User guide

From OCG Test Wiki

Jump to: navigation, search

The forecasting system contains two components:

  • the ROMS model and all programs to create the necessary forcing files. This component is called the West Florida Shelf Forecasting System or WFSFCS.
  • The web-based visualization program (called pyocean)


Contents

[edit] The West Florida Shelf Forecasting System

The West Florida Shelf Forecasting System (WFSFCS) is essentially written in octave scripts and shell scripts. Octave is a high-level scripting language for numerical computing. The scripts can also be executed without change in Matlab. It contains also some Python and Fortran code. The following filename extensions are used:


Extension Language
.m Octave/Matlab
.sh bash shell scripts
.py Python


[edit] Prerequisites

The following software need to be installed to run the WFSFCS:

All these programs are open-source. Some are already available in Linux distributions. The compilation page contains some instructions to compile these packages from source.

[edit] Downloading

Source code is available under CVS and can be downloaded by: 

export CVSROOT=:pserver:abarth@ocgmod1.marine.usf.edu:/var/cvs
cvs checkout WFSFCS

[edit] Directory structure

The directory WFSFCS contains the following sub-folders:

bin
Shell and Python scripts and Fortran executables
Conf
configuration files defining, e.g., the directory where the model will run
Fortran
Fortran source files
Octave
Octave-specific files
Scripts
Octave/Matlab scripts
roms-2.0_op4
ROMS code without tides
roms-2.0_op5
ROMS code with tides

[edit] Compilation

To compile the ROMS model without tides: 

cd roms-2.0_op4
make -f Makefile-hostname

To compile the ROMS model with tides: 

cd ../roms-2.0_op5
make -f Makefile-hostname

To compile some Fortran utilities: 

cd ../Fortran
make FORT=ifort
make install

Octave functions: Grib import: 

cd Octave/loadgrid
make

Curl backend (included in octave since at least octave 2.9.12): 

cd Octave/urlwrite
make

UFill for spatial extrapolation: 

cd Octave/UFill
FLIBS="-L/opt/intel/fc/9.0/lib -lifcore_pic  -lguide" make FC=ifort
octave --eval test_ufill

[edit] Installation

In the folder Conf there is a file named 'wfsfcs.cron'. This file contains all necessary instructions to make the forecast system run every day. The crontab can be installed by: 

crontab wfsfcs.cron

This will replace any existing crontab. The shell script get_ncep_an.sh downloads the NCEP analysis every day at 6:06 PM and the shell script wfs_run_cronjob.sh launches the model run at 0:05 AM.

[edit] Output files

All files are created in the directory $model_op_root (this variable is defined in WFSFCS/Conf/globals.sh). Every day a directory named B<YEAR><MONTH><DAY> is created. This file contains the folowing subdirectories and files:

Atmo
all atmospheric forcing files
Atmo/atm.nc
NetCDF file with a forcing fields from NCEP
Atmo/oi_sst.nc
NetCDF file with the OI SST
Log
log files of the whole process
IC
initial condition
IC/IC.nc
NetCDF file with the initial condition, either ROMS of the previous forecast or HYCOM
IC/HAB_*.txt
Text file with the initial position for the HAB forecasts in the HAB data format.
Run
Model run without tides
Run/WFS_avr.nc
Daily averages for the model run
Run/WFS_flt.nc
Drifter trajectories
RunTides
like the folder Run but with tides.

[edit] Launching the model scripts explicitly

Use the same environment as the cronjon. To find which variables are defined by the cronjob, type: 

crontab -l

You will see: 

PATH=/home/abarth/WFSFCS/Conf:/home/abarth/WFSFCS/bin:/opt/python2.4/bin:/home/abarth/Python/pyocean/:/usr/local/bin:/bin:/usr/bin:
PYTHONPATH=/home/abarth/Python
LD_LIBRARY_PATH=/opt/intel/cc/9.0/lib
[....]

Execute the lines setting the PATH, PYTHONPATH and LD_LIBRARY_PATH. Run the system with: 

wfs_run.sh $(mjd 20070921)

The date is given here in YYYYMMDD format. The command mjd computes the Modified Julian Day number.

Retrieved from "http://ocgmod1.marine.usf.edu/wiki/index.php/User_guide"