Grid'5000 experiment

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VSM-G project - step 2 (Application)

Conducted by

Alexandre Beautrait, Xavier Delaruelle, Leo Ghemtio, Emmanuel Jeannot, Bernard Maigret

Description

Use of grid computing for solving a in silico drug discovery problem using the VSM-G platform.

The proposed experiment deals with the second step of the funnel, i.e the flexible docking algorithm, on a computational grid. Indeed, this Grid'5000 experiment will allow us for the first time to use the GOLD program on grid clusters and to test its parallel implementation (PVM) at a large scale. GOLD uses a genetic algorithm to dock a flexible ligand to a semi-flexible protein. The program takes into account the position and conformation of the ligand and also the hydrogen bonding network in the binding site. Then, an empirical scoring function is used to rank the ligands according to their computed affinity with the protein target.
This experiment will highlight the behaviour of the program, estimate the profit time, and also estimate the effect of the size of the files needed for this calculation over the total computing time (granularity). Different times will be monitored such as the total processing time, the time for data transfer and the computing time. The ultimate goal of this experiment is to tune at best the parameters of the program to optimally spread the calculation on the grid. Moreover, we will estimate the best tool to distribute jobs on the grid cluster in order to interface later in optimal way VSM-G with a grid system.

This experiment being concluded, the best candidate molecules will be then submitted to the final module of the funnel, i.e. Molecular Dynamics simulations. This step will constitute another Grid'5000 experiment.

Status

achieved

Resources

  • Nodes involved: >1000
  • Sites involved: >3
  • Minimum walltime: 8h
  • Batch mode: yes
  • Use kadeploy: yes
  • CPU bound: yes
  • Memory bound: no
  • Storage bound: yes
  • Network bound: yes
  • Interlink bound: yes

Tools used

GOLD (evaluation version); APST; OAR;

Results

Not yet

Shared by: Alexandre Beautrait, Xavier Delaruelle, Leo Ghemtio, Emmanuel Jeannot, Bernard Maigret
Last update: 2011-07-03 14:51:38
Experiment #370

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