Although you could just work within the source code distribution
using the Makefile, it's cleaner and will be better for you in the
future if you learn to use the {{{build.sh}}} script that allows you to
leave the source code directory unmodified, and have all the project
specific stuff in project directories.  Here's how it works:

1. Make a project directory
On our Opteron cluster, I have one directory where I keep the source code
{{{/home/rsignell/models/roms_rutgers/trunk}}}
and another where I actually do model runs
{{{/home/rsignell/projects/}}}

So on my system, for a new test, I make a directory called
{{{/home/rsignell/projects/test1}}}

2. Checkout the source code using SVN (or unpack the source code if
you grabbed my tarfile) and copy the {{{build.sh}}} script (which you will
find in {{{./ROMS/Bin}}} subdirectory) to your project directory.

3. Edit {{{build.sh}}}

I  edit {{{build.sh}}} to specify:
{{{
MY_ROMS_APPLICATION=LAKE_SIGNELL
MY_ROMS_SRC=/home/rsignell/models/roms_rutgers/trunk
MY_PROJECT_DIR=/home/rsignell/projects/test1
}}}
and set which compiler I want to use (e.g. {{{pgi}}}, {{{ifort}}}) and what type
of executable I want (MPI, OpenMP, or Serial)

Even though I use the pgi compiler on our cluster, I actually build
MPI code using the {{{mpif90}}} script, so I set {{{USE_MPIF90}}} on as well as
{{{pgi}}}.

4. Compile.
Run the {{{build.sh}}} script.  If you have more than one processor on the
machine you are compiling on you can use the {{{-j}}} option to build
faster.  For example, to use 2 cpus:
{{{
./build.sh -j 2
}}}
5. Set up the input files for the run
ROMS uses an ASCII input file to specify some of the run parameters,
and we use the {{{.in}}} extension by convention to indicate these files.
For the test cases, these are found in the {{{~/ROMS/External directory}}}.
So to run ROMS from our project directory, we need to copy over the
right input file for the {{{LAKE_SIGNELL}}} case.  We also want a copy of
{{{varinfo.dat}}}, which defines NetCDF parameters.
{{{
cp ~/models/ROMS/External/{ocean_lake_signell.in,varinfo.dat} ~/projects/test1
}}}
6. Run.
{{{./oceanS < ocean_lake_signell.in}}}  (Serial)
{{{./oceanO < ocean_lake_signell.in}}}  (OpenMP)
{{{mpirun -n 16 -hostfile node_file ./oceanM lake_signell.in}}}   (MPI)