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support:systems:tribe:software

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

Software Package Version License Module Name Prerequisites Notes
citcoms 3.0.2 GPL geo/citcoms-3.0.2 Python
gale 1.3.0 GPL geo/gale-1.3.0-pathscale-3.2 Pathscale, PetSc,OpenMPI, Compiled with Pathscale

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
support/systems/tribe/software.txt · Last modified: 2011/11/01 14:22 by tlknight