Software

Environment overview | Software packages

The Yellowstone system and the Geyser and Caldera analysis and visualization clusters have nearly all software in common. Notable exceptions are GPU-related packages provided for the Geyser and Caldera systems.

Because of the similarities between systems, your non-GPU codes will run on any of them. Which system to use depends largely on the needs of your project.

As you will see below, CISL makes available an array of open-source and commercial third-party products that you can load as needed for programming, compiling, computing, analysis, and file management tasks.


Environment overview

The following are common to the HPC, analysis, and visualization clusters' system software:

Operating system: Red Hat Enterprise Linux.

Scheduler: Platform LSF (load sharing facility) is used to schedule jobs.

Shells: Four shells are supported on login and compute nodes: tcsh, csh, bash, and ksh. The default is tcsh.

Compilers: Intel, PathScale, PGI, GNU, and NVIDIA compilers are provided. CUDA and OpenCL are available for developing GPGPU codes for the Geyser and Caldera clusters.

Environment modules

Our Consulting Services Group (CSG) provides an extensive collection of environment modules to help you manage the many environment variables, compilers, libraries, and other software. With the variety of compilers, in particular, using the environment modules is especially important to ensuring that your programs work as intended.

You can use some modules regardless of which compiler is loaded, while others are compiler-dependent.

See the following pages for searchable lists of software packages and descriptions that are drawn from their module help files:

Also see Python modules information.


Software packages

The following section lists many of the software packages that are available now or that will be added. If you have suggestions for software to include, please contact the CISL Help Desk.

Applications and analysis packages

  • CDAT - Climate Data Analysis Tools
  • CDO - Climate Data Operators
  • Ferret
  • GEMPAK - GEneral Meteorology PAcKage
  • Gnuplot
  • GrADS - Grid Analysis and Display System
  • IDL - Interactive Data Language
  • ImageMagick
  • Mathematica
  • MATLAB and toolboxes
  • NCAR Graphics
  • NCL - NCAR Command Language
  • Ncview
  • Octave
  • OpenGrADS
  • ParaView*
  • R
  • VAPOR* - Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers
  • VirtualGL*
  • Vis5D*
  • VisIt*
  • VTK* - Visualization ToolKit

Community models

  • CESM - Community Earth System Model
  • DART - Data Assimilation Research Testbed
  • ESMF - Earth System Modeling Framework
  • MM5 - PSU/NCAR Mesoscale Model
  • MOZART - Model for OZone and Related chemical Tracers
  • NRCM - Nested Regional Climate Model
  • WRF - Weather Research & Forecasting

Libraries

  • BLAS - Basic Linear Algebra Subprograms
  • Charm++
  • FFTW - Fastest Fourier Transform in the West
  • HDF5
  • JasPer
  • LAPACK - Linear Algebra PACKage
  • Linux math libraries - GSL, MKL
  • NetCDF - Network Common Data Form
  • PETSc - Portable, Extensible Toolkit for Scientific Computation
  • PnetCDF - Parallel netCDF
  • Trilinos

Performance and optimization tools

  • hpccount
  • IPM - Integrated Performance Monitoring
  • PAPI - Performance Application Programming Interface
  • Scalasca
  • TAU - Tuning and Analysis Utilities
  • Threadspotter
  • VTune

Programming support

  • Bazaar
  • Git
  • IPython
  • Mercurial
  • Perl
  • Python, PyNGL, PyNIO
  • Ruby
  • SVN - Subversion
  • TcL
  • TotalView

Utilities

  • BBCP
  • CMake
  • Emacs
  • Ghostscript
  • GNU Screen
  • NCO - netCDF Operators
  • NEdit
  • Vim
  • VNC* - Virtual Network Computing
  • WGRIB / WGRIB2
  • XDiff
  • Xxdiff

 

* Those marked with an asterisk should be run only on the Geyser and Caldera clusters because of their graphics and GPU requirements. Others can be used on the Yellowstone supercomputer. Check the man pages for any program to get additional information.