AOS Wiki

On top of regular software included as part of your Linux distribution, the following software packages are available centrally to all Linux users of Atmospheric and Oceanic Sciences computing systems:

Eclipse is a multi-language software development environment comprising an integrated development environment (IDE) and an extensible plug-in system. It is written mostly in Java. It can be used to develop applications in Java and, by means of various plug-ins, other programming languages including Ada, C, C++, COBOL, Haskell, Perl, PHP, Python, R, Ruby (including Ruby on Rails framework), Scala, Clojure, Groovy, Android and Scheme. It can also be used to develop packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others.

To use Eclipse, issue eclipse in the terminal.

Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. It runs on most Unix systems, and on Windows XP/NT/9x using X windows for display. It can transparently access extensive remote Internet data sources using OPeNDAP (formerly known as DODS)

To use ferret, please source /aos/shared/ferret/default/ferret_paths.sh. Once sourced, you may use ferret as discussed in the documentation

GEMPAK, the GEneral Meteorology PAcKage, is an analysis, display, and product generation package for meteorological data. It is developed by NCEP (the National Centers for Environmental Prediction) for use by the National Centers (Storm Prediction Center (SPC), Tropical Prediction Center (TPC), Aviation Weather Center (AWC), Hydrologic Prediction Center (HPC), Marine Prediction Center (MPC), Environmental Modeling Center (EMC), etc.) in producing operational forecast and analysis products such as those distributed as Redbook Graphics and others displayed on the NWS web pages and utilized internally within the centers. Graphical User Interfaces provide convenient access to interactive data manipulation. A comprehensive set of decoders enables integration of real-time and archive data, products, and bulletins. The GEMPAK distribution consists of a suite of application programs, Graphical User Interfaces (GUIs), meteorologic computation libraries, graphic display interfaces, and device drivers for the decoding, analysis, display and diagnosis of geo-referenced and meteorological data.

To use GEMPAK, please source /aos/shared/gempak/default/Gemenviron.profile. Once sourced, you may use GEMPAK as discussed in the documentation.

The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. GrADS has two data models for handling gridded and station data. GrADS supports many data file formats, including binary (stream or sequential), GRIB (version 1 and 2), NetCDF, HDF (version 4 and 5), and BUFR (for station data). GrADS has been implemented worldwide on a variety of commonly used operating systems and is freely distributed over the Internet.

To use GRADS, please see binaries in /aos/shared/grads/default/bin

HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. Using HDFView, you can:

• view a file hierarchy in a tree structure
• create new file, add or delete groups and datasets
• view and modify the content of a dataset
• add, delete and modify attributes
• replace I/O and GUI components such as table view, image view and metadata view

To use HDFView, simply issue hdfview at the command-line on any 64-bit Linux system in the department.

IDL, short for Interactive Data Language, is a programming language used for data analysis. IDL is vectorized, numerical, and interactive, and is commonly used for interactive processing of large amounts of data (including image processing). The syntax includes many constructs from Fortran and some from C.

To use IDL, please issue idl at the command-line. To use IDL graphically, please issue idlde.

The Integrated Data Viewer (IDV) from Unidata is a Java-based software framework for analyzing and visualizing geoscience data. This IDV release includes a software library and a reference application made from that software.

To use IDV, issue IDV in the terminal.

Intel Fortran Compiler, also known as IFORT, is a Fortran compiler developed by Intel. It generates code for IA-32, Intel 64 processors. Compilers are available for Linux, Microsoft Windows and Mac OS X. On Windows, it is known as Intel Visual Fortran. On Linux and Mac OS X, it is known as Intel Fortran.

Intel C++ Compiler (also known as icc or icl) is a group of C and C++ compilers from Intel Corporation available for GNU/Linux, Mac OS X, and Microsoft Windows.

To use the Intel C++ or Fortran compilers, please issue icc or ifort respectively.

Mathematica is a computational software program used in scientific, engineering, and mathematical fields and other areas of technical computing. It was conceived by Stephen Wolfram and is developed by Wolfram Research of Champaign, Illinois

To use Mathematica, please issue Mathematica in the terminal.

