For users' convenience, many software packages and compilers have been installed on Queen Bee.
You can use SoftEnv which is a utility to help users manage complex user environments.
Using the softenv command, a user may view the list of available packages.
If a package you need to use is not on the default environment, you can add the softenv
entry to the .soft file in your home directory and then update the environment by using
command resoft after modifying this file or log out and login again.
If there are tools that you want to use that are not
installed on Queen Bee or if you have questions or comments about the content of this
page, please send us e-mail at sys-help@loni.org.
| application |
|---|
| Name | version | softenv | docs | description |
|---|
| APBS | 0.5.1. | +apbs-0.5.1 | | APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE) . |
| Apache Ant | 1.6.5. | +apache-ant-1.6.5 | [docs] | A portable compilation utility written in java. |
| CPMD | 3.11.1. | +cpmd-3.11.1 | [docs] | A parallelized plane wave/pseudopotential implementation of Density Functional Theory. |
| Cactus utilities | n/a. | +cactus | | such as GetCactus, and environmental variables |
| FFTW | 3.1.2-GNU. | +fftw-3.1.2-gnu | | |
| 3.1.2-Intel10.1. | +fftw-3.1.2-intel10.1 |
| 3.1.2-Intel9.1. | +fftw-3.1.2-intel9.1 |
| GX Map | 0.5.3.2 | +gx-map-0.5.3.2-r1 | | |
| Gnuplot | 4.2.0-gcc3.4.6. | +gnuplot-4.2.0-gcc3.4.6 | [docs] | A portable command-line driven interactive data and plotting utility. |
| Mesa | 6.4.2. | +Mesa-6.4.2 | | |
| NAMD | 2.6_Linux-i686-TCP. | +NAMD_2.6_Linux-i686-TCP | [docs] | A computational biochemistry package. |
| 2.6_Linux-i686. | +NAMD_2.6_Linux-i686 |
| Octave | 2.1.73. | +octave-2.1.73 | | Free MatLab replacement |
| Pacman | 3.20 | +pacman | | |
| 3.20-r1 | +pacman-3.20-r1 |
| TAU | 2.16-gcc3.4.6. | +tau-2.16-gcc3.4.6 | [docs] | A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. |
| VISIT | 1.8.1. | +visit | [docs] | VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. |
| gaussianview | 4.1.2. | +gaussianview-4.1.2 | | A graphical user interface designed to help prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces. |
| git | 1.5.4. | +git-1.5.4 | | git is a version control software. |
| lammps | 2.1.4 | +lammps | | A molecular dynamics code |
| quantum monte carlo simulations | 0.95 | +qumax-0.95 | | |
| valgrind | 3.2.3. | +valgrind-3.2.3 | | a suite of simulation-based debugging and profiling tools for programs running on Linux, functions include memory check, cache grind, etc. |
| library |
|---|
| Name | version | softenv | docs | description |
|---|
| Atlas | gcc3.4.6. | +atlas | [docs] | Automatically Tuned Linear Algebra Software |
| BLACS | 1.1-gnu. | +blacs-mvapich-gnu | [docs] | Basic Linear Algebra Communication Subprograms |
| 1.1-intel9.1. | +blacs-mvapich2-intel9.1 |
| GSL | 1.9-gcc | +gsl-1.9-gcc-3.4.2 | [docs] | 3.4.2. The GNU Scientific Library. |
| 1.9-gcc. | +gsl-1.9-gcc | The GNU Scientific Library. |
| 1.9-intel9.1. | +gsl-1.9-intel9.1 |
| HDF5 | 1.6.5-gnu. | +hdf5-1.6.5_gnu | [docs] | Hierarchical Data Format is software for converting, visualizing, and storing data in a portable way. |
| 1.6.5_intel10.1. | +hdf5-1.6.5_intel10.1 |
