Table of Contents
This section describes the custom software available on the frontend. The frontend is running CentOS 5 so any software that is available there is also installed. All custom software is compiled with Pathscale 3.2 compilers unless otherwise stated. All of this software has been installed in /share/apps and is available on all compute nodes unless otherwise stated.
Compilers and Interpreters
The following compilers and interpreters are installed on tribe. All of the non-standard software is available through the module commands.
| Software Package | Version | License | Module Name | Prerequisites | Notes |
|---|---|---|---|---|---|
| GCC | 4.4 | GPL | gcc-4.4 | MPFR and GMP | C, C++, and Fortran support |
| GCC | 4.5 | GPL | gcc-4.5 | MPFR and GMP | C, C++, and Fortran support |
| Pathscale | 3.2 | One Concurrent User | pathscale-3.2 | none | C, C++, and Fortran support |
| PGI | 9-9.0 | One Concurrent User | pgi-9-9.0 | none | Fortran suport only |
| PGI | 10-10.0 | One Concurrent User | pgi-10-10.0 | none | Fortran support only |
| python | 2.6.4 | GPL | none | none | |
| python | 3.1.1 | GPL | python-3.1.1 | none | 3.1.1 is built with many common scientific libraries |
Job Schedulers
We currently only have one job scheduler in use on this cluster. Sun Grid Engine is one of the best job schedulers currently available for tightly coupled cluster computing. A job scheduler allows an administrator to set up and enforce a policy on utilizing cluster resources. Bypassing the job scheduler is considered malicious and jobs will be killed if they are not submitted through the batch queue.
| Software Package | Version | License | Module Name | Prerequisites | Notes |
|---|---|---|---|---|---|
| Grid Engine | 6.1 | SISSL | n/a | none | Configured with fair-share scheduling for multiple queues depending on your PI's contribution. |
Parallel Environments
There are more than one MPI layers installed on this cluster. OpenMPI is now very stable and many vendors are getting behind their implementation. We use it exclusively mostly because it offers features that the vendor-specific implementations don't offer. If you have loaded gcc (module load gcc) then you will get openmpi compiled with gcc when you issue “module load openmpi”. If you have load the Pathscale compiler “module load pgi” then “module load openmpi” will load the openmpi compiled with the Pathscale compiler.
| Software Package | Version | License | Module Name | Prerequisites | Notes |
|---|---|---|---|---|---|
| Open MPI | 1.4.1 | BSD | openmpi14-1.4 | Pathscale, GCC, or Open64 compiler | Compiled with the Pathscale, GCC, and Open64 compilers |
| QLogic MPI | 2.5.1 | Commercial | qlogic-2.5.1 | none | This is the MPI layer distributed by QLogic for Infinipath cards |
General Purpose Libraries
The following are general purpose libraries that are used in many other software packages.
| Software Package | Version | License | Module Name | Prerequisites | Notes |
|---|---|---|---|---|---|
| ACML | 4.4.0 | Commercial | acml-4.4.0 | PGI, GCC, or Open64 compiler | For use with the PGI, GCC, and Open64 compilers |
| LAPACK | 3.1.1 | BSD | lapack-3.2.2 | none | Reference LAPACK implementation |
| ATLAS | 3.8.2 | BSD | atlas-3.9.25 | GCC, OpenMPI | LAPACK and Blas |
| FFTW | 2.1.5 | GPL | fftw-2.1.5 | GCC, Pathscale, or Open64 compiler, OpenMPI | Some packages do not support the new FFTW3 API |
| FFTW | 3.2.2 | GPL | fftw-3.2.2 | GCC, Pathscale, or Open64 compiler, OpenMPI | The recommended version (if it supports the new API) |
| HDF | 5.1.8.1 | OS | hdf5 | GCC | |
| netCDF | 4.1.1 | OS | netcdf-4.1.1 | Pathscale, Open64, or GCC compiler | |
| PetSc | 2.3.2 | OS | petsc-2.3.2-p10-pathscale-3.2 | Pathscale, SCALAPACK, BLACS, LAPACK, BLAS | PetSc is used by Gale. |
Geo Dynamics
Geodynamics applications from http://geodynamics.org
Molecular Dynamics/Chemistry
The following packages are used in MD simulations and are available on this cluster.
| Software Package | Version | License | Module Name | Prerequisites | Notes |
|---|---|---|---|---|---|
| ABINIT | 6.0.4 | GPL | abinit6-6.0.4 | Pathscale, ACML, OpenMPI, netCDF, FFTW | Compiled with the Pathscale compiler |
| FFTW | 2.1.5 | fftw-2.1.5 | OpenMPI | ||
| FFTW | 3.2.2 | fftw-3.2.2 | OpenMPI | ||
| LAMMPS | 2010.05.27 | GPL | lammps-2010.05.27 | Pathscale, ACML, FFTW | Compiled with the Pathscale compiler |
| VASP | 4.6 | Commercial | vasp4-4.6 | Pathscale, ACML,OpenMPI | Compiled with the Pathscale compiler |
| VASP | 5.2 | Commercial | vasp5-5.2 | Pathscale, ACML, OpenMPI | Compiled with the Pathscale compiler |
