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<HEAD> |
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<!-- installunix.html --> |
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<!-- version 1.2b 3:10 PM 3/7/2002 --> |
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<TITLE>NEURON Installation for UNIX and Linux</TITLE> |
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</HEAD> |
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<BODY BGCOLOR="#ffffff"> |
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<H1> |
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NEURON Installation for UNIX and Linux |
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</H1> |
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|
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This version of InterViews and NEURON |
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uses autoconf and should |
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be much easier to install than with the older Imake installation method |
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(e.g. 4.2.1 and earlier). |
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I (Michael Hines) am extremely grateful to Gary Holt (holt@LNC.usc.edu) |
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for writing the original autoconf scripts for this package. |
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I have modified these scripts in several ways and all bugs should be |
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considered my own. Please notify me (michael.hines@yale.edu) if this |
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package does not install properly on your machine. |
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<p> |
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In general there should no longer be any requirement for CPU, NEURONHOME, |
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or LD_LIBRARY_PATH environment variables. However, if you have trouble |
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launching NEURON it may be because I am not using libtool generically in |
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the configuration files and need an explicit LD_LIBRARY_PATH for interviews |
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or for the compiler libraries. |
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<p> |
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A very important addition to NEURON is the |
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<a href="#java">ability to use JAVA.</a> At this time, installation of |
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this feature requires the explicit invocation of the |
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<a href="#withnrnjava">--with-nrnjava</a> |
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argument to the configure command when configuring nrn-5.3. |
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I am very grateful to Fred Howell (fwh@anc.ed.ac.uk) of Nigel Goddard's lab |
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for designing and providing a sample implementation of the NEURON to Java |
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interface. |
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|
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<H2> Quick Installation Instructions </H2> |
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|
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Note: Neuron may be installed in its extraction directory. Use |
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--prefix=`pwd` in the ./configure command. |
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|
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<H3>Full installation with InterViews (strongly recommended)</H3> |
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Download |
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<a href="ftp://ftp.neuron.yale.edu/neuron/unix/iv-15.tar.gz">iv-15.tar.gz</a> |
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into home directory and then |
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<pre> |
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cd $HOME |
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gunzip -c iv-15.tar.gz | tar xf - |
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cd iv-15 |
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./config.guess #your hostcpu is printed in the form hostcpu-vendor-osversion |
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./configure --prefix=$HOME/iv |
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make |
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make install |
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</pre> |
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|
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Download |
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<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz"> |
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nrn-5.3.tar.gz</a> |
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into home directory and then |
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<pre> |
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cd $HOME |
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gunzip -c nrn-5.3.tar.gz | tar xf - |
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cd nrn-5.3 |
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./configure --prefix=$HOME/nrn --with-iv=$HOME/iv <a href="#withnrnjava">--with-nrnjava</a> |
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|
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make |
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make install |
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</pre> |
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|
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Finally, test NEURON by running its "demonstration" program. |
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<pre> |
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#hostcpu is the output of config.guess in the form hostcpu-vendor-osversion |
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$HOME/nrn/hostcpu/bin/neurondemo |
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</pre> |
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|
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If the last instruction fails, try the last instruction again after |
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<pre> |
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setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib:${HOME}/iv/hostcpu/lib" |
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</pre> |
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|
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<H3>Installation of NRNIV without GUI classes (no GUI) </H3> |
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Download |
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<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz"> |
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nrn-5.3.tar.gz</a> |
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into home directory and then |
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<pre> |
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cd $HOME |
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gunzip -c nrn-5.3.tar.gz | tar xf - |
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cd nrn-5.3 |
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./configure --prefix=$HOME/nrn --without-iv |
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make |
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make install |
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cd $HOME/nrn/share/nrn/demo/release |
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$HOME/nrn/hostcpu/bin/nrnivmodl |
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hostcpu/special |
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</pre> |
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|
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If the last command fails you may need a |
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<pre> |
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setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib" |
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</pre> |
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|
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<H3>NRNOC only (no c++ classes)</H3> |
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Download |
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<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz"> |
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nrn-5.3.tar.gz</a> |
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into home directory and then |
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<pre> |
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cd $HOME |
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gunzip -c nrn-5.3.tar.gz | tar xf - |
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cd nrn-5.3 |
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./configure --prefix=$HOME/nrn --without-nrniv |
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make |
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make install |
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cd $HOME/nrn/share/nrn/demo/release |
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$HOME/nrn/hostcpu/bin/nrnocmodl |
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hostcpu/special |
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</pre> |
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|
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If the last command fails you may need a |
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<pre> |
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setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib" |
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</pre> |
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|
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<H2> More details </H2> |
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To install the package first download |
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<pre> |
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<a href="ftp://ftp.neuron.yale.edu/neuron/unix/iv-15.tar.gz">iv-15.tar.gz</a> |
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</pre> |
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and then download |
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<pre> |
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<a href="ftp://ftp.neuron.yale.edu/neuron/unix/nrn-5.3.tar.gz">nrn-5.3.tar.gz</a> |
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</pre> |