MATLAB (matrix laboratory) is a numerical computing environment and fourth-generation programming language. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, and Fortran.

To use Matlab, please issue matlab in the terminal.

Mendeley is a desktop and web program for managing and sharing research papers, discovering research data and collaborating online. It combines Mendeley Desktop, a PDF and reference management application (available for Windows, Mac and Linux) with Mendeley Web, an online social network for researchers. Mendeley requires the user to store all basic citation data on its servers - storing copies of documents is at the user's discretion. Upon registration, Mendeley provides the user with 1 GB of free web storage space, which is upgradeable at a cost.

To use Mendeley, please issue mendeleydesktop.sh in the terminal

The NCAR Command Language (NCL) is a free interpreted language designed by the National Center for Atmospheric Research for scientific visualization and data processing. NCL has robust file input and output. It can read in netCDF, HDF4, HDF4-EOS, GRIB, binary and ASCII data.

To use NCL/NCARG, please export NCARG_ROOT=/aos/shared/ncl_ncarg/default. Once exported, you may issue ncl to start ncl.

NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. The project homepage is hosted by the Unidata program at the University Corporation for Atmospheric Research (UCAR). They are also the chief source of netCDF software, standards development, updates, etc. The format is an open standard. NetCDF Classic and 64-bit Offset Format are an international standard of the Open Geospatial Consortium.

If you would like to use NetCDF as a library, you will need to tell the compiler and linker to find it in /aos/shared/lib/centos6/netcdf/4/gnu/include and /aos/shared/lib/centos6/netcdf/4/gnu/lib respectively

Skype is a proprietary voice-over-Internet Protocol service and software application originally created in 2003 by Swedish entrepreneur Niklas Zennström and his Danish partner Janus Friis. It has been owned by Microsoft since 2011.

The service allows users to communicate with peers by voice, video, and instant messaging over the Internet. Phone calls may be placed to recipients on the traditional telephone networks. Calls to other users within the Skype service are free of charge, while calls to landline telephones and mobile phones are charged via a debit-based user account system. Skype has also become popular for its additional features, including file transfer, and videoconferencing. Competitors include SIP and H.323-based services, such as Linphone, as well as the Google Talk service, Mumble and Hall.com.

To use Skype, please issue skype at the command-line.

PyNGL and PyNIO provide Python interfaces to most of the graphics and file input/output functionality existing in the NCAR Command Language (NCL). A knowledge of NCL would give you a leg up in using these modules, but they are meant to be independent from NCL and used as a stand-alone suite of Python functions. In a few circumstances where the NCL documentation applies directly to PyNGL and PyNIO and there is no ambiguity, links are made to the NCL documentation from the PyNGL documentation. PyNGL and PyNIO represent recent developments in the evolution of a package that dates back several decades. Those who are interested can view the

In order to use python NGL and NIO, you will need to export PYTHONPATH=/aos/shared/lib/centos6/python/lib/python2.6/site-packages

netcdf4-python module can read and write files in both the new netCDF 4 and the old netCDF 3 format, and can create files that are readable by HDF5 clients. The API modelled after Scientific.IO.NetCDF, and should be familiar to users of that module.

Most new features of netCDF 4 are implemented, such as multiple unlimited dimensions, groups and zlib data compression. All the new numeric data types (such as 64 bit and unsigned integer types) are implemented. Compound and variable length (vlen) data types are supported, but the enum and opaque data types are not. Mixtures of compound and vlen data types (compound types containing vlens, and vlens containing compound types) are not supported.

In order to use python-netcdf4, you will need to export PYTHONPATH=/aos/shared/lib/centos6/python/lib/python2.6/site-packages

Numeric is a Python module for high-performance, numeric computing. It provides much of the functionality and performance of commercial numeric software such as Matlab; in some cases, it provides more functionality than commercial software.

In order to use python-numeric , you will need to export PYTHONPATH=/aos/shared/lib/centos6/python/lib/python2.6/site-packages