Software packages installed on Ducky
For users' convenience, many software packages and compilers have been installed on Ducky.
You can use SoftEnv which is a utility to help users manage complex user environments.
Let's say you want to use the Gaussian 03 on this cluster. The softenv
entry in the table is '+gaussian-03'. Here are the steps you
Step 1: Add /usr/local/packages/softenv-1.6.2/bin to
your PATH variable and export it. Ideally you would do this
in your .cshrc or .bashrc. Using the softenv command, a user may view the list of available packages.
Step 2: To utilize Gaussian03, you need to add +gaussian-03 to the .soft file in your home directory.
To update the environment when modifying this file, one simply uses the resoft command
or log out and login again.
|Amber||8||+amber-8||[docs]||Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids. |
|Charm++||5.9||+charm-5.9||[docs]||Charm++ is a machine independent parallel programming system. |
|GROMACS||3.2.1||+gromacs-3.2.1||[docs]||GROMACS is a versatile package to perform molecular dynamics. |
|Gaussian||03||+gaussian-03||[docs]||Gaussian predicts energies, molecular structures, etc. starting from basic laws of quantum mechanics. |
|Globus Environment||4.0.3||+globus-4.0.3||[docs]||A set of tools for programming on the grid. |
|Grace||5.1.18||+grace-5.1.18||[docs]||Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. |
|LoadLeveler||3.3||+loadleveler-3.3||[no docs available]||LoadLeveler�is a job scheduler designed to maximize resource utilization and throughput in a cluster environment to get the most out of the resources. |
|Metis||4.0||+metis-4.0||[docs]||METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. |
|NAMD||2.6b1||+namd-2.6b1||[docs]||A computational biochemistry package. |
|NCARG||4.4.0||+ncarg-4.4.0||[docs]||NCAR Graphics is a Fortran and C based software package for scientific visualization. |
|NWChem||4.6||+nwchem-4.6||[docs]||A computational chemistry package. |
|Open Babel||1.100.1-xlc||+openbabel-1.100.1||[docs]||Openbabl is a continuation of the 'babel' program used to convert file formats used by chemists. |
|PINY_MD||2005.8||+piny_md||[docs]||PINY_MD(c) is a multipurpose, object-oriented molecular simulation. |
|Program Database Toolkit||3.9||+pdtoolkit-3.9||[docs]||PDT is a framework for analyzing source code written in several programming languages. |
|Tuning and Analysis Utilites||2.16||+tau-2.16||[docs]||TAU is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. |
|GNU Compilers||3.4.4||+gnu-3.4.4||[docs]||Free compilers from GNU. Note: compiled for AIX 5.2|
|4.0.1||+gnu-4.0.1||Free compilers from GNU. This version includes gfortran, a fortran 95 compiler. Note: compiled for AIX 5.2|
|4.1.1||+gnu-4.1.1||Free compilers from GNU. Note: compiled for AIX 5.3|
|XL C/C++ Compiler||7.0||+xlc-7.0||[no docs available]||XL C/C++ Enterprise Edition for AIX can be used for large, complex, computationally intensive programs, including interlanguage calls with Fortran programs |
|XL Fortran Compiler||9.1||+xlf-9.1||[no docs available]||XL Fortran Enterprise Edition for AIX can be used for large, complex, computationally intensive programs, including interlanguage calls with C and C++ programs. |
|ESSL||4.2||+essl-4.2||[no docs available]||ESSL is a state-of-the-art collection of subroutines providing a wide range of mathematical functions for many different scientific and engineering applications. |
|GSL||1.7||+gsl-1.7||[docs]||The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. |
|HDF5||1.6.4-xlc||+hdf5-1.6.4||[docs]||Hierarchical Data Format is software for converting, visualizing, and storing data in a portable way. |
|NetCDF||3.5.1||+netcdf-3.5.1||[docs]||NetCDF stands for Network Common Data Form and is an interface/implementation of a library for storing data. |
|PESSL||3.2||+pessl-3.2||[no docs available]||Parallel ESSL is a scalable mathematical subroutine library that supports parallel processing applications on clusters of processor nodes optionally connected by a high-performance switch. |
|Scalapack||1.7-xlc-32-bit||+scalapack-1.7-xlc-32||[docs]||Parallel Dense Linear Algebra library Package configure options: SLmake.inc and BLACS/Bmake.inc |
|GridMPI||1.1||+gridmpi-1.1||[docs]||GridMPI is an implementation of the MPI (Message Passing Interface) standard designed for high performance computing in the Grid. |
|MPICH||1.2.6-gnu3.2.3||+mpich-1.2.6-gnu||[docs]||Mpich is an implementation of MPI |
|Paralll Environment||4.2||+pe-4.2||[no docs available]||IBM Parallel Environment for AIX (PE) software lets you develop, debug, analyze, tune, and execute parallel applications written in Fortran, C, and C++. PE conforms to existing standards like UNIX� and MPI. |