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.
A very important addition to NEURON is the ability to use JAVA. At this time, installation of this feature requires the explicit invocation of the --with-nrnjava argument to the configure command when configuring nrn-5.2. 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.
cd $HOME gunzip -c iv-14.tar.gz | tar xf - cd iv-14 ./config.guess #your hostcpu is printed in the form hostcpu-vendor-osversion ./configure --prefix=$HOME/iv make make installDownload nrn-5.2.tar.gz into home directory and then
cd $HOME gunzip -c nrn-5.2.tar.gz | tar xf - cd nrn-5.2 ./configure --prefix=$HOME/nrn --with-iv=$HOME/iv --with-nrnjava make make installFinally, test NEURON by running its "demonstration" program.
#hostcpu is the output of config.guess in the form hostcpu-vendor-osversion $HOME/nrn/hostcpu/bin/neurondemoIf the last instruction fails, try the last instruction again after
setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib:${HOME}/iv/hostcpu/lib"
cd $HOME gunzip -c nrn-5.2.tar.gz | tar xf - cd nrn-5.2 ./configure --prefix=$HOME/nrn --without-iv make make install cd $HOME/nrn/share/nrn/demo/release $HOME/nrn/hostcpu/bin/nrnivmodl hostcpu/specialIf the last command fails you may need a
setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib"
cd $HOME gunzip -c nrn-5.2.tar.gz | tar xf - cd nrn-5.2 ./configure --prefix=$HOME/nrn --without-nrniv make make install cd $HOME/nrn/share/nrn/demo/release $HOME/nrn/hostcpu/bin/nrnocmodl hostcpu/specialIf the last command fails you may need a
setenv LD_LIBRARY_PATH "${HOME}/nrn/hostcpu/lib"
iv-14.tar.gzand then download
nrn-5.2.tar.gzIn most cases the following should be sufficient for a complete installation
gunzip -c iv-14.tar.gz | tar xf - cd iv-14 #read the INSTALL file. ./configure --prefix=/where/you/want/it make make install cd .. rm -r -f iv-14
If you don't specify a prefix it defaults to /usr/local/iv
I use:
./configure --prefix=$HOME/iv
To install the NEURON part
gunzip -c nrn-5.2.tar.gz | tar xf - cd nrn-5.2 #read the INSTALL file ./configure --prefix=/where/you/want/it --with-iv=/where/you/installed/interviews make make install cd .. rm -r -f nrn-5.2
If you don't specify a prefix it defaults to /usr/local/nrn
If you don't specify a --with-iv it first looks in prefix/../iv and then
in /usr/local/iv
I use:
./configure --prefix=$HOME/nrn --with-iv=$HOME/ivNotice that in my case
./configure --prefix=$HOME/nrnwould suffice because interviews was installed in $HOME/iv
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
/where/you/want/it/hostcpu/bin/neurondemocreates /where/you/want/it/share/nrn/demo/neuron (if it doesn't already exist) and launches the demo.
If this is not the case then set these environment variables manually. After configuration, these environment variables are no longer needed.
On my machine these end up as
JDKDIR=/usr/j2se JDKLIBARCH=sparc JDKINCLUDEARECH=solarisAfter 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:
setenv LD_LIBRARY_PATH $HOME/iv/sparc/lib:/local/gnu/lib setenv LD_LIBRARY_PATH $JDKDIR/jre/lib/sparc:$LD_LIBRARY_PATH
Your PATH should be set so that it can find java, javac, and javah. On my machine I use:
set path=($JDKDIR/bin $path)
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 <~>%The key is for jni.h to have
#define JNI_VERSION_1_2 0x00010002