A+ A A-

Running Jobs

PBS WorkLoad Manager

All jobs on the GPU and SUN are scheduled by PBSPro

How to submit on GPU:

1. Compile your code

2. Run your submit script. (Please click here to view example scripts for customization)

Please note that you need to use an MPI inorder to call an mpi program. The system installed MPI is under /GPU/opt/open-mpi-new/.

export the mpi using the following command or add the lines on your .profile

 

1. export PATH=/GPU/opt/open-mpi-new/bin:$PATH

2. export LD_LIBRARY_PATH=/GPU/opt/open-mpi-new/lib:$LD_LIBRARY_PATH

 

Partitions available on GPU:

1. C2070

2. C1060

 

Moab Job Submit:

msub  scriptname -l feature=feature-name

allows users to submit jobs directly to Moab.

top of the page

 


Moab job submit on SUN:

1. Compile your code (Please click here on how to compile on SUN)

2. Run your submit script (Please click here to view example scripts for customization)

Partitions available on SUN

1. nehalem

2. westmere

3. dell

4. sparc

5. test

6. viz

Moab Job Submit:

msub  scriptname -l feature=feature-name

Allows users to submit to Moab.

top of the page


How to cancel jobs

Cancel jobs on GPU and SUN cluster:

mjobctl -c jobid

used to selectively cancel the specified job(s) (active, idle, or non-queued) from the queue


Debugging

mpirun_dbg.dbx, mpirun_dbg.ddd, mpirun_dbg.gdb


Monitoring

For monitoring on nodes use one of

  • nmon
  • vmstat
  • top
  • xloadl(X11)

and of course ps and free

top of the page

Last Updated on Tuesday, 03 June 2014 14:37

Hits: 1980

Scientific codes running on Sun cluster

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

 

Last Updated on Tuesday, 03 June 2014 14:12

Hits: 2378

Scientific codes running on 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

 

Last Updated on Tuesday, 03 June 2014 14:13

Hits: 146

Scientific codes running on the Sun cluster (3)

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

 

Last Updated on Tuesday, 03 June 2014 14:17

Hits: 137

Documentation for users:

CHPC Student Cluster Competition 2013

Tsessebe Cluster Available

Graphical Processing Unit Cluster Available

CHPC SAGrid Cluster Available

Dirisa Storage Unit Available

Social Share

FacebookTwitterGoogle BookmarksLinkedin

Website developed by Multidimensions