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In most cases the following should be sufficient for a complete installation |
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<pre> |
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gunzip -c iv-15.tar.gz | tar xf - |
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cd iv-15 |
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#read the <a href="iv15-install">INSTALL</a> file. |
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./configure --prefix=/where/you/want/it |
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make |
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make install |
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cd .. |
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rm -r -f iv-15 |
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</pre> |
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<p> |
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|
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If you don't specify a prefix it defaults to /usr/local/iv<br> |
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I use: |
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<pre> |
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./configure --prefix=$HOME/iv |
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</pre> |
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<p> |
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|
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To install the NEURON part |
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<pre> |
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gunzip -c nrn-5.3.tar.gz | tar xf - |
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cd nrn-5.3 |
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#read the <a href="nrn-install">INSTALL</a> file |
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./configure --prefix=/where/you/want/it --with-iv=/where/you/installed/interviews |
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make |
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make install |
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cd .. |
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rm -r -f nrn-5.3 |
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</pre> |
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<p> |
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|
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If you don't specify a prefix it defaults to /usr/local/nrn<br> |
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If you don't specify a --with-iv it first looks in prefix/../iv and then |
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in /usr/local/iv |
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<br> |
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I use: |
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<pre> |
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./configure --prefix=$HOME/nrn --with-iv=$HOME/iv |
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</pre> |
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Notice that in my case |
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<pre> |
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./configure --prefix=$HOME/nrn |
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</pre> |
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would suffice because interviews was installed in $HOME/iv |
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<p> |
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|
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In general there should no longer be any requirement for CPU, NEURONHOME, |
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or LD_LIBRARY_PATH environment variables. However, if you have trouble |
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launching NEURON it may be because I am not using libtool generically in |
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the configuration files and need an explicit LD_LIBRARY_PATH for interviews |
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or for the compiler libraries. |
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Installation is successful if |
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<pre> |
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/where/you/want/it/hostcpu/bin/neurondemo |
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</pre> |
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creates /where/you/want/it/share/nrn/demo/neuron |
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(if it doesn't already exist) and launches the demo. |
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<P> |
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<a name="java"></a> |
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<h1>NEURON and Java together</h1> |
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When Java is built into NEURON, launching NEURON (with nrniv, special, |
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nrngui, etc) also initializes the java virtual machine. |
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With load_java("java.class.name") or load_java("java.class.name", "HocName") |
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one loads and registers Java classes |
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and their methods with the hoc interpreter. From the |
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hoc interpreter, one can then instantiate and use java objects. |
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Furthermore, user developed java classes |
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can obtain information from NEURON and execute |
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NEURON statements. It is likely that all future GUI development |
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for NEURON will take place in java. |
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<br> |
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<a href="src/nrnjava/nrnjava.html">src/nrnjava/nrnjava.html</a> |
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<p> |
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<a name="withnrnjava"></a> |
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<h1>Building Java into NEURON</h1> |
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Configure makes some half hearted attempts to figure out where |
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the java development environment, include files, and libjvm are |
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located but may not always be successful. We assume |
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<br> |
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1) jni.h is in $JDKDIR/include and that may include a file in |
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$JDKDIR/include/$JDKINCLUDEARCH. Generally, java, javac, etc. |
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are located in $JDKDIR/bin. |
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<br> |
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2) libjvm... is in $JDKDIR/jre/lib/$JDKLIBARCH |
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<p> |
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<a href="#important">Important Note!! README!</a> |
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<p> |
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If this is not the case then set these environment variables |
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manually. After configuration, these environment variables |
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are no longer needed. |
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<p> |
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On my machine these end up as |
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<pre> |
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JDKDIR=/usr/j2se |
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JDKLIBARCH=sparc |
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JDKINCLUDEARECH=solaris |
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</pre> |
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After building NEURON, you may need a LD_LIBRARY_PATH |
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addition to tell where to find this library at run time. On my machine |
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I use: |
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<pre> |
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setenv LD_LIBRARY_PATH $HOME/iv/sparc/lib:/local/gnu/lib |
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setenv LD_LIBRARY_PATH $JDKDIR/jre/lib/sparc:$LD_LIBRARY_PATH |
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</pre> |
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<p> |
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Your PATH should be set so that it can find java, javac, and javah. |
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On my machine I use: |
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<pre> |
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set path=($JDKDIR/bin $path) |
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</pre> |
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<p> |
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<a name="important"></a> |
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<h1> Important Note </h1> |
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You must have a relatively recent version of Java installed. |
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Mine is |
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<pre> |
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hines <~>% java -version |
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java version "1.3.0_02" |
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Java(TM) 2 Runtime Environment, Standard Edition (build 1.3.0_02) |
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Java HotSpot(TM) Client VM (build 1.3.0_02, mixed mode) |
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hines <~>% |
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</pre> |
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The key is for jni.h to have |
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<pre> |
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#define JNI_VERSION_1_2 0x00010002 |
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</pre> |
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|
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<hr> |
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<FONT size = -1><EM> Page and graphics copyright © 1999-2002 N.T. Carnevale and M.L. Hines, |
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All Rights Reserved.</EM></FONT> |
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</BODY></HTML> |
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