Search found 35 matches

by MBeining
Thu May 30, 2019 5:22 am
Forum: MSWin
Topic: Compiling script fails with newer NEURON versions due to $N
Replies: 2
Views: 184

Re: Compiling script fails with newer NEURON versions due to $N

Thanks for that hint!

After also adding a check to add the correct mingw path (in this case $N/mingw/mingw64/bin) it worked!
by MBeining
Sun May 26, 2019 5:26 am
Forum: MSWin
Topic: Compiling script fails with newer NEURON versions due to $N
Replies: 2
Views: 184

Compiling script fails with newer NEURON versions due to $N

Hi there, I am the dev of T2N, the Matlab-NEURON interface, where I also implemented auto compiling of the mod files. For this I used this script which is modification of the original mknrndll.sh and which allows to hand over the NEURON path from Matlab via the console: if test -f $1/bin/cygpath ; t...
by MBeining
Sat Nov 18, 2017 8:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Which libnrnmech.so file to load on linux/mac
Replies: 3
Views: 12112

Re: Which libnrnmech.so file to load on linux/mac

The problem is that, as the interface can start NEURON simulations in parallel, there are several folders each containing the hoc files for each run (e.g. several current steps for calculating an F-I relationship). Hence I would have to copy that x86_64 folder (or what ever it is called on that syst...
by MBeining
Fri Nov 17, 2017 8:42 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Which libnrnmech.so file to load on linux/mac
Replies: 3
Views: 12112

Which libnrnmech.so file to load on linux/mac

I am testing a NEURON interface on different OS and I am a bit confused concerning the libnrnmech file which has to be loaded on linux/mac with the nrn_load_dll function in order to implement the compiled mechanisms. The reason is that these files have slightly different names on different machines ...
by MBeining
Tue Nov 07, 2017 5:19 am
Forum: Parallel NEURON
Topic: mpiexec fails on linux
Replies: 1
Views: 9565

Re: mpiexec fails on linux

Ok, I found out that using Open MPI, the test0.hoc works.
Guess Neuron is not compatible with mpich, only with mpich2? (which was not available to install via apt on that machine)
by MBeining
Sun Nov 05, 2017 8:05 am
Forum: Parallel NEURON
Topic: mpiexec fails on linux
Replies: 1
Views: 9565

mpiexec fails on linux

This is a kind of follow-up post of this thread about mpiexec problems in Windows: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=31&t=3769&p=16167#p16167 Trying to run the test0.hoc on Ubuntu gave me this error: mpiexec -n 2 nrniv -mpi /usr/local/nrn/test0.hoc Try loading openmpi load_mpi: libmp...
by MBeining
Sun Nov 05, 2017 6:22 am
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Re: Neuron's mpiexec fails on Windows 10

ok thanks!
by MBeining
Fri Nov 03, 2017 9:52 am
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Re: Neuron's mpiexec fails on Windows 10

Thank you so much, it works now with Neurons mpiexec again! :-) I still get the "post close command" error when trying to run this version with Microsofts MPI. I don't mind, but maybe it is of interest for you. Last question: mpiexec is not part of the Linux/Mac distributions, right? So I cannot ass...
by MBeining
Fri Nov 03, 2017 3:18 am
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Re: Neuron's mpiexec fails on Windows 10

Thank you for testing! I had now the opportunity to run the test0.hoc with different NEURON versions under two different Windows 10 machines and the outcome was that it is not the Windows version but the combination of mpiexec and Neuron version: Windows 10 Pro 64 bit, Version 1703 (OS Build 15063.6...
by MBeining
Thu Nov 02, 2017 7:41 am
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Re: Neuron's mpiexec fails on Windows 10

Ok I simplified the problem even more by just using the test0.hoc The following section shows you the input/output from the NEURON bash shell when 1) starting parallel Neuron as described in the Neuron tutorial 2) checking which mpiexec the bash shell used 3) testing the two other mpiexec executable...
by MBeining
Sun Oct 29, 2017 1:54 pm
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Re: Neuron's mpiexec fails on Windows 10

Unfortunately, I have to withdraw my latest post, as the problems continue with Microsoft MPI and using neuron. Actually using Microsoft MPI works with other programs (test batch scripts etc) and works when running neuron without the -mpi argument, but as soon as I use "C:\Program Files\Microsoft MP...
by MBeining
Fri Oct 27, 2017 8:23 am
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Re: Neuron's mpiexec fails on Windows 10

ok thanks!
by MBeining
Tue Oct 24, 2017 2:13 pm
Forum: Parallel NEURON
Topic: Neuron's mpiexec fails on Windows 10
Replies: 13
Views: 13765

Neuron's mpiexec fails on Windows 10

When I use the mpi exec provided by NEURON (7.3 and 7.5, others not tested) on Windows 10 64 bit using this code C:\nrn\bin\mpiexec -n 4 nrniv -nobanner -nogui -mpi "neuron_runthis.hoc" -c quit() I get this error: ERROR: Failed to post close command error 1726 ERROR: unable to tear down the job tree...
by MBeining
Thu Sep 14, 2017 8:24 am
Forum: Parallel NEURON
Topic: NetCon threshold and parallel context
Replies: 0
Views: 11962

NetCon threshold and parallel context

In the documentation of the ParallelContext it would be good to explicitly state that the threshold of the NetCon cannot be set on the NetCon that is returned by gid_connect, while delay and weight can be set.
It took me some time to find out that this is the reason why my network does not spike =)
by MBeining
Tue Sep 12, 2017 10:06 am
Forum: Parallel NEURON
Topic: parallelized NEURON does not start with pnm.run()
Replies: 7
Views: 8845

Re: parallelized NEURON does not start with pnm.run()

thanks Ted for the detailed explanation! I'll change it =)