WikiROMS - User contributions [en]

Tools

2006-11-06T22:35:23Z

Hetland:

== NetCDF tools ==

ROMS output files are NetCDF CF-1.0 Compliant files.

There are a variety of tools you can use for visualizing ROMS output.

* [http://meteora.ucsd.edu/~pierce/ncview_home_page.html NcVIEW]: A general non-ROMS specific NetCDF viewer, good for quick exploration and animation. Plots in coordinate index space only, however.

== Python ==

Python is a scripting language that is easy to learn and use (like MATLAB), is object-oriented and very powerful, and is rapidly becoming a standard language for scientific scripting. Many scientists are developing packages and toolboxes in python, for example www-pcmdi.llnl.gov/software-portal/cdat, www.pyngl.ucar.edu, and countless other, smaller packages. Many utilities are being developed with python hooks build in (like VTK, a 3D visualization library). Python has all of the basic tools required for working with numerical model data, in particular NetCDF support. Python can also be used as a wrapper for C and FORTRAN code, so you can have the speed of FORTRAN for number crunching with the ease of a high level language for data I/O. Finally, python is free and open source, and is available on all major computer platforms.

A good place to learn about scientific computing using Python is http://www.scipy.org. You will need a few packages installed in order to work with ROMS output in Python:

* numpy: http://numpy.scipy.org (basic numeric array mathematics)
* matplotlib: http://matplotlib.sourceforge.net (and the basemap toolkit for geospatial plotting)
* python-netcdf4: http://code.google.com/p/netcdf4-python/ (follow the install directions *exactly)

You can find a number of scripts designed to work explicitly with ROMS files at http://pong.tamu.edu/svn/python/trunk/. You can either browse online, or download the entire reposatory with [subversion (http://subversion.tigris.org/)]. Check out the repository with:

$ svn co http://pong.tamu.edu/svn/python/trunk/ python-roms

Install each of the packages by going to the top of the directory, say the 'roms' package for the basic ROMS tools by

$ cd python-roms/roms

$ python setup.py build

$ sudo python setup.py install

== MATLAB ==

** [http://marine.rutgers.edu/~jevans/rslice/rslice/doc/html/ch01.html RSLICE]: A GUI specifically for ROMS files. Works with ROMS files served via OpenDAP also.
** [http://www.brest.ird.fr/Roms_tools/ ROMS_TOOLS]: GUI and tools specifically for ROMS output files (ROMS-AGRIF).
* The [http://www.unidata.ucar.edu/software/idv/ Integrated Data Viewer (IDV)]: A GUI for visualizing a variety of file formats, including CF-Compliant NetCDF. A 100% Java application that uses the NetCDF-Java library.
* NCAR_Graphics Environment

Tools

2006-11-06T22:34:07Z

Hetland:

== NetCDF tools ==

ROMS output files are NetCDF CF-1.0 Compliant files.

There are a variety of tools you can use for visualizing ROMS output.

* [http://meteora.ucsd.edu/~pierce/ncview_home_page.html NcVIEW]: A general non-ROMS specific NetCDF viewer, good for quick exploration and animation. Plots in coordinate index space only, however.

== Python ==

Python is a scripting language that is easy to learn and use (like MATLAB), is object-oriented and very powerful, and is rapidly becoming a standard language for scientific scripting. Many scientists are developing packages and toolboxes in python, for example www-pcmdi.llnl.gov/software-portal/cdat, www.pyngl.ucar.edu, and countless other, smaller packages. Many utilities are being developed with python hooks build in (like VTK, a 3D visualization library). Python has all of the basic tools required for working with numerical model data, in particular NetCDF support. Python can also be used as a wrapper for C and FORTRAN code, so you can have the speed of FORTRAN for number crunching with the ease of a high level language for data I/O. Finally, python is free and open source, and is available on all major computer platforms.

A good place to learn about scientific computing using Python is http://www.scipy.org. You will need a few packages installed in order to work with ROMS output in Python:

* numpy: http://numpy.scipy.org (basic numeric array mathematics)
* matplotlib: http://matplotlib.sourceforge.net (and the basemap toolkit for geospatial plotting)
* python-netcdf4: http://code.google.com/p/netcdf4-python/ (follow the install directions *exactly)

You can find a number of scripts designed to work explicitly with ROMS files at http://pong.tamu.edu/svn/python/trunk/. You can either browse online, or download the entire reposatory with subversion (http://subversion.tigris.org/). Check out the repository with:

$ svn co http://pong.tamu.edu/svn/python/trunk/ python-roms

Install each of the packages by going to the top of the directory, say the 'roms' package for the basic ROMS tools by

$ cd python-roms/roms

$ python setup.py build

$ sudo python setup.py install

== MATLAB ==

** [http://marine.rutgers.edu/~jevans/rslice/rslice/doc/html/ch01.html RSLICE]: A GUI specifically for ROMS files. Works with ROMS files served via OpenDAP also.
** [http://www.brest.ird.fr/Roms_tools/ ROMS_TOOLS]: GUI and tools specifically for ROMS output files (ROMS-AGRIF).
* The [http://www.unidata.ucar.edu/software/idv/ Integrated Data Viewer (IDV)]: A GUI for visualizing a variety of file formats, including CF-Compliant NetCDF. A 100% Java application that uses the NetCDF-Java library.
* Python Tools
* NCAR_Graphics Environment

