md on the grid using the wenmr gromacs web portal
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MD ON THE GRID USING THE WENMR GROMACS WEB PORTAL Marc van Dijk - PowerPoint PPT Presentation

MD ON THE GRID USING THE WENMR GROMACS WEB PORTAL Marc van Dijk Utrecht University The Netherlands GROMACS on the Grid: basics Ported GROMACS version: 4.5.3 with rotational constraint support Installed on 16 sites supporting


  1. MD ON THE GRID USING THE WENMR GROMACS WEB PORTAL Marc van Dijk Utrecht University The Netherlands

  2. GROMACS on the Grid: basics • Ported GROMACS version: 4.5.3 with rotational constraint support • Installed on 16 sites supporting the eNMR Virtual Organization Always in search • Together they support ~47500 