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INSTALL.md

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Brief instructions:

First, install the interviews distribution that comes from the same place as you got the neuron distribution (see the INSTALL file there for details).

following:

% gzip -dc nrn-4.2.3.tar.gz | tar -xf - # You've already done this if you're % # reading this file. % cd nrn-4.2.3 % ./configure --prefix=/where/you/want/neuron --with-iv=/where/you/put/interviews % make % make install % cd .. % rm -rf nrn-4.2.3 # You don't need this directory any more. % /where/you/want/neuron/bin/neurondemo

the above line tests the nrnivmodl script and runs the demo. alternatively

you can run the bare executable (with only built in model descriptions

with

% /where/you/want/neuron/bin/nrniv

% cd (directory where you have all your .mod files) % /where/you/want/neuron/bin/nrnivmodl % i686/special # Will be in a different subdirectory depending % # on your architecture.

the above special may be only a script with the actual executable in

i686/.libs/special

this latter can be moved to another location and executed.

MACHINE PROBLEMS

Some machines have problems which have work arounds specifically incorporated into the configure script. Those machines are listed here as examples of what has gone occasionally wrong in the past with generic installation attempts and how to fix them. If installation on your machine does not work the first time execute config.guess and see if your machine appears in this list for some hints about how to install. If your machine does not appear in this list but it still doesn't install, look at the list of occasional problems.

No machines in list.

OCCASIONAL INSTALLATION PROBLEMS (machines indicated for each problem automatically do the indicated work around within the configure file)

bison exists but it doesn't work alpha-cray-unicosmk2.0.4.90 (at least on the t3e at sdsc)

force use of yacc with
setenv YACC yacc ; configure ....

parse1.c or lex.c does not compile alpha-cray-unicosmk2.0.4.90 (at least on the t3e at sdsc)

force the re-translation of .y and .l files with
touch `find . -name \*.\[yl\] -print`

too many ld warnings mips-sgi-irix6.2

suppress warnings with:
setenv LDFLAGS -w ; configure ....

compiler internal error gcc-2.8.1

compile c++ files without optimization
setenv CXXFLAGS -g

applications fail to launch because shared libraries cannot be found setenv LD_LIBRARY_PATH /list/of:/library/paths:/to/find/them/in

More detailed instructions:

When neuron is configured it checks to see if the GNU readline library is already installed. If not then it builds an old version of the readline library which is located in src/readline.

In addition, you will need to install the interviews library. You cannot use the vanilla interviews library that may come packaged with X11, or may be available as a separate package with your operating system. You must use the custom-modified interviews library which is available from the neuron web site neuron.yale.edu or wherever you got the this neuron distribution from. Read the INSTALL file in that distribution for details. Again, you can install the interviews library in the same directory that you're going to install neuron in.

Once you've got these libraries installed, do

./configure --prefix=/where/you/want/neuron

If you don't specify a prefix, it defaults to /usr/local. Unlike previous versions of neuron, it is difficult to move neuron once you've installed it, so pick your installation directory carefully.

There are a couple of options to configure that you may need:

--with-iv=/where/you/put/interviews
		Use this if you didn't install your interviews
		distribution in a standard place (like /usr/local).

--with-readline=/where/you/put/readline
		Use this if you didn't install readline in a
		standard place.

--enable-static --enable-debug
		This may be useful if you're trying to debug the
		neuron sources themselves.  This builds static
		libraries in addition to the shared libraries.

--with-nrnpython=/where/you/put/python
                    Access the NEURON python API

It's possible that you need to specify the location of your X11 files, if they aren't in some standard place like /usr/X11R6/lib or /usr/lib/X11; do "configure --help" and look at the --with-X options.

You may also need to specify the name of your C++ compiler. (The configure script can guess the name of the C++ compiler for many systems.) Do this with a command like this:

CXX=/some/weird/place/bin/my_special_c++ ./configure

or on systems with the env command,

env CXX=/some/weird/place/bin/my_special_c++ ./configure

You might also need to specify the LIBS variable in the same way if there are special libraries you need to link with.

