How to install and run a simple NCS example

This assumes you have a fairly standard Linux installation.  Any hardware
should work: I do most of my development on an 800 MHz P3 laptop.

1) Obtain the MPICH software from www-unix.mcs.anl.gov/mpi/mpich/ and
install it.  Other MPI implementations should work, but we have not
tested them.

2) Obtain the NCS source from brain.cs.unr.edu/ncsDocs and unpack it.

3) Edit the Makefile.  Make sure the line "SYSTEM = local" is uncommented.
Skip down to the lines following "ifeq ($(SYSTEM),local)", and change them
to reflect the paths where you installed MPICH.

4) Other flags you may want to change are:

  USE_AIO - normally "no".  Set to "yes" if you want to use the
  Asynchronous I/O library.  This is not a concern for small tests, but
  will speed up processing considerably on larger models with many output
  files.

  QQ_ENABLE - should be "no" unless you are doing development.  Enables a
  high-resolution profiling library.

5) Type make.

6) If compilation is successful, edit the Perl script "ncs5".  Change the
line "$cmd = " to reflect the path to your mpirun script.

7) Get the sample input file "onecell.in" from the web site.

8) On the command line, type "./ncs5 1 onecell.in > outputfile"

9) NCS should run.  On completion, "outputfile" will contain a program log,
"one-Vcell.txt" will contain cell voltages at each timestep.