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Scientific codes running in the e1350, Blue Gene/P & Sun cluster (2)

Sun Microsystems cluster

Code

version

directory

Notes

GROMACS

4.0.5

/opt/gridware
/gromacs

A molecular dynamics package primarily designed for biomolecular. For more information, click HERE.

DL_poly

3.07,
2.18

/opt/gridware
/dlpoly

A general purpose serial and parallel Molecular dynamic simulation package, this version of Dl_poly has a wider range of structure optimisation features to help with setting up the starting configuration. For more info about this code click HERE and to see the script for running DL_poly_3.07 and 2.18 in the Sun, e1350 and BG/P systems, click HERE.

EMBOSS

6.2.0

/opt/gridware
/EMBOSS

EMBOSS is an open source software package developed to meet the needs of molecular biology community. For more information about this package, click HERE.

ATLAS

3.9

/opt/gridware
/atlas3.9

ATLAS is an Automatically Tuned Linear Algebra Software. For more information about this software, click HERE.

GAUSSIAN

g09

/opt/gridware
/gaussian

Gaussian is a structure calculation software. For more information about this software, click HERE and to see the script for running GAUSSIAN in the Sun, e1350 and BG/P systems, click HERE.

SEADAS

6.1

/opt/gridware
/SeaDas

SEADAS is a comprehensive image analysis package. For more information about this package, click HERE.


 

Graphical Processing Unit (GPU)

Code

version

directory

Notes

EMBOSS

6.3.1

/GPU/opt/emboss-intel-new

Intel Compilation:EMBOSS is an open source software package developed to meet the needs of molecular biology community. For more information on how to run EMBOSS on the GPU cluster HERE

EMBOSS

6.3.1

/GPU/opt/emboss-gcc-6.3

GCC Compilation:EMBOSS is an open source software package developed to meet the needs of molecular biology community. For more information on how to run EMBOSS on the GPU cluster HERE

NAMD

2.8

/GPU/opt/namd/NAMD_2.8_Source/

NAMD is a free-of-charge molecular dynamics simulation package written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems (millions of atoms) HERE

 

CHPC Student Cluster Competition 2013

Tsessebe Cluster Available

Graphical Processing Unit Cluster Available

CHPC SAGrid Cluster Available

Dirisa Storage Unit Available

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