Once the configure procedure has successfully run, type "make". This will take a few minutes and will build everything in neuron. (Unlike previous versions of neuron, this builds both nrnoc and nrniv.)

If you run into compilation errors with the files "lex.c", then you will need to rerun lex or flex on the .l files. In this case, you must have lex or flex installed on your system and in your path. (Flex is freely available from the Free Software Foundation, www.gnu.org.) Delete all the files named "lex.c" (there are several in different directories), and make should automatically rebuild them for you using the version of flex that you have installed on your system.

Similarly, if you run into compilation errors with the files "ytab.c" or "d_ytab.c", then you will probably need to rerun bison or yacc on the .y files. To do this, simply delete the offending .c files and the make procedure will automatically rebuild them for you using the bison that you have on your system. If your problem is with d_ytab.c, then you must have bison (yacc isn't good enough, sorry). Bison is freely available from www.gnu.org.

Once compilation is complete, you will need to install neuron in order to use it. (This is different from previous versions.) Type "make install" to do so. Once you've installed neuron, no files in the directory tree that you untarred neuron into are needed any more; you may delete the whole thing. (This is also different from previous versions.)

As with any other unix package, it is not a good idea to move neuron around once you've installed it, because the directory names are coded into the files themselves. If you need to move it, put a soft link in its original location that points to the new location (so the old filenames will still work). Better yet, simply recompile neuron specifying the new installation directory.

In previous versions of NEURON, you needed to set the NEURONHOME environment variable and the CPU variable, and often LD_LIBRARY_PATH as well. This should no longer be necessary. Simply run the binaries that are installed. E.g., if you did "configure --prefix=/usr/local/stow/neuron-4.2.2", then you would run

/usr/local/stow/neuron-4.2.2/bin/nrniv

Or you can put that directory in your path.

To compile your own special purpose .mod files into neuron, use the following procedure:

  1. Cd to the directory that contains your .mod files.
  2. Type "/where/you/put/neuron/bin/nrnivmodl" (or, if you put that directory in your path, just type "nrnivmodl"). This will create a subdirectory of the current directory which is your CPU name (e.g., if you're running neuron on a pentium II or III, the subdirectory is called "i686". Inside this directory is created the program "special", which is the neuron binary that you want to run.

Automake and autoconf scripts were originally done for this package by Gary Holt (holt@LNC.usc.edu). These replace the treacherous primitive Imakefile jungle with the modern temperate forest of autoconf. If you wish to modify the Makefile.am files, you will need both autoconf and automake. I used autoconf-2.13 and automake-1.4; I doubt you can use earlier versions.

Following are the generic installation instructions for any package with a configure script.

Basic Installation

These are generic installation instructions.

The configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a Makefile' in each directory of the package. It may also create one or more .h' files containing system-dependent definitions. Finally, it creates a shell script config.status' that you can run in the future to recreate the current configuration, a file config.cache' that saves the results of its tests to speed up reconfiguring, and a file config.log' containing compiler output (useful mainly for debugging `configure').

If you need to do unusual things to compile the package, please try to figure out how configure' could check whether to do them, and mail diffs or instructions to the address given in the README' so they can be considered for the next release. If at some point `config.cache' contains results you don't want to keep, you may remove or edit it.

The file configure.ac' is used to create configure' by a program called autoconf'. You only need configure.ac' if you want to change it or regenerate configure' using a newer version of autoconf'.

The simplest way to compile this package is:

  1. cd' to the directory containing the package's source code and type ./configure' to configure the package for your system. If you're using csh' on an old version of System V, you might need to type sh ./configure' instead to prevent csh' from trying to execute configure' itself.

    Running `configure' takes awhile. While running, it prints some messages telling which features it is checking for.