Tools

2006-11-06T22:30:50Z

Hetland:

== Python ==

Python is a scripting language that is easy to learn and use (like MATLAB), is object-oriented and very powerful, and is rapidly becoming a standard language for scientific scripting. Many scientists are developing packages and toolboxes in python, for example www-pcmdi.llnl.gov/software-portal/cdat, www.pyngl.ucar.edu, and countless other, smaller packages. Many utilities are being developed with python hooks build in (like VTK, a 3D visualization library). Python has all of the basic tools required for working with numerical model data, in particular NetCDF support. Python can also be used as a wrapper for C and FORTRAN code, so you can have the speed of FORTRAN for number crunching with the ease of a high level language for data I/O. Finally, python is free and open source, and is available on all major computer platforms.

A good place to learn about scientific computing using Python is http://www.scipy.org. You will need a few packages installed in order to work with ROMS output in Python:

numpy: http://numpy.scipy.org (basic numeric array mathematics)
matplotlib: http://matplotlib.sourceforge.net (and the basemap toolkit for geospatial plotting)
python-netcdf4: http://code.google.com/p/netcdf4-python/ (follow the install directions *exactly)

You can find a number of scripts designed to work explicitly with ROMS files at http://pong.tamu.edu/svn/python/trunk/. You can either browse online, or download the entire reposatory with subversion (http://subversion.tigris.org/). Check out the repository with:

$ svn co http://pong.tamu.edu/svn/python/trunk/ python-roms

Install each of the packages by going to the top of the directory, say the 'roms' package for the basic ROMS tools by

$ cd python-roms/roms

$ python setup.py build

$ sudo python setup.py install

== Visualization ==

ROMS output files are NetCDF CF-1.0 Compliant files.

There are a variety of tools you can use for visualizing ROMS output.

* [http://meteora.ucsd.edu/~pierce/ncview_home_page.html NcVIEW]: A general non-ROMS specific NetCDF viewer, good for quick exploration and animation. Plots in coordinate index space only, however.
* Matlab Tools
** [http://marine.rutgers.edu/~jevans/rslice/rslice/doc/html/ch01.html RSLICE]: A GUI specifically for ROMS files. Works with ROMS files served via OpenDAP also.
** [http://www.brest.ird.fr/Roms_tools/ ROMS_TOOLS]: GUI and tools specifically for ROMS output files (ROMS-AGRIF).
* The [http://www.unidata.ucar.edu/software/idv/ Integrated Data Viewer (IDV)]: A GUI for visualizing a variety of file formats, including CF-Compliant NetCDF. A 100% Java application that uses the NetCDF-Java library.
* Python Tools
* NCAR_Graphics Environment

Tools

2006-11-06T22:29:25Z

Hetland:

Tools

2006-11-06T22:29:08Z

Hetland:

Getting Started

2006-11-06T22:24:10Z

Hetland: /* Basic Steps */

ROMS is a very complex model with many options and capabilities. ROMS
is composed of many Fortran files (*.F), a few header files (*.h),
various input script files (*.in), a metadata variable definition file
([[varinfo.dat]]), and a single [[makefile]]. The ROMS algorithms are
distributed with the following directory structure:

<span class="blue">
src/ main root directory
-------- Compilers/ make configuration files
-------- Lib/ external libraries
-------- makefile a single makefile
-------- Master/ main programs
-------- ROMS/ ROMS root directory
-------- Adjoint/ adjoint model
-------- Bin/ executable scripts
-------- Drivers/ computational drivers
-------- External/ input scripts
-------- Include/ configuration header files
-------- Modules/ declaration modules
-------- Nonlinear/ nonlinear model
-------- Obsolete/ discontinued files
-------- Programs/ support programs
-------- SeaIce/ sea-ice model
-------- Representer/ representer model
-------- Tangent/ tangent linear model
-------- Utility/ generic utility files
-------- Version version information</span>

ROMS uses extensively [[C-preprocessing]] to activate and/or deactivate
the various numerical and physical algorithm options. It also uses
[[NetCDF]] to manage input and output data streams. It is highly
recommended that first time users learn the basics about NetCDF
before starting working with ROMS.

==Basic Steps==

* Register at the ROMS website ([http://www.myroms.org www.myroms.org]) to get access to the algorithms and other user privileges. Select an username and password which will be used in the future to login and post messages in the ROMS forum, algorithm downloads, and contributing to wikiROMS.

* Download the ROMS distribution file, unzip and untar to the desired directory. After unpacking, the ROMS files are placed in the directory tree structure shown above.

* Make roms by typing 'make' This will run the makefile at the top of the directory structure. This file will include a special makefile particular to your operating system and compiler, found in the Compilers subdirectory. You may need to edit this so that ROMS can find your netcdf libraries. You can also modify the compiler flags here if you want to, say, compile ROMS to run with the MPI libraries.

