Software packages installed on Neptune
For users' convenience, many software packages and compilers have been installed on Neptune.
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
follow.
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
resoft
or log out and login again.
| Applications |
|---|
| Name | version | softenv | docs | description |
|---|
| 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 | [docs] | 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. |
| Compilers |
|---|
| Name | version | softenv | docs | description |
|---|
| 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 | [docs] | 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 | [docs] | XL Fortran Enterprise Edition for AIX can be used for large, complex, computationally intensive programs, including interlanguage calls with C and C++ programs. |
| Libraries |
|---|
| Name | version | softenv | docs | description |
|---|
| ESSL | 4.2 | +essl-4.2 | [docs] | 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 | [docs] | 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 |
| 1.7-xlc-64-bit | +scalapack-1.7-xlc-64 |
| Parallel-Compilers |
|---|
| Name | version | softenv | docs | description |
|---|
| 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 |
| 1.2.6-xlc | +mpich-1.2.6-xlc |
| Paralll Environment | 4.2 | +pe-4.2 | [docs] | 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. |