  2. Type `make' to compile the package.

  3. Optionally, type `make check' to run any self-tests that come with the package.

  4. Type `make install' to install the programs and any data files and documentation.

  5. You can remove the program binaries and object files from the source code directory by typing make clean'. To also remove the files that configure' created (so you can compile the package for a different kind of computer), type make distclean'. There is also a make maintainer-clean' target, but that is intended mainly for the package's developers. If you use it, you may have to get all sorts of other programs in order to regenerate files that came with the distribution.

Compilers and Options

Some systems require unusual options for compilation or linking that the configure' script does not know about. You can give configure' initial values for variables by setting them in the environment. Using a Bourne-compatible shell, you can do that on the command line like this: CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure

Or on systems that have the `env' program, you can do it like this: env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure

Compiling For Multiple Architectures

You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their own directory. To do this, you must use a version of make' that supports the VPATH' variable, such as GNU make'. cd' to the directory where you want the object files and executables to go and run the configure' script. configure' automatically checks for the source code in the directory that configure' is in and in ..'.

If you have to use a make' that does not supports the VPATH' variable, you have to compile the package for one architecture at a time in the source code directory. After you have installed the package for one architecture, use `make distclean' before reconfiguring for another architecture.

Installation Names

By default, make install' will install the package's files in /usr/local/bin', /usr/local/man', etc. You can specify an installation prefix other than /usr/local' by giving configure' the option --prefix=PATH'.

You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you give configure' the option --exec-prefix=PATH', the package will use PATH as the prefix for installing programs and libraries. Documentation and other data files will still use the regular prefix.

In addition, if you use an unusual directory layout you can give options like --bindir=PATH' to specify different values for particular kinds of files. Run configure --help' for a list of the directories you can set and what kinds of files go in them.

If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving configure' the option --program-prefix=PREFIX' or `--program-suffix=SUFFIX'.

Optional Features

Some packages pay attention to --enable-FEATURE' options to configure', where FEATURE indicates an optional part of the package. They may also pay attention to --with-PACKAGE' options, where PACKAGE is something like gnu-as' or x' (for the X Window System). The README' should mention any --enable-' and --with-' options that the package recognizes.

For packages that use the X Window System, configure' can usually find the X include and library files automatically, but if it doesn't, you can use the configure' options --x-includes=DIR' and --x-libraries=DIR' to specify their locations.

Specifying the System Type

There may be some features configure' can not figure out automatically, but needs to determine by the type of host the package will run on. Usually configure' can figure that out, but if it prints a message saying it can not guess the host type, give it the --host=TYPE' option. TYPE can either be a short name for the system type, such as sun4', or a canonical name with three fields: CPU-COMPANY-SYSTEM

See the file config.sub' for the possible values of each field. If config.sub' isn't included in this package, then this package doesn't need to know the host type.

If you are building compiler tools for cross-compiling, you can also use the --target=TYPE' option to select the type of system they will produce code for and the --build=TYPE' option to select the type of system on which you are compiling the package.

Sharing Defaults

If you want to set default values for configure' scripts to share, you can create a site shell script called config.site' that gives default values for variables like CC', cache_file', and prefix'. configure' looks for PREFIX/share/config.site' if it exists, then PREFIX/etc/config.site' if it exists. Or, you can set the CONFIG_SITE' environment variable to the location of the site script. A warning: not all configure' scripts look for a site script.

Operation Controls

`configure' recognizes the following options to control how it operates.

--cache-file=FILE' Use and save the results of the tests in FILE instead of ./config.cache'. Set FILE to /dev/null' to disable caching, for debugging configure'.

--help' Print a summary of the options to configure', and exit.

--quiet' --silent' -q' Do not print messages saying which checks are being made. To suppress all normal output, redirect it to /dev/null' (any error messages will still be shown).

--srcdir=DIR' Look for the package's source code in directory DIR. Usually configure' can determine that directory automatically.

--version' Print the version of Autoconf used to generate the configure' script, and exit.

`configure' also accepts some other, not widely useful, options.