zAlign INSTALL instructions
---------------------------

First of all, let's compile zAlign, shall we? See if there is a 'configure'
script on the top-level directory; if you don't see any file with that name (if
you checked out source from our Bazaar repository that will be the case), run:

  $ tree_setup.sh
  [ Note that the script above requires GNU's Autoconf, Automake and Libtool. ]

Okay, now the 'configure' script has been created. Let's execute it:

  $ ./configure
  [ Note that the installation prefix can be customized with '--prefix'. ]

The above step should work. You can, however, get the following error if you
don't have any MPI implementation available in you $PATH:

  $ ./configure
  [output snipped]
  checking for mpic++... no
  checking for mpicxx... no
  checking for mpiCC... no
  checking for hcp... no
  checking for mpxlC_r... no
  checking for mpxlC... no
  checking for mpCC... no
  checking for cmpic++... no
  checking for MPI_Init... no
  checking for MPI_Init in -lmpi... no
  checking for MPI_Init in -lmpich... no
  configure: creating ./config.status
  config.status: creating Makefile
  config.status: creating src/Makefile
  config.status: creating config.h
  config.status: executing depfiles commands
  config.status: executing libtool commands

As you can see, 'configure' wasn't able to find any MPI implementation to use.
You can solve this problem either by installing an MPI implementation (such as
Open MPI or MPICH), or if it's already installed, by including its location in
your $PATH.

Finally, we have to compile zAlign:

 $ make

Two executables will be placed under the 'src' directory, 'zalign' and
'mpialign'. The first should be used in standalone environments, and the second
in distributed ones.

To install to a system-wide location you'll probably need to become root first
(or use 'sudo'):

  $ su
  Password: <root password>

And, to install:

  # make install

To learn how to use both programs, run:

  $ zalign -h

or

  $ mpirun -np 1 mpialign -h
  [ Note that 'mpialign' should be invoked using the 'mpirun' command provided
    by your MPI implementation. ]

And, we're done!
