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Integrated Environment for Computational Chemistry on the APAC Grid Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University,

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Presentation on theme: "Integrated Environment for Computational Chemistry on the APAC Grid Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University,"— Presentation transcript:

1 Integrated Environment for Computational Chemistry on the APAC Grid Dr. Vladislav Vassiliev Supercomputer Facility, The Australian National University, ACT 0200, Canberra, Australia

2 Concept of the National Grid Other Grids: Institutional National International Other Grids: Institutional National International Data Centres Instruments Sensor Networks Research Teams grid-based portals distributed computation federated data access remote control collaboratories

3 QPSF ANU VPAC ac3 TPAC CSIRO Job Monitoring: Scope Job Management: Globus, PBS Nimrod LCG Job Submission: Command Line Portals Computing Systems: Peak Mid-range Special IVEC SAPAC APAC National Facility APAC National Grid Computing Grid Infrastructure QPSF (JCU) Systems coverage Users can access ALL systems at APAC partners About 4600 processors and 100’s of Tbytes of disk Around 3Pbytes of disk cached HSM systems

4 Integrated Environment for Computational Chemistry on the APAC Grid Supercomputer(s) Client

5 What does it mean “Integrated Environment” ?

6 “Integrated Environment”: Overall Architecture JMolEditor Shelves Gaussian Amber Gamess Gromacs Job submission Job Monitoring Getting results Providers: GT2 GT4 SSH Local Tripos Mol2 PDB Input File Formats Input File Preparation Gaussian Amber Gamess Gromacs Database JMolEditor There are two standalone programs, JMolEditor and Shelves

7 “Integrated Environment”: Rich User Interface High- performance 3D rendering Intuitive interface for unexperienced users

8 “Integrated Environment”: Support for popular Computational Chemistry Formats Gaussian GAMESS Mopac PBD Tripos Mol2 Amber Gromacs etc.

9 The most popular Computational Chemistry Programs on the National Facility (1920 CPUs) Chemistry SoftwareUsage (%) gaussian18.1 gamess0.01 mopac0.32 amber3.1 gromacs1.02 charmm3.8 molpro2.1 vasp8.5 namd4.4 nwchem0.03 siesta1.9 Our primary targets are the most popular programs in the Computational Chemistry community Of total wall time on the Altix cluster (1920 CPUs)

10 “Integrated Environment”: Preparation of input files for popular programs Simple Gaussian Input Editor

11 “Integrated Environment”: On-line and in-built help system and tutorials Tracking Help Help

12 “Integrated Environment”: Molecular Builder/Editor Adding/deleting Atoms Adding Fragments Adding Molecules Modifying atoms, bonds, angles, dihedral angles Automatic filling of empty valences with hydrogens

13 “Integrated Environment”: Visualizing Volumetric Data (Gaussian cubes)

14 “Integrated Environment”: Implementing a Full Production Cycle Structure Preparation Input File Preparation Job Submission Job Status Query Output Files Download Calculated Structure Visualization

15 “Integrated Environment”: Job Submission Common options for all programs Program specific options Provider Specific Options Scheduler Specific Options All complexities of the Grid job submission are hidden behind a dialog

16 “Integrated Environment”: Job Status Monitoring To download output files To kill selected jobs

17 System requirements Mac OS All is already there… MS Windows and Linux 1) The Java Runtime Environment (JRE) ≥ 1.5 2) Download and install Java3d (freeware optional component)

18 Download Site for JMolEditor Option 1: Download a program to run it on a desktop Option 2: Run from a website using Java Web Start On-line Help

19 What will be next? Support for more Computational Chemistry Programs (visualization, input files preparation, analysis of final results) Adding new features according to the user’s requests…


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