Search found 1594 matches

by hines
Fri Sep 16, 2005 2:01 am
Forum: Anatomically detailed models
Topic: Creating 3d shapes from swc files
Replies: 1
Views: 4833

send me your original swc file (the one that
imports correctly) and your modified file (the
one that does not import) and I will take a look.
Send them to michael.hines@yale.edu
by hines
Fri Sep 16, 2005 1:57 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Line too long error
Replies: 4
Views: 5970

please send me your mod file. michael.hines2yale.edu it will save me the time of writing a test file. Anyway, the limit is 512 characters per line. That could be changed in nrn/src/nmodl/io.c if you compiled the unix version. Just look for the Fgets calls and where the buffer it uses is declared and...
by hines
Wed Sep 07, 2005 8:35 am
Forum: UNIX/Linux
Topic: RHEL 4 problem?
Replies: 4
Views: 7394

Re: dlopen failed on an x86 w/ RHEL

dlopen failed - /home/atm/Bennet sims/i686/.libs/libnrnmech.so: cannot open shared object file: No such file or directory First, does the file exist? If so, the problem may be spaces in the path. I only remember supportting path name spaces on mac and mswin. You can edit the i686/special file and t...
by hines
Sat Sep 03, 2005 8:58 pm
Forum: OS X
Topic: multiple mod files
Replies: 4
Views: 6342

are you by any chance running tiger instead of panther. If so install
http://www.neuron.yale.edu/ftp/neuron/v ... SX10.4.dmg
by hines
Wed Aug 31, 2005 2:08 pm
Forum: OS X
Topic: multiple mod files
Replies: 4
Views: 6342

> if i drag the entire folder onto mknrndll, it seems to only compile one of the mod files. That is probably because there is an error in the mod file which stops everything. > if i drag multiple files onto mknrndll it deletes all but one of them I programmed for folder and single file dragging, so ...
by hines
Wed Aug 31, 2005 1:50 pm
Forum: Other questions
Topic: reuse oc module to qualify software to parse .hoc data
Replies: 8
Views: 8794

by hines
Thu Aug 25, 2005 11:01 am
Forum: Modeling networks
Topic: Hf Stimulus Network Performance: Event Delivery or Pointers?
Replies: 10
Views: 11410

I'd recommend you do some profiling to find out what the rate limiting parts of the simulation are. You are right that cvode may be way too fastidious given the rate of synaptic input but that just means that if the fixed step method is faster and accurate enough, switch to that. Also try the local ...
by hines
Tue Aug 23, 2005 2:11 pm
Forum: Modeling networks
Topic: parallel simulations of networks
Replies: 6
Views: 8758

The latest alpha version: http://www.neuron.yale.edu/ftp/neuron/versions/alpha/nrn-5.8.53.tar.gz supports parallel network simulations. Further information can be found at: http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/classes/parnet.html#ParallelNetManager This has been implement...
by hines
Tue Aug 23, 2005 9:10 am
Forum: Other questions
Topic: Attaching specific jvm
Replies: 2
Views: 3203

I know that was done by the NEOSIM project though I don't see their code on the http://www.neosim.org website. However, you could certainly ask one of the contacts, specifically, Fred.Howell@ed.ac.uk how he did it.
by hines
Tue Aug 16, 2005 12:07 pm
Forum: Other questions
Topic: run neuron from a java class
Replies: 4
Views: 5150

But if NEURON is NOT built with the --with-nrnjava configure option it can still be controlled by java via stdin/stdout. Just have Java launch NEURON with the -isatty argument and everytime java sees the oc> prompt NEURON is ready for another command. I have an example that uses a pair of files call...
by hines
Tue Aug 16, 2005 11:46 am
Forum: Other questions
Topic: run neuron from a java class
Replies: 4
Views: 5150

When one builds NEURON with the --with-nrnjava configure option, it means that immediately after NEURON is launched, it will load a JVM java virtual machine. In this case, instead of calling a main program in java which then loads NEURON, call a java control routine from NEURON. Consider the file, t...
by hines
Mon Aug 08, 2005 6:19 am
Forum: UNIX/Linux
Topic: RHEL 4 problem?
Replies: 4
Views: 7394

The rpm is built on a i686 machine and perhaps there are problems using that when the shared object is constructed on a x86_64 machine. However, the specific error message points to something a bit different. The _cal_reg is derived from the name of the cal.mod file and that is being called not from...
by hines
Wed Aug 03, 2005 11:20 am
Forum: Getting started
Topic: Passing an objref array by reference to a function
Replies: 3
Views: 4736

There is no direct way to pass an objref array to a function. Probably the least violent transformation to existing code is to make use of a wrapper object as is done with strdef. The every occurrence of an array variable becomes variable.o and instead of declaring objref variable[n] one declares ob...
by hines
Sun Jul 31, 2005 9:21 am
Forum: Other questions
Topic: real time data output
Replies: 1
Views: 3187

I believe that Gwendal LeMasson <gwendal.lemasson@bordeaux.inserm.fr> uses NEURON in this way for his dynamic clamp. See the nrn/src/nrnoc/fadvance.c file and look at the function nrn_fixed_step(). Basically, you feed a double buffered DAC with output values, wait for a clock pulse that strobes the ...
by hines
Thu Jul 28, 2005 1:11 pm
Forum: Anatomically detailed models
Topic: import of neurolucida .asc
Replies: 6
Views: 8779

Edit the nrn/lib/hoc/import3d/read_nlcda3.hoc file and search for proc spine() then change the "properties() points()" line so that it looks like // properties() points() while (current.token != rightsp) { read_next_token() } that will ignore the spines. The import3d tool in the alpha version has so...