Information on how to run the Land Ice V&V (LIVV) post-processing software.
KJE 1/2013

The /livv directory contains all the scripts and code to run the LIVV kit.
The $machine.bash script contains the inputs needed to run on a data processing style machine.
An example scripts for Carver (NERSC) (and Lens (OLCF) will be updated when 
Titan comes on line to submit jobs) are provided.

If you want to run on another machine, these are the software packages and versions that worked 
on both NERSC and OLCF machines as of 1/2013:
hdf5/1.8.6
python/2.7            
ncl/6.0.0  (at NERSC this is called, inexplicably, ncar/6.0.0)  
nco/4.0.7
netcdf/4.1.3

Filepaths for the python script are defined in the bash shell script, and most are required.

The command to run the python script along with all of the necessary/optional files is the 
last line of the script. 
/bin: the python processing code 
/plots: the ncl code 
/data: the solver data from each processed run is placed here in a $case.asc format 

To run the shell script:
1. Create a mirror copy of everything in the /seacism/tests/higher-order directory in your scratch space
2. Put the 4 currently evaluated executables of simple_glide into the mirror /higher-order directory
(this is done automatically by the master build scripts in the /cmake-scripts directory)
In the mirror directory:
3. in the carver.bash file in the /livv directory it will automatically:
	a. specifies the global scratch path for all the scripts it calls: $SCRIPT_PATH
	b. sets the $HTML_PATH on where to post results
	c. sets config path and output path (if you want to run the optional 5km GIS and have followed the same
naming convention)
4. in the carver.bash file in the /livv directory you set:
	a. USERNAME: it doesn't have to be your machine user name. Its the name of the subdirectory where your 
files will be placed to be on the web and also to ID folks who go to you website of who ran the kit
	b. COMMENT: case details so those who view the website will know the goal of that run
5. type "bash $machine.bash" at the command line in the main directory.
(right now, use KJE GIS 5km output, or have run using the associated config scripts if you want the LIVV kit 
to process a production 5km case)
	c. whether to run production cases or not (RUN_$, right now it will only run reg_tests)

If its successful, there will be some output from ncl telling you that plots have 0 values, indicating that the test cases you ran are exact with the benchmarks.

When you are done, the script tells you the website location to go look at the output.

TODOs (feel free to add to this as needed)

Major:
*have the picard runs also post processed for solver and convergence details, right now its just JFNK
*plot the solver and convergence info more usefully for all relevant runs
*parse data from trilinos_options.xml file as well as configure settings
*create a more general user interface to process the GIS production output
*enable the option to read from FELIX data (in exodus format) using visit

Minor:
*have the input and output information from the benchmark runs set in the software rather than the user 
specify (or at least have a default)
*parse more detailed data from the output files about the solver and preconditioner
n VV_outprocess
