Search found 127 matches

by Keivan
Sun Sep 06, 2009 1:27 am
Forum: UNIX/Linux
Topic: compile neuron with intel compiler for linux?
Replies: 8
Views: 8739

Partial Success Report

finally I could compile neuron with interviews using Intel compilers. I used the latest 7.1 alpha version of neuron. The trick is to completely delete your previous compiled neuron and use a clean source and pass no flages to compilers. note: It seems that the "make clean" command is very buggy and ...
by Keivan
Sat Sep 05, 2009 5:25 pm
Forum: UNIX/Linux
Topic: Bug report
Replies: 1
Views: 1513

Bug report

I was looking the neuron configuration file and maybe find a problem in it. I have changed this part: # Check whether --with-iv or --without-iv was given. if test "${with_iv+set}" = set; then withval="$with_iv" HAVE_IV=1 if test "$with_iv" = "no" ; then HAVE_IV=0 echo "Not compiling with interviews....
by Keivan
Sat Sep 05, 2009 1:13 am
Forum: UNIX/Linux
Topic: compile neuron with intel compiler for linux?
Replies: 8
Views: 8739

My Experience

I have recently compiled neuron with Intel compiler suit. As Thomas said if interviews are compiled with Intel compilers neuron would not compile correctly. The speedup with Intel-compiled neuron 7 was more than 100% in the single thread mode and about 10% in threaded mode compared to GNU compilers....
by Keivan
Tue Sep 01, 2009 1:42 am
Forum: NEURON hacks
Topic: Syntax Highlighting for GNU Linux and MS Windows
Replies: 11
Views: 31855

Syntax Highlighting for GNU Linux and MS Windows

Updated: 28 September 2013 Updated: 13 October 2013 -> begintemplate endtemplate Syntax Highlighnting in Geany Geany seems to be one of the preferred IDEs for NEURON simulation environment in GNU Linux. To enable syntax highlighting for geany: 1) edit or create ~/.config/geany/filetype_extensions.co...
by Keivan
Mon Aug 31, 2009 10:27 pm
Forum: Parallel NEURON
Topic: how config mpich2 on a standalone PC?
Replies: 9
Views: 8485

Re: how config mpich2 on a standalone PC? {solved}

thank you hines.
by Keivan
Mon Aug 31, 2009 10:24 pm
Forum: Parallel NEURON
Topic: Error LoadBalance failure
Replies: 9
Views: 3093

Re: Error LoadBalance failure {solved}

thank you ted. I am now enjoying my parallel neuron.
by Keivan
Mon Aug 31, 2009 5:04 pm
Forum: Parallel NEURON
Topic: how config mpich2 on a standalone PC?
Replies: 9
Views: 8485

Re: how config mpich2 on a standalone PC?

Thank you hines. I am really tired of struggling with my computer. this is my stat now: I have compiled mich2 with the following series of commands: ./configure --prefix=$HOME/mpich2 --with-device=ch3:nemesis --enable-sharedlibs=gcc --with-pm=gforker --enable-fast=O3 MPICH2LIB_CFLAGS=-march=native M...
by Keivan
Mon Aug 31, 2009 10:06 am
Forum: Parallel NEURON
Topic: Error LoadBalance failure
Replies: 9
Views: 3093

Re: Error LoadBalance failure

The best solution is to have one segment for the soma. It does not matter how many or few segments the other sections have. Multisplit works only when no subtree has more than two split points and, although the soma uniquely is allowed to have a split point in its interior, there can be only one of...
by Keivan
Mon Aug 31, 2009 12:53 am
Forum: Parallel NEURON
Topic: Error LoadBalance failure
Replies: 9
Views: 3093

Re: Error LoadBalance failure

Do you have a special reason for sticking with these nseg values, or can you change them?
there is no special reason using these nseg values. I will try your recomendations on my machine.
by Keivan
Mon Aug 31, 2009 12:42 am
Forum: Parallel NEURON
Topic: how config mpich2 on a standalone PC?
Replies: 9
Views: 8485

how config mpich2 on a standalone PC?

I want to test parallel neuron on a standalone multiprocessor computer. previously I could compile neuron using pvm3, however I realized that mpich2 is a better package. according to the article "Translating network models to parallel hardware in NEURON" I have compiled mpich2. but I do not want to ...
by Keivan
Sun Aug 30, 2009 11:51 am
Forum: Parallel NEURON
Topic: Error LoadBalance failure
Replies: 9
Views: 3093

Re: Error LoadBalance failure

I've sent required files
by Keivan
Sun Aug 30, 2009 10:38 am
Forum: Parallel NEURON
Topic: Error LoadBalance failure
Replies: 9
Views: 3093

Error LoadBalance failure

I am experimenting new parallel neuron 7. I have just imported a dendritic tree to neuron without anything else. but I have encountered error activating multispilit from tools > parallel computing keivan@ubuntu:~/Desktop/TemporalGate$ nrngui main.hoc NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-...
by Keivan
Sat Jan 05, 2008 8:45 pm
Forum: Other questions
Topic: What are the basic requirments to change the source code?
Replies: 1
Views: 1782

What are the basic requirments to change the source code?

I want to know if I want to change the neuron source code what I must know? and where is the starting point?
by Keivan
Sat Jan 05, 2008 8:40 pm
Forum: Other questions
Topic: Compiling NEURON
Replies: 1
Views: 1497

SSE & Intel compiler

1) I want to know is neuron benefits from SSE instructions?
2) Is it possible to compile neuron with intel compilers in windows or linux?
by Keivan
Wed Jan 02, 2008 6:02 am
Forum: General questions and discussions about computational neuroscience
Topic: sugesstions about the tools and technologies users require.
Replies: 5
Views: 9563

Philosophy of Neuron and the multithreading

As every one knows The Neuron was a revolution in the simplification of the computational neuroscience. I think using a simulator like neuron we could focus on the problem instead of thinking the ways we could write our code or thinking the ways to improve our speed of computation. In this regard I ...