Connecting Infrastructure, Connecting Research

NGS Scientific Software Applications

DNA zeolite gadget engineering analysis

Many sites on the NGS make available a range of Scientific Software. These applications are available for use via the UI/WMS resource broker or via globus commands. The table below shows which applications are available at which sites.

The UI/WMS can select the most appropriate site for you or you can request your job to run at a specific site. The links in the table will take you to pages showing you how to submit grid jobs to use the application from the UI using the WMS, the NGS portal, or via direct globus commands. In some instances the software may not be fully grid enabled and may need to be run by logging into the site first. These documentation pages give instructions for how to do this where appropriate.

Click on the categories below to see the applications available. Click on an application to see which versions are available and at which NGS sites. Click on the Documentation links to see how to run that application on the NGS. Click on a site name, on the right hand side, to see which applications are available at that site.


Application Categories


  • AstroPhysics Overview 
  • BioInformatics Overview 
    • EXONERATE Documentation 
      • 1.4 STFC-RAL
    • Emboss Documentation 
      • 4.1.0 STFC-RAL
      • 6.0.1 STFC-RAL
    • FASTA Documentation 
      • 34.26.5 STFC-RAL
    • GROMACS Documentation 
      • 3.3.1 Manchester STFC-RAL
      • 3.3.3 Oxford Super Computing Westminster
      • 4.0.7 Oxford Super Computing
      • 4.0 STFC-RAL
      • 4.0.5 Westminster
    • Mrbayes Documentation 
      • 3.1.2 Oxford Super Computing STFC-RAL
      • 3.1.2.1 STFC-RAL
    • NAMD Documentation 
      • 2.6 Manchester Oxford Super Computing STFC-RAL helena.esc.rl.ac.uk
      • 2.7b2 Manchester
      • 2.7b1 Oxford Super Computing STFC-RAL helena.esc.rl.ac.uk
    • NCBI BLAST Documentation 
      • 2.2.16 STFC-RAL
      • 2.2.17 STFC-RAL
      • 2.2.18 STFC-RAL SuperMicro svr026.gla.scotgrid.ac.uk
      • 2.2.24 STFC-RAL
    • NCBI BLAST Toolbox Documentation 
      • 25032007 STFC-RAL
    • SIESTA Documentation 
      • 2.01 Manchester STFC-RAL
      • 3.0 Oxford Super Computing
    • mpiBlast Documentation 
      • 1.4.0 STFC-RAL
  • BioMedical Overview 
    • GATE Documentation 
      • 3.1 STFC-RAL
      • 3.1.1-1 STFC-RAL
      • 3.1.1-2 STFC-RAL
      • 4.0.0 STFC-RAL
  • Chemistry Overview 
    • AMBER Documentation 
      • 10.0 Huddersfield STFC-RAL Westminster
      • 9.0 STFC-RAL Westminster
    • Autodock Documentation 
      • 4.0.1 STFC-RAL Westminster
      • 4.2.2.1 STFC-RAL Westminster
    • Autogrid Documentation 
      • 4.0.0 STFC-RAL Westminster
      • 4.2.2.1 STFC-RAL Westminster
    • CASTEP Documentation 
      • 4.3-r3 Manchester
      • 5.0.1 Manchester STFC-RAL
      • 5.5.2 RAL SCARF
      • 4.2 STFC-RAL
      • 4.3 STFC-RAL
      • 5.5.1 STFC-RAL helena.esc.rl.ac.uk
    • Castep Utilities Documentation 
      • 4.3-r3 Manchester
      • 5.0.1 Manchester STFC-RAL
      • 5.5.2 RAL SCARF
      • 4.2 STFC-RAL
      • 4.3 STFC-RAL
      • 5.5.1 STFC-RAL helena.esc.rl.ac.uk
    • DL_POLY 2 Documentation 
      • 2.14 Huddersfield
      • 2.20 Huddersfield RAL SCARF STFC-RAL helena.esc.rl.ac.uk
      • 2.16 STFC-RAL helena.esc.rl.ac.uk
      • 2.19 STFC-RAL
    • DL_POLY 3 Documentation 
      • 3.10 Huddersfield STFC-RAL helena.esc.rl.ac.uk
      • 3.09 RAL SCARF STFC-RAL
      • 3.06 STFC-RAL helena.esc.rl.ac.uk
    • Dock Documentation 
      • 6.1 STFC-RAL
    • Firefly Documentation 
      • 7.1.G STFC-RAL
      • 7.1.H STFC-RAL
    • Firefly/PC-GAMESS Documentation 
      • 7.1.11 STFC-RAL
      • 7.1.4 STFC-RAL
      • 7.1.9 STFC-RAL
      • 7.1.C STFC-RAL
      • 7.1.D STFC-RAL
      • 7.1.E STFC-RAL
      • 7.1.F STFC-RAL
      • 7.1.G STFC-RAL
    • GAMESS (US) Documentation 
      • 7.0 STFC-RAL
    • GAMESS-UK Documentation 
      • 7.0 STFC-RAL
    • GROMACS Documentation 
      • 3.3.1 Manchester STFC-RAL
