installunix.html

.....2<HTML>
<HEAD>
  <!-- installunix.html -->
  <!-- version 1.2b 3:10 PM 3/7/2002 -->
  <TITLE>NEURON Installation for UNIX and Linux</TITLE>
</HEAD>
<BODY BGCOLOR="#ffffff">
<H1>
NEURON Installation for UNIX and Linux
</H1>

This version of InterViews and NEURON 
uses autoconf and should
be much easier to install than with the older Imake installation method
(e.g. 4.2.1 and earlier).
I (Michael Hines) am extremely grateful to Gary Holt (holt@LNC.usc.edu)
for writing the original autoconf scripts for this package.
I have modified these scripts in several ways and all bugs should be
considered my own. Please notify me (michael.hines@yale.edu) if this
package does not install properly on your machine.
<p>
In general there should no longer be any requirement for CPU, NEURONHOME,
or LD_LIBRARY_PATH environment variables. However, if you have trouble
launching NEURON it may be because I am not using libtool generically in
the configuration files and need an explicit LD_LIBRARY_PATH for interviews
or for the compiler libraries.
<p>
A very important addition to NEURON is the
<a href="#java">ability to use JAVA.</a> At this time, installation of
this feature requires the explicit invocation of the
<a href="#withnrnjava">--with-nrnjava</a>
argument to the configure command when configuring nrn-5.3.
I am very grateful to Fred Howell (fwh@anc.ed.ac.uk) of Nigel Goddard's lab
for designing and providing a sample implementation of the NEURON to Java
interface.

<H2> Quick Installation Instructions </H2>

Note: Neuron may be installed in its extraction directory. Use
--prefix=`pwd` in the ./configure command.

<H3>Full installation with InterViews (strongly recommended)</H3>
Download
<a href="ftp://ftp.neuron.yale.edu/neuron/unix/iv-15.tar.gz">iv-15.tar.gz</a>
into home directory and then
<pre>
cd $HOME
gunzip -c iv-15.tar.gz | tar xf -
cd iv-15
./config.guess #your hostcpu is printed in the form hostcpu-vendor-osversion
./configure --prefix=$HOME/iv
make
make install
</pre>

Download
<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz">
nrn-5.3.tar.gz</a>
into home directory and then
<pre>
cd $HOME
gunzip -c nrn-5.3.tar.gz | tar xf -
cd nrn-5.3
./configure --prefix=$HOME/nrn --with-iv=$HOME/iv <a href="#withnrnjava">--with-nrnjava</a>

make
make install
</pre>

Finally, test NEURON by running its "demonstration" program.
<pre>
#hostcpu is the output of config.guess in the form hostcpu-vendor-osversion
$HOME/nrn/hostcpu/bin/neurondemo
</pre>

If the last instruction fails, try the last instruction again after
<pre>
setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib:${HOME}/iv/hostcpu/lib"
</pre>

<H3>Installation of NRNIV without GUI classes (no GUI) </H3>
Download
<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz">
nrn-5.3.tar.gz</a>
into home directory and then
<pre>
cd $HOME
gunzip -c nrn-5.3.tar.gz | tar xf -
cd nrn-5.3
./configure --prefix=$HOME/nrn --without-iv
make
make install
cd $HOME/nrn/share/nrn/demo/release
$HOME/nrn/hostcpu/bin/nrnivmodl
hostcpu/special
</pre>

If the last command fails you may need a
<pre>
setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib"
</pre>

<H3>NRNOC only (no c++ classes)</H3>
Download
<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz">
nrn-5.3.tar.gz</a>
into home directory and then
<pre>
cd $HOME
gunzip -c nrn-5.3.tar.gz | tar xf -
cd nrn-5.3
./configure --prefix=$HOME/nrn --without-nrniv
make
make install
cd $HOME/nrn/share/nrn/demo/release
$HOME/nrn/hostcpu/bin/nrnocmodl
hostcpu/special
</pre>

If the last command fails you may need a
<pre>
setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib"
</pre>

<H2> More details </H2>
To install the package first download
<pre>
<a href="ftp://ftp.neuron.yale.edu/neuron/unix/iv-15.tar.gz">iv-15.tar.gz</a>
</pre>
and then download
<pre>
<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz">nrn-5.3.tar.gz</a>
</pre>