* TIP: You can type make -j <number of processors> to make ROMS faster. This will spread the make process over more than one processor. Often, you can also compile in debug mode (FFLAG=-g) -- that will typically compile much faster, so you can make sure the code compiles. However, it will cause the code to run *much* more slowely. Usually, you will want to optimize the code with a compiler flag -O. We have found that level 2 optimization (FFLAG=-O2) is usually good enough, and compiles faster than higher level optimization.

==Questions from New Users==

* My build finished with no errors. Where is the ROMS executable?
It is either in oceanS (serial), oceanO (OpenMP), oceanM (MPI), or oceanG (debug). Check the makefile to see which options are on.

* What do I have to do to run an application?
There are basically four levels of complexity in running an application.
# Canned applications that come with the ROMS distribution and don't need input. These can be run by editing ./Include/cppdefs.h to #define one (all others should be #undef) of the pre-defined model applications. Then make (good practice to make clean first) and, if you are lucky, the program will build. It should run with the command ./oceanS
# Canned applications that come with ROMS and require input files. Same as above, but now they have to be run with a command like ./oceanS < External/ocean_some_predefined_app.in. These may also require netCDF input files with names like ocean_some_predefined_app.nc.
# User-specified applications with no input data. These are the best test beds for new users or new algorithms. They consist of a set of selected cpp options in /Include/cppdefs.h, a user-generated .in file, and usually modifications to /Nonlinear/analytical.F to specify intial, boundary, and forcing conditions internally.
# User applications with input data...the real deal. These require changes to cppdefs.h, some_app.in, and appropriate input files for initialization and forcing.

*Why the _r8 at the end of real constants?
Some computers use 32 bits for single precision real numbers and 64 bits for double precision, and some use 64 and 128, respectively. For consistent results on various machines, ROMS takes advantage of the intrinsic F90/95 function SELECTED_REAL_KIND( ). (See ./Modules/mod_kinds.F). This allows you to associate an integer parameter with a specific data type...in this case r8 is associated with 64-bit precision. RTFM (Read the Fortran90 Manual), or better yet, chapter 11 in Chapman, 2004.

Tools

2006-11-06T22:18:49Z

Hetland:

Tools

2006-11-06T22:17:42Z

Hetland:

Python is a scripting language that is easy to learn and use (like MATLAB), is object-oriented and very powerful, and is rapidly becoming a standard language for scientific scripting. Many scientists are developing packages and toolboxes in python, for example www-pcmdi.llnl.gov/software-portal/cdat, www.pyngl.ucar.edu, and countless other, smaller packages. Many utilities are being developed with python hooks build in (like VTK, a 3D visualization library). Python has all of the basic tools required for working with numerical model data, in particular NetCDF support. Python can also be used as a wrapper for C and FORTRAN code, so you can have the speed of FORTRAN for number crunching with the ease of a high level language for data I/O. Finally, python is free and open source, and is available on all major computer platforms.

A good place to learn about scientific computing using Python is http://www.scipy.org. You will need a few packages installed in order to work with ROMS output in Python:

numpy: http://numpy.scipy.org (basic numeric array mathematics)
matplotlib: http://matplotlib.sourceforge.net (and the basemap toolkit for geospatial plotting)
python-netcdf4: http://code.google.com/p/netcdf4-python/ (follow the install directions *exactly)

You can find a number of scripts designed to work explicitly with ROMS files at http://pong.tamu.edu/svn/python/trunk/. You can either browse online, or download the entire reposatory with subversion (http://subversion.tigris.org/). Check out the repository with:

svn co http://pong.tamu.edu/svn/python/trunk/ python-roms

Install each of the packages by going to the top of the directory, say the 'roms' package for the basic ROMS tools by

cd python-roms/roms
python setup.py build
sudo python setup.py install

Tools

2006-11-06T22:15:46Z

Hetland:

Tools

2006-11-06T22:12:10Z

Hetland:

Python is a scripting language that is easy to learn and use (like MATLAB), is object-oriented and very powerful, and is rapidly becoming a standard language for scientific scripting. Many scientists are developing packages and toolboxes in python, for example www-pcmdi.llnl.gov/software-portal/cdat, www.pyngl.ucar.edu, and countless other, smaller packages. Many utilities are being developed with python hooks build in (like VTK, a 3D visualization library). Python has all of the basic tools required for working with numerical model data, in particular NetCDF support. Python can also be used as a wrapper for C and FORTRAN code, so you can have the speed of FORTRAN for number crunching with the ease of a high level language for data I/O. Finally, python is free and open source, and is available on all major computer platforms.

A good place to learn about scientific computing using Python is http://www.scipy.org. You will need a few packages installed in order to work with ROMS output in Python:

numpy: http://numpy.scipy.org (basic numeric array mathematics)
matplotlib: http://matplotlib.sourceforge.net (and the basemap toolkit for geospatial plotting)
python-netcdf4: http://code.google.com/p/netcdf4-python/ (follow the install directions *exactly)

http://pong.tamu.edu/svn/python/trunk/

http://subversion.tigris.org/

Tools

2006-11-06T22:11:10Z

Hetland:

Tools

2006-11-06T22:09:08Z

Hetland: