Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Rboinc 22jan Vph R2

155 views

Published on

  • Be the first to comment

Rboinc 22jan Vph R2

  1. 1. WP3 Tools: distributed molecular simulations and remote submission interface Toni Giorgino Computational Biochemistry and Biophysics Lab / GRIB-IMIM www.multiscalelab.org 22-23 jan 2009
  2. 2. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 13 MD at the microsecond scale Full-atom MD is computationally expensive All solvation water molecules modeled Non-bonded interactions All degrees of freedom in a protein z
  3. 3. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 14 MD at the microsecond scale Full-atom MD is computationally expensive All solvation water molecules modeled Non-bonded interactions All degrees of freedom in a protein z
  4. 4. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 15 Tackled at several scales Combine advances of large-scale infrastructures ⇒ distributed computing ...with those in commodity computing architectures ⇒ GPU One node (CPU) 0.4 ns/day 1
  5. 5. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 16 Tackled at several scales Combine advances of large-scale infrastructures ⇒ distributed computing ...with those in commodity computing architectures ⇒ GPU One node (CPU) 0.4 ns/day Within-node 1
  6. 6. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 17 Tackled at several scales Combine advances of large-scale infrastructures ⇒ distributed computing ...with those in commodity computing architectures ⇒ GPU One node (CPU) 0.4 ns/day One node, accelerated 4.5 ns/day Within-node 1
  7. 7. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 18 Tackled at several scales Combine advances of large-scale infrastructures ⇒ distributed computing ...with those in commodity computing architectures ⇒ GPU One node (CPU) 0.4 ns/day One node, accelerated 4.5 ns/day Within-node Among-nodes1
  8. 8. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 19 Tackled at several scales Combine advances of large-scale infrastructures ⇒ distributed computing ...with those in commodity computing architectures ⇒ GPU One node (CPU) 0.4 ns/day One node, accelerated 4.5 ns/day Distributed computing X 1,700, growing Within-node Among-nodes1
  9. 9. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 20 Tools One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing X 1,700, growing Within-node Among-nodes1
  10. 10. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 21 Tools One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing X 1,700, growing Within-node Among-nodes1 AceMD
  11. 11. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 22 Tools One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing X 1,700, growing Within-node Among-nodes1 AceMD Boinc
  12. 12. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 23 Tools One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing X 1,700, growing Within-node Among-nodes1 AceMD Boinc
  13. 13. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 24 Computing architecture Based on BOINC (Berkeley Open Infrastructure for Network Computing) Allows (loosely-coupled) computations to be distributed over the Internet Volunteers contribute CPU cycles Not MD-specific Public statistics at www.boincstats.com
  14. 14. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 25 Using computing power • The infrastructure becomes useful for the community with a distributed submission system One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing × 2,000, growing Within-node Among-nodes1
  15. 15. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 26 Using computing power • The infrastructure becomes useful for the community with a distributed submission system One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing × 2,000, growing Within-node Among-nodes1 Sim.entry point
  16. 16. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 27 Using computing power • The infrastructure becomes useful for the community with a distributed submission system One node (CPU) 0.25 ns/day One node, accelerated 4.6 ns/day Distributed computing × 2,000, growing Within-node Among-nodes1 Sim.entry point Research team 1 – hERG Scientist 2 – gA … Research team N – protN
  17. 17. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 28 Remote simulation submission • Pre-defined “best practice” submission protocols • Researchers stage in/out files – They are taken in charge by Boinc • Accounting: – Given the scale of deployment, increasing “trustedness” associated to each simulation – FLOPS consumed
  18. 18. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 29 Example: submission 1. Client parses local files and prepares a description of the simulation (may contain user-supplied metadata) 2. Inputs are uploaded to a staging area 3. Execution • Consis check • Move to execution area • Launch simulation 4. Results continuously produced; “work units” spanned until the protocol ends (# of ns × bins) 5. Clients periodically retrieve & delete results
  19. 19. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 30 Technically boinc_submit − Uploads local input files − Creates config, launches WUs, etc − Returns immediately boinc_stat boinc_retrieve [boinc_cancel et al]
  20. 20. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 31 Common traits All client commands have a notion of username and password to send for authentication Authentication checked with Boinc protocol Server remembers uploaded files for later deletion (server-side “RemoteWU” entity) A RemoteWU has an ID for the clients to retrieve − ideally equal to the usual WU id
  21. 21. VPH NoE Meeting - Oxford Thursday, January 22, 2009 Toni Giorgino 32 Outlook • Expose remote submission interfaces • Identify ontologies for inclusion of relevant annotations • Introduce metadata at least for annotating inputs (to be carried out in outputs)

×