Index of /pub/misc2/neuron/unix

      Name                                               Last modified       Size  Description


[DIR] Parent Directory                                   12-Apr-2001 23:40      -  
[TXT] README                                             10-Feb-1999 20:45     8k  
[   ] bison-1.25.tar.gz                                  25-Nov-1996 17:18   281k  GZIP compressed docume>
[CMP] celbild.tar.Z                                      01-Mar-1999 14:49    24k  tar archive
[TXT] changelog4.1.1                                     10-Feb-1999 20:42    42k  
[   ] gcc-2.7.2.tar.gz                                   04-Jan-1996 22:41   6.8M  GZIP compressed docume>
[CMP] iv3.2a.hines9.tar.Z                                10-Feb-1999 20:42   1.4M  tar archive
[   ] libg++-2.7.1.tar.gz                                04-Jan-1996 22:41   1.5M  GZIP compressed docume>
[CMP] nrn4.1.1.tar.Z                                     10-Feb-1999 20:43   3.1M  tar archive
[CMP] nrn4.1.1a.tar.Z                                    01-Mar-1999 18:52   3.1M  tar archive
[CMP] nrn411to411a.tar.Z                                 01-Mar-1999 18:56    69k  tar archive
[CMP] unzip512.tar.Z                                     03-Oct-1995 19:33   514k  tar archive
[   ] zip201.zip                                         03-Oct-1995 01:00   240k  

This is version 4.1.1 of NEURON with the CVODE variable time
step variable order integration method, two extracellular layers
(compilable with more if needed), local variable
time step method (separate dt per cell), network connection
objects (NetCon), graphical CellBuilder, and Multiple Run Fitter.

Installation is similar to that of
nrn4.1. Changes since 4.1 are listed in the
changelog4.1.1 file.

Configuration is set up for Matrix and CVode class and the CC compiler.

To eliminate Matrix and/or CVode classes
edit the $NEURONHOME/src/config/(usematrix.def and/or usecvode.def)
definitions to 0. More information about these classes can be found in
the matrix.html and cvode.html files in the help system.
http://www.neuron.yale.edu/neuron/help/neuron/general/classes/matrix/matrix.html
http://www.neuron.yale.edu/neuron/help/neuron/neuron/classes/cvode.html

The complete set of html help files is in the ../mswin/html.zip file.

You DO NOT need to get the mesch or cvode tar files from ../../old/v4.0.1
as all the needed
sources are in the nrn4*.tar.Z files. These files do have extra
documentation however.

To compile with gcc2.7.2 edit the relevant line in
$NEURONHOME/src/config/InterViews/local.def.

If you do not currently have iv3.2a.hines8.tar.Z with the regexp.c fix
installed then install
iv3.2a.hines9.tar.Z. This should install without modification under LINUX.

---
following is a edited copy of the old 3.2.3 README file which contains
further installation hints.
---
This is a version of neuron whose interpreter, now "OC",
has been enhanced to allow object oriented programming (strictly
speaking, encapsulated data structures, since there is no inheritance
or polymorphism) and dynamic creation of arrays. It also uses the
gnu readline library for emacs-like command line editing. Oc
can be event driven which is the handle for the graphical user interface.
Finally, it contains hooks for interfacing C++ classes for use in the
interpreter.

All documentation is found aat
http://www.neuron.yale.edu/neuron.html
The files may be installed on your machine by getting the html source from
ftp://ftp.neuron.yale.edu:neuron/unix/html4.1.1.zip.

The neuron specific portion, now "NRNOC", allows the user to create and
maintain lists of sections which can be very efficiently iterated.
Creation of sections can be done piecemeal instead of having to use
a single "create" statement. Sections can be created inside objects.
The number crunching has been vectorized for vastly increased efficiency
on machines like a CRAY (passive nodes take about half the time on
regular machines as well).

The point process syntax using vectors of point processes has been
abandoned in favor of treating them as objects. The .oc and .hoc file
differences in nmodl/examples illustrate the syntax differences.
Fortunately or unfortunately this is a serious break with past versions
of NEURON and will require modifications to any hoc file using point
processes.

All neuron sources are in nrn4.1.1.tar.Z
You need approximately 30Mb of disk space not counting
the compressed tar file.

The graphical interface portion which has nothing to do with neurons ( ie.
graphs and menus) is independently linked with OC to form IVOC and lives
in the IVOC directory. All interface files are written in C++ and make
use of the public domain InterViews library from stanford. This part also
adds the built-in List class to construct lists of objects and a File
class to allow more than one open file for reading and writing data.