      • 3.3.3 Oxford Super Computing Westminster
      • 4.0.7 Oxford Super Computing
      • 4.0 STFC-RAL
      • 4.0.5 Westminster
    • Gaussian Documentation 
      • E.01 RAL SCARF STFC-RAL helena.esc.rl.ac.uk
      • C.02 STFC-RAL
    • Gaussian Utilities Documentation 
      • C.02 RAL SCARF STFC-RAL helena.esc.rl.ac.uk
    • Gaussian09 Documentation 
      • B.01 RAL SCARF STFC-RAL helena.esc.rl.ac.uk
      • A.02 STFC-RAL helena.esc.rl.ac.uk
    • Gaussian09 Utilities Documentation 
      • A.02 RAL SCARF STFC-RAL helena.esc.rl.ac.uk
    • Gulp Documentation 
      • 3.1 Huddersfield STFC-RAL
    • LAMMPS Documentation 
      • 101012 Huddersfield
      • 070622 Manchester STFC-RAL
      • 090714 Manchester
      • 070810 STFC-RAL
      • 080521 STFC-RAL
      • 090417 STFC-RAL
    • NAMD Documentation 
      • 2.6 Manchester Oxford Super Computing STFC-RAL helena.esc.rl.ac.uk
      • 2.7b2 Manchester
      • 2.7b1 Oxford Super Computing STFC-RAL helena.esc.rl.ac.uk
    • ORCA Documentation 
      • 2.6.35 Oxford Super Computing
      • 2.7.0 STFC-RAL
      • 2.8.0 STFC-RAL
    • Siesta Documentation 
      • 2.01 Manchester STFC-RAL
      • 3.0 Oxford Super Computing
    • VASP Documentation 
      • 4.6 STFC-RAL
  • Data Analysis Overview 
    • IDL Documentation 
      • 7.0 STFC-RAL helena.esc.rl.ac.uk
    • MGL Tools Documentation 
      • 1.5.2 Westminster
    • Octave Documentation 
      • 2.1.73 Manchester STFC-RAL
      • 3.0.0 Manchester STFC-RAL
      • 2.1.57 STFC-RAL SuperMicro svr026.gla.scotgrid.ac.uk
    • R Documentation 
      • 2.6.0 Manchester STFC-RAL Westminster helena.esc.rl.ac.uk
      • 2.9.2 Oxford Super Computing
      • 2.4.1 STFC-RAL
      • 2.6.2 SuperMicro svr026.gla.scotgrid.ac.uk
      • 2.12.1 lcgce03.gridpp.rl.ac.uk lcgce05.gridpp.rl.ac.uk lcgce07.gridpp.rl.ac.uk lcgce08.gridpp.rl.ac.uk lcgce09.gridpp.rl.ac.uk sl5-1000.gridpp.rl.ac.uk sl5-2000.gridpp.rl.ac.uk sl5-3000.gridpp.rl.ac.uk sl5-4000.gridpp.rl.ac.uk sl5-500.gridpp.rl.ac.uk sl5-6000.gridpp.rl.ac.uk sl5-700.gridpp.rl.ac.uk sl5-wholenode.gridpp.rl.ac.uk
    • Root Documentation 
      • 5.12 STFC-RAL
      • 5.14 STFC-RAL
    • Sabre Documentation 
      • 4.0 STFC-RAL
      • 5.0 STFC-RAL
      • 6.0 STFC-RAL
    • Weka Documentation 
      • 3.4.9 STFC-RAL
  • Engineering Overview 
    • Abaqus Documentation 
      • 6.10.2 Huddersfield STFC-RAL
      • 6.8.2 Huddersfield
      • 6.9 RAL SCARF STFC-RAL helena.esc.rl.ac.uk
      • 6.6.1 STFC-RAL
      • 6.7.1 STFC-RAL
      • 6.8 STFC-RAL
  • Image Analysis Overview 
  • Uncategorised
    • BLAST
      • TOOLBOX.NCBI SuperMicro svr026.gla.scotgrid.ac.uk
      • TOOLBOX.NCBI-test.sh SuperMicro svr026.gla.scotgrid.ac.uk
      • TOOLBOX.NCBI.25032007 SuperMicro svr026.gla.scotgrid.ac.uk
    • BSOFT32
      • 1.5.4 STFC-RAL SuperMicro svr026.gla.scotgrid.ac.uk
    • EM3DR2
      • 2.0.2 STFC-RAL SuperMicro svr026.gla.scotgrid.ac.uk
    • GAMESS-US
      • R1.11Apr08 STFC-RAL
      • R6 STFC-RAL
    • HARC
      • CLIENT Manchester
      • CLIENT.1.9.5 Manchester
    • HMMER
      • 3.0 Huddersfield
    • JAVA
      • 1.5.0 STFC-RAL Westminster
      • 1.6.0 STFC-RAL Westminster
      • 1.4.2 Westminster
    • MPI
      • START STFC-RAL
    • PFT2
      • 2.0.4 STFC-RAL SuperMicro svr026.gla.scotgrid.ac.uk
    • PYTHON
      • 2.6 Manchester
    • VMD
      • 1.8.6 Westminster
    • 1

Sites


Huddersfield
Manchester
Oxford Super Computing
RAL SCARF
STFC-RAL
SuperMicro
Westminster
helena.esc.rl.ac.uk
lcgce03.gridpp.rl.ac.uk
lcgce05.gridpp.rl.ac.uk
lcgce07.gridpp.rl.ac.uk
lcgce08.gridpp.rl.ac.uk
lcgce09.gridpp.rl.ac.uk
sl5-1000.gridpp.rl.ac.uk
sl5-2000.gridpp.rl.ac.uk
sl5-3000.gridpp.rl.ac.uk
sl5-4000.gridpp.rl.ac.uk
sl5-500.gridpp.rl.ac.uk
sl5-6000.gridpp.rl.ac.uk
sl5-700.gridpp.rl.ac.uk
sl5-wholenode.gridpp.rl.ac.uk
svr026.gla.scotgrid.ac.uk
 

 

Applications Support

The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.

Acknowledgements

Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.

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