In most cases the following should be sufficient for a complete installation
<pre>
gunzip -c iv-15.tar.gz | tar xf -
cd iv-15
#read the <a href="iv15-install">INSTALL</a> file.
./configure --prefix=/where/you/want/it
make
make install
cd ..
rm -r -f iv-15
</pre>
<p>

If you don't specify a prefix it defaults to /usr/local/iv<br>
I use:
<pre>
./configure --prefix=$HOME/iv
</pre>
<p>

To install the NEURON part
<pre>
gunzip -c nrn-5.3.tar.gz | tar xf -
cd nrn-5.3
#read the <a href="nrn-install">INSTALL</a> file
./configure --prefix=/where/you/want/it --with-iv=/where/you/installed/interviews
make
make install
cd ..
rm -r -f nrn-5.3
</pre>
<p>

If you don't specify a prefix it defaults to /usr/local/nrn<br>
If you don't specify a --with-iv it first looks in prefix/../iv and then
in /usr/local/iv
<br>
I use:
<pre>
./configure --prefix=$HOME/nrn --with-iv=$HOME/iv
</pre>
Notice that in my case
<pre>
./configure --prefix=$HOME/nrn
</pre>
would suffice because interviews was installed in $HOME/iv
<p>

In general there should no longer be any requirement for CPU, NEURONHOME,
or LD_LIBRARY_PATH environment variables. However, if you have trouble
launching NEURON it may be because I am not using libtool generically in
the configuration files and need an explicit LD_LIBRARY_PATH for interviews
or for the compiler libraries.
Installation is successful if
<pre>
/where/you/want/it/hostcpu/bin/neurondemo
</pre>
creates /where/you/want/it/share/nrn/demo/neuron
(if it doesn't already exist) and launches the demo.

<P>
<a name="java"></a>
<h1>NEURON and Java together</h1>
When Java is built into NEURON, launching NEURON (with nrniv, special,
nrngui, etc) also initializes the java virtual machine.
With load_java("java.class.name") or load_java("java.class.name", "HocName")
one loads and registers Java classes
and their methods with the hoc interpreter. From the
hoc interpreter, one can then instantiate and use java objects.
Furthermore, user developed java classes
can obtain information from NEURON and execute
NEURON statements. It is likely that all future GUI development
for NEURON will take place in java.
<br>
<a href="src/nrnjava/nrnjava.html">src/nrnjava/nrnjava.html</a>
<p>
<a name="withnrnjava"></a>
<h1>Building Java into NEURON</h1>
Configure makes some half hearted attempts to figure out where
the java development environment, include files, and libjvm are
located but may not always be successful. We assume
<br>
1) jni.h is in $JDKDIR/include and that may include a file in
$JDKDIR/include/$JDKINCLUDEARCH. Generally, java, javac, etc.
are located in $JDKDIR/bin.
<br>
2) libjvm... is in $JDKDIR/jre/lib/$JDKLIBARCH
<p>
<a href="#important">Important Note!! README!</a>
<p>
If this is not the case then set these environment variables
manually. After configuration, these environment variables
are no longer needed.
<p>
On my machine these end up as
<pre>
JDKDIR=/usr/j2se
JDKLIBARCH=sparc
JDKINCLUDEARECH=solaris
</pre>
After building NEURON, you may need a LD_LIBRARY_PATH
addition to tell where to find this library at run time. On my machine
I use:
<pre>
setenv LD_LIBRARY_PATH $HOME/iv/sparc/lib:/local/gnu/lib
setenv LD_LIBRARY_PATH $JDKDIR/jre/lib/sparc:$LD_LIBRARY_PATH
</pre>
<p>
Your PATH should be set so that it can find java, javac, and javah.
On my machine I use:
<pre>
set path=($JDKDIR/bin $path)
</pre>
<p>
<a name="important"></a>
<h1> Important Note </h1>
You must have a relatively recent version of Java installed.
Mine is
<pre>
hines <~>% java -version
java version "1.3.0_02"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.3.0_02)
Java HotSpot(TM) Client VM (build 1.3.0_02, mixed mode)
hines <~>% 
</pre>
The key is for jni.h to have
<pre>
#define JNI_VERSION_1_2 0x00010002
</pre>

  <hr>
<FONT size = -1><EM> Page and graphics copyright &copy; 1999-2002 N.T. Carnevale and M.L. Hines,
All Rights Reserved.</EM></FONT>
</BODY></HTML>