Search found 1576 matches

by hines
Tue Jul 19, 2005 9:14 am
Forum: UNIX/Linux
Topic: compile neuron with intel compiler for linux?
Replies: 8
Views: 8664

I suppose that is possible and there is certainly a lot of room for greater optimization by sophisticated compilers. But I have no experience with the intel compiler and so can't speak to any performance gains with respect to its use. That said, on linux it should be very easy to use that instead of...
by hines
Thu Jun 30, 2005 7:15 am
Forum: UNIX/Linux
Topic: Problems with nrn5.7 on sun/sparc
Replies: 2
Views: 6395

The first step is to try again with the alpha version at http://www.neuron.yale.edu/ftp/neuron/versions/alpha/nrn-5.8.12.tar.gz There have been a number of configuration updates so that it compiles on gcc4.0.0 on mac os x 4. That may help with gcc3.2.2 on the sparc. The next step is to try configuri...
by hines
Mon Jun 27, 2005 7:54 am
Forum: Other questions
Topic: Debug in Neuron
Replies: 2
Views: 3553

I forgot to mention that the old error message from the previous incarnation of the help system was (note the 11 year out of date email address): ------------------------------ ?1 segmentation bus segmentation violations and bus errors Implies an error in your hoc code that was mishandled by the sys...
by hines
Mon Jun 27, 2005 7:45 am
Forum: Other questions
Topic: Debug in Neuron
Replies: 2
Views: 3553

I need to update that old message. When it arises, it reflects the lack of an error check in the executable at a more reasonable diagnostic point. The first clue as to what went wrong is in the in the interpreter stack trace that is printed after the message which tells which user function was being...
by hines
Fri Jun 24, 2005 7:15 pm
Forum: Other questions
Topic: reuse oc module to qualify software to parse .hoc data
Replies: 8
Views: 8567

For user defined formats for output files you will need to know about several idioms and classes that access NEURON's internal information about the simulated model. E.g. forall for (x) print secname, x, v(x) prints all voltages for all sections. See SectionRef, MechanismType, and MechanismStandard....
by hines
Fri Jun 24, 2005 4:49 pm
Forum: Other questions
Topic: Simulations without GUI
Replies: 1
Views: 3170

What happens if you take the simulation code that includes the GUI (I assume you launch with something like "nrngui myfile.hoc") and launch with nrngui --bbs_nhost 0 myfile.hoc The option was obviously intended for other purposes but for you it has the desirable side effect of turning off the gui wi...
by hines
Tue Jun 21, 2005 7:28 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Calling C functions from NEURON
Replies: 2
Views: 5391

The easiest way to add c code to NEURON is with a mod file. Search for VERBATIM in ModelDB. NMODL provides many of the interface details automatically. But if you do want to add a c function directly into the nrn/src/oc interpreter then you are very close, only missing 3 points. Don't forget to add ...
by hines
Tue Jun 21, 2005 6:56 pm
Forum: OS X
Topic: Is NEURON 5.7.159 slow compared to the previous 5.7?
Replies: 2
Views: 5418

That slowdown is certainly not supposed to happen. Could you
zip up all the ses/mod/hoc files needed to reproduce the problem
and send them to me so I can determine the cause of the problem.
I'll have a mac osx 4 available next Monday and can get back to
you a few days after that.
by hines
Tue Jun 21, 2005 6:26 pm
Forum: UNIX/Linux
Topic: Compilation of iv-17 on SGI IRIX64 6.5 fails
Replies: 3
Views: 5703

I have not seen the strange X and $X prefixes before on the SGI or anywhere else. I'd recommend using the http://www.neuron.yale.edu/ftp/neuron/versions/alpha/iv-17.tar.gz version since it has been slightly updated to compile under gcc-4.0.0 on osx 4 but that seems a longshot for the sgi. If that ma...
by hines
Tue Jun 21, 2005 9:30 am
Forum: Other questions
Topic: Vector manipulation and play
Replies: 4
Views: 4658

I did an experiment to see if one can use pointers to weights and it indeed works. Consider the NEURONDEMO after choosing the Synchronizing Net demo. oc>NetCon[5].weight -0.3 oc>objref pp oc>pp = new Pointer(&NetCon[5].weight) oc>pp.val -0.3 oc>pp.val = -1 oc>NetCon[5].weight -1 oc> Of course the us...
by hines
Tue Jun 07, 2005 3:27 am
Forum: UNIX/Linux
Topic: Compilation error on sparc/sunOS
Replies: 2
Views: 5079

Did you have a previously installed version and overwrote the old sources with the new version? If so there has been a recent upgrade to the sundials integrators that removed and added many files. It may be that you need to do a make clean to get rid of the old .o files before doing a make. If this ...
by hines
Fri May 27, 2005 11:34 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Single Channel Simulation
Replies: 3
Views: 5443

I should also mention that a PointProcess instance of a ChannelBuilder specification, when "Allow Single Channels" is selected, can be switched between macroscopic current mode and single channel mode by setting the value of Nsingle. When Nsingle has the value of 0 then it is a macroscopic current, ...
by hines
Fri May 27, 2005 11:26 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Single Channel Simulation
Replies: 3
Views: 5443

Single channel models can only be constructed with NEURONMainMenu/Build/ChannelBuilder/Point There can only be a single gate defined as a kinetic scheme raised to the first power. At that point you can select the Properties/AllowSingleChannels checkbox. For an example, launch the NEURONDEMO and sele...
by hines
Wed May 25, 2005 7:57 am
Forum: NEURON + Python
Topic: request for comments
Replies: 13
Views: 14880

request for comments

I have a question primarily directed to those who understand quite a bit about Python and a bit about NEURON's conceptual idea of the section. Several months ago, Mike Neubig suggested that NEURON's usefulness would be greatly enhanced if Python could be used as an alternative interpreter. To this p...
by hines
Sun May 22, 2005 10:06 pm
Forum: The GUI
Topic: can't reconstitute an Impedance Path tool from a ses file
Replies: 1
Views: 4455

I see that none of the Impedance tools have the ability to save themselves into a session file. And none of them use the proper idiom for properly opting out of the session file, i.e. when the box holding the gui for the object is created one should use VBox.save("") where the argument is an empty s...