INSTALLATION

Quick Start
===========

This MEAD distribution is set up for compilation on Unix-like systems.
(See end of file for some info about MEAD on Windows.)  You will need
a reasonably up-to-date C++ and C compilers, including support for
templates, namespaces, run-type type identification, and the C++
standard libraries, including containers.  You will also need a
standard Unix "make" program.  You should then be able to build the
MEAD programs with just two commands:

	./configure
        [this tests for compilers etc., and generates makefiles]
	make
        [this compiles and links]
        make check
        [runs some simple test cases.  Diffs should be in small decimals.]
        make install
        [installs in /usr/local, or some specified place (see below).]

On a Mac, if configure complains about being unable to guess the build
type, give it "--build=powerpc" on the command line.

If you're going to build mead for more than one architecture, or if
you think you may want to tinker with the source code, it's a good
idea to build in a separate directory from the sources.  This can be
done if you have a make program that supports the VPATH feature.  If
the current directory is the mead top-level source directory,
mead-2.2.0:

   mkdir ../build
   cd ../build
   ../mead-2.2.0/configure
   [this generates makefiles in the build directory]
   make
   [this will work because the makefiles know how to look in source dir]   
    

If you want to use different C++ and C compilers than what configure
comes up with, you can set the CXX and CC environment variables,
respectively, before running configure, for example:

   ../mead-2.2.0/configure CXX=KCC CC=acc 

Configure can also be invoked with flags to control whether the
Python interface is generated, where installed files go, etc. (see below).

You should end up with libmead.a in subdirectory libmead and executables
in the apps subdirectory (each app has its own subdirectory):

	potential
	sav-driver
	solvate
	solinprot
	multiflex
	redti
	mulsidecomp
	potscan

At this point, you may wish to do "make check" which will run
a few of the apps on sample data and compare the output with expected
results using diff.  Don't too be alarmed if diff reports some
differences.  Close examination of them should show that it's just in
the last digit or two of floating point precision.

To install the libraries and executables, use the command:

	make install

This will copy libmead.a into /usr/local/lib, MEAD header files (.h
files) into /usr/local/include/MEAD, and the executables into
/usr/local/bin.  docmutented below.  If you've built the python
interface (see --with-python, below) "make install" will try to
install it in your python site-packages directory.  You can specify
different installation directories using the configure flags
documented below.  Of course, installation will fail if you don't have
the permissions to write in the appropriate directories.

Supported Platforms
===================

With this release, MEADs use of C++ is more standards compliant but
also depends more on compiler's to fully implement the standard.  This
may cause problems with older compilers.

So far, MEAD, including the Python wrapping mentioned below has been
sucessfully built and run on Red Hat and Fedora Linux systems
(i.e. Linux2 kernels) using gcc-3.1 or better.  I think other Linux2
systems with the same compiler should do as well.

MEAD without the Python system has been compiled and tested successfully
on Mac OS X 10.2.  I didn't do the Python because I couldn't get NumPy
to build on my Mac.

If you have an older compiler, you may wish to try an older version.
Older versions were more extensively tested on SGI, Sun, Dec Alpha,
and other non-Linux Unix systems.



MEAD-Specific Configuration Options
===================================

MEAD configuration of can be customized by using command-line options to
the ./configure script.  Type "./configure --help" to list the full set.
In addition to the usual options such as `--prefix' and `--bindir' (see
"generic installation instructions" below), MEAD supports the following:

* --with-python   (Default: disabled)
  Look for a suitable Python installation and enable building and
  installation of a dynamically shared library so that MEAD functions
  can be called from Python scripts.  A "suitable" Python means that the
  python interpreter has the Numeric extension built in, headers and
  library files are available to compile and link against.
  See swig/README for more.
  IMPORTANT NOTE: Python extensions written in C++ typically only work
  if Python itself was compiled with a C++ compiler, and if the
  extension (MEAD in this case) is compiled with the same C++ compiler
  as Python.
 