The graphical interface portion which is neuron specific is linked with
OC, IVOC, and NRNOC to make NRNIV. The nrniv specific files live in the
nrniv directory.

DO NOT EVEN BOTHER to run InstallNRNIV until after you have successfully
built InterViews from 
iv3.2a.hines9.tar.Z in this directory (an already installed hines7
version of InteViews will work as well. hines6 and before WILL NOT work)
To do that you will need a C++ compiler
and about 70 MBytes of disk space.
(The source to gcc2.7.2 are here as well. See GCCinstall).

COMPILING:

Although a shell script may get made that will build the whole thing
silently, at this point the process is too lengthy to trust to a single
command.

1)
	The nrn4....tar.Z file has a main directory of nrn. Use
	zcat nrn4*Z |tar tf -|more to see the names of the files
	that will be extracted (When extracted, a nrn directroy will be
	created and all files will go there).
	Move to the parent directory where you want the nrn directory to
	be and extract with:
		zcat nrn4*.tar.Z|tar xf -
	You may rename the nrn directory if you wish.
	Move to the nrn directory.
	Run InstallNRNOC or else build
		memacs, readline, scopmath, sparse, modlunit, nmodl,
		ivoc, nrnoc, CVODE, and mesch
	   in that order. You will need the enviroment variables CPU and
		NEURONHOME. On my machine they are SUN4 and /home/hines/nrn

The most common problem that prevents proper installation is
a non-standard location for X11 include files and libraries.
If you don't have a directory called /usr/include/X11 then
be sure to read the info about X11 paths in
$NEURONHOME/config/InterViews/local.def
You may also need to change the hardwired path in
$NEURONHOME/bin/imknrn

Because it is not easy to configure makedepend, by default it is defined
as
#define DependCmd true
at the front of  $NEURONHOME/src/config/local.def

Success is achieved if you get $NEURONHOME/bin/$CPU/nrnoc and the
libraries: lib/$CPU/libcvode... and lib/$CPU/libmesch...

2)
	Build and install my version of InterViews from the file
	iv3.2a.hines7.tar.Z. Do it in a place that has about
	40 MBytes of free space. I extract in a directory called
	interviews3.2 which extracts everything into
	a subdirectory called iv and also extracts a README file.
	On my machine, a SUN4 under Solaris2.5 and an SGI it installs out
	of the box under gcc2.7.2 and CC respectively.

	Another possible difficulty is that some machines have installed
	x window include and library directories in a nonstandard place.
	If you don't have /usr/include/X11 and/or /usr/lib/X11 then
	make sure you look in config/InterViews/local.def which will
	tell you what to do.
	
	If you are installing under LINUX, do NOT change local.def. Instead
	look at iv/src/config/InterViews/iv-linux.cf to see the
	InstalledRoot where the installation will end up (/usr/interviews).

	Make the symbolic link between /interviews and iv/installed. On my
	machine I said.
		ln -s /timshel2g/interviews3.1-beta2/iv/installed /interviews
	If you can't do that then you'd better read the iv/README file about
	how to install it in a nonstandard place.

	If using gcc under solaris, make the indicated change in
	iv/src/config/InterViews/local.def

	Make sure the environment variable CPU is set.
	in iv say
		make World
	in such a way that all the output gets saved to a file so
	you can make sure it was successful. I say
		sh
		make World 1>worldoutput 2>&1
	This takes at least an hour.
	Then test it by moving to iv/src/bin/idraw/SUN4 and typeing
		a.out
	If you get a macdraw like drawing editor then go back to
	iv and say make install.

3)
	Build nrniv, (neuron with a graphical user interface)
	in the NEURONHOME directory
	It can be done by executing the InstallNRNIV script.

4)	The environment variables needed for a .cshrc on a SUN using gcc
are:
# source this in the nrn directory to get proper environment
setenv CPU SUN4
setenv NEURONHOME `pwd`
setenv N $NEURONHOME
setenv IV /local/interviews
set path=($N/bin $N/bin/$CPU $IV/bin/$CPU $path)
setenv LD_LIBRARY_PATH "$N/lib/${CPU}:$IV/lib/${CPU}:/usr/openwin/lib:\
/local/gnu/lib"

On linux instead of a LD_LIBRARY_PATH it is better to rebuild the
configuration file with:
echo /usr/local/interviews/lib >> /etc/ld.so.conf ; ldconfig
echo /usr/local/neuron/lib >> /etc/ld.so.conf ; ldconfig

5)	Build the demo and play with it by executing neurondemo
	and following the instructions until it works.