| 1.6.5_intel10.1_MPI_enabled. | +hdf5-1.6.5-mvapich2-0.98-intel10.1 |
| 1.6.5_intel9.1. | +hdf5-1.6.5_intel9.1 |
| Intel Math Kernel Library | 9.0 | +mkl-9.0 | [docs] | Highly optimized thread-safe math routines for high performance computing. |
| 9.1 | +mkl-9.1 |
| Latest. | +intel-mkl | A pointer to the latest version. |
| LAPACK | 3.1.1-g77. | +lapack-3.1.1-g77 | [docs] | Linear Algebra PACKage |
| 3.1.1-intel9.1. | +lapack-3.1.1-intel9.1 |
| Mpich | 1.2.7p1-Intel-fc-9.1+gcc-3.4.6. | +mpich-1.2.7p1-Intel-fc-9.1+gcc-3.4.6 | [docs] | Mpich is a free, portable implementation of the message passing libraries. |
| Mvapich | 0.98-gcc. | +mvapich-0.98-gcc | [docs] | Mvapich is a free, portable implementation of the message passing libraries. |
| 0.98-intel10.1. | +mvapich-0.98-intel10.1 |
| 0.98-intel9.1. | +mvapich-0.98-intel9.1 |
| 0.98-pgi6.1. | +mvapich-0.98-pgi6.1 |
| 1.0-beta-intel9.1 | +mvapich-1.0-beta-intel-9.1 |
| 1.0-intel. | +mvapich-1.0-intel10.1-tvdbg | | This version of mvapich is for using Totalview to debug your parallel program. |
| 1.0beta-intel10.1. | +mvapich-1.0-intel10.1 | [docs] | Mvapich is a free, portable implementation of the message passing libraries. |
| LATEST | +mvapich2 |
| Mvapich2 | 0.98-gcc. | +mvapich2-0.98-gcc | [docs] | Mvapich2 is a free, portable implementation of the message passing libraries. |
| 0.98-intel10.1. | +mvapich2-0.98-intel10.1 | Mvapich is a free, portable implementation of the message passing libraries. |
| 0.98-intel9.1. | +mvapich2-0.98-intel9.1 | Mvapich2 is a free, portable implementation of the message passing libraries. |
| 1.01-intel10.1. | +mvapich2-1.01-intel10.1 | Mvapich is a free, portable implementation of the message passing libraries. |
| 1.01-intel9.1. | +mvapich2-1.01-intel9.1 | Mvapich2 is a free, portable implementation of the message passing libraries. |
| 1.02p1-intel10.1. | +mvapich2-1.02p1-intel10.1 | Mvapich is a free, portable implementation of the message passing libraries. |
| NWChem | 5.0. | +nwchem-5.0 | [docs] | A computational chemistry package. |
| 5.1. | +nwchem-5.1-mpich |
| NetCDF | 3.5.1-gnu. | +netcdf-3.6.2-pgi | [docs] | NetCDF stands for Network Common Data Form and is an interface/implementation of a library for storing data. |
| 3.6.2. | +netcdf-3.6.2-intel.10.1 |
| Open Babel | 2.1.0-gcc3.4.6. | +openbabel-2.1.0-gcc3.4.6 | [docs] | Openbabl is a continuation of the 'babel' program used to convert file formats used by chemists. |
| OpenMPI | 1.2.2-gcc. | +openmpi-1.2.2-gcc | | |
| 1.2.2-intel9.1. | +openmpi-1.2.2-intel9.1 |
| 1.2.4-intel10.1. | +openmpi-1.2.4-intel10.1 |
| PETSc | 2.2.1-gnu-mvapich. | +petsc-2.2.1-gnu-mvapich | [docs] | PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. |
| 2.3.3-gnu-mvapich. | +petsc-2.3.3-gnu-mvapich |
| 2.3.3-gnu-openmp. | +petsc-2.3.3-gnu-openmp |
| 2.3.3-intel9.1-mvapich2. | +petsc-2.3.3-intel9.1-mvapich2 |
| 2.3.3-p11 | +petsc-2.3.3-p11-intel10.1-mvapich2 |
| ScaLAPACK | 1.8-gnu. | +scalapack-mvapich2-gnu | [docs] | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers |
| 1.8-intel9.1. | +scalapack-mvapich-intel9.1 |
| hypre | 2.0.0-Intel9.1-mvapich10.98 | +hypre-2.0.0_intel-9.1-mvapich1-0.98 | | |