* --with-py-site-packages-dir=DIRECTORY
  When `--with-python' is specified, the ./configure may fail if it
  cannot determine Python's "site-packages" directory.  If this happens,
  use `--with-py-site-packages-dir' to specify DIRECTORY manually.

* --with-swig  Don't use this, it's broken!

* --disable-exceptions  (Default: enabled)
  If an error is detected inside the MEAD library, a MEAD-supplied error
  function is called (see libmead/globals.cc) which prints out an
  error message and then either calls exit with an error condition, or
  throws an exception according to whether this option is enabled.
  If mead is being run as a python module, the python wrapping of
  mead should catch the exception and turn it into a python error.
  However, if exceptions are disabled and MEAD calls exit, then
  the python interpreter will have an unexpected forced exit.
  You should only disable this option if your compiler and linker
  system can't deal with C++ exceptions.

Troubleshooting
===============

Trouble?  Maybe the configure script gave up because it couldn't find
a C++ compiler, or maybe it found the wrong one (such as the GNU
compiler when you wanted your system's native compiler).  To force the
use of the compiler of your choice see the section, "Compilers and
Options," below.  The relevant environment variables are CXX and
CXXFLAGS for controlling C++ compilation.

If that doesn't work you should probably read the "generic installation
instructions" below, but first I'll explain a bit about this "configure"
stuff.

The configure program used with MEAD accomplishes two things: creation
of a Makefile suitable for building MEAD on your system, and setting
up a few files and symbolic links that might be necessary.  You probably
do not need to tell configure what kind of system you have, what
features of C or C++ are supported or not, and so on.  Configure is
supposed to figure this stuff out for it self by sniffing around on
your system, trying to compile little tests, and so on.  The Makefile
generated by configure is based on the file, Makefile.in, which looks
pretty much like an ordinary Makefile except that it contains
constructs like "@THING@," for which configure makes substitutions in
the Makefile, depending on what it determines about your system.

The main system-dependencies that MEAD's configure file must deal with
pertain to the C++ compiler's characteristics and the availability
certain C++ library classes and functions.  In particular, MEAD uses
the bool built-in variable type which is now part of the standard.  If
it is still unsupported by your compiler, it can be usually be "faked"
well enough be preprocessor defines.  Configure also tries to come up
with optimization and code generation option flags that will give good
performance, but this is limited by my (Bashford's) experience on
local machines.  This is an area where you may well wish to tinker.

C++ is not the only source of trouble.  MEAD uses regular expressions
which are part of the C library on most Unix systems, but are not part
of either the standard C library or POSIX 1.  As with String,
configure checks to see if your system has regex, uses it if found,
but otherwise compiles and uses a GNU regex supplied here with MEAD.
(NOTE: The 64-bit version of SGI's IRIX 6.2 regex has a bug.
This is why MEAD's configure forces the CC "-n32" option on SGI).

Configure sounds like a pretty hairy program doesn't it?  Don't worry,
I didn't write it myself.  It is a Unix shell script generated
semi-automatically by the GNU project's program, autoconf, which takes
a much simpler file which I did write, configure.in, and performs
elaborate macro substitutions to generate configure.  As you can see,
MEAD owes a great deal to the Free Software Foundation's GNU project.

-Donald Bashford
bashford@scripps.edu

----------------- generic installation instructions --------------

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.in' is used to create `configure' by a program
called `autoconf'.  You only need `configure.in' 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.


Windows
========
I (Don Bashford) don't have a Windows machine, or know much about
them.  But my colleague, Michel Sanner has built the MEAD library and
the python interface using MS Visual C++.  For Windows, the whole
configuration and Makefile machinery described here is apparently not
meaningful, but Visual C++ can somehow help you turn the MEAD or
libmead directory and the swig directory into "projects", which do the
job of Makefiles.  Some Michel needed some twiddling with project
parameters, but no changes to the source code.


[INSTALLATION ends here]