 153

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: 23
Views: 153

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: 23
Views: 153

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: 23
Views: 153

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: 23
Views: 153

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: 23
Views: 153

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...
by hines
Fri Sep 14, 2018 11:18 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 11
Views: 134

Re: Installation problem Neuron

I've been unable to successfully install mojave as a virtual box guest. It will be away for two weeks and can get back to the problem at that time.
by hines
Wed Sep 12, 2018 3:07 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 11
Views: 134

Re: Installation problem Neuron

The otool output for nrniv is seriously perplexing. Mine is much lengthier with... Michaels-MacBook-Pro:~ michaelhines$ otool -L /Applications/NEURON-7.6/nrn/x86_64/bin/nrniv /Applications/NEURON-7.6/nrn/x86_64/bin/nrniv: /Applications/NEURON-7.6/nrn/x86_64/lib/libnrnoc.0.dylib (compatibility versio...
by hines
Wed Sep 12, 2018 7:10 am
Forum: OS X
Topic: Installation problem Neuron
Replies: 11
Views: 134

Re: Installation problem Neuron

one last diagnostic test using a terminal window. What is the output of
otool -L /Applications/NEURON-7.6/nrn/x86_64/bin/nrniv
The executable expects to get those variables from /usr/lib/libedit.3.dylib
Also what is the result of
ls -l /usr/lib/libedit*
ls -l /usr/lib/libreadline*
by hines
Tue Sep 11, 2018 8:34 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 11
Views: 134

Re: Installation problem Neuron

I'd like to know the result of the terminal experiment I mentioned earlier. That will generate several further questions.
by hines
Mon Sep 10, 2018 9:39 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 11
Views: 134

Re: Installation problem Neuron

I tried to install the mojave beta on a virtual box clone of high sierra. Gets what seems to be close to success but will not boot. Hangs at the
boot message
/dev/disk0s2 on / (hfs, local, journaled)
by hines
Mon Sep 10, 2018 6:10 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 11
Views: 134

Re: Installation problem Neuron

Did you build from sources or use the pkg file distribution. If the latter, have you intalled the software from xquartz.org and the command line tools. If the latter what configure line did you use. What python do you have installed. Does the following work? Start a terminal window and in the termin...
by hines
Wed Aug 29, 2018 8:20 am
Forum: Neurons in Action
Topic: NIA 2 crashes Firefox
Replies: 1
Views: 99

Re: NIA 2 crashes Firefox

I'm not actually certain the following is relevant but you might try (from a terminal window) curl https://nia2.sinauer.com/nrngui.forNIA2EX.txt > /Applications/NIA2Ex.app/Contents/MacOS/HelperApps/NEURON/nrn/i686/bin/nrngui.sh Probably a good idea to first make a copy of the original nrngui.sh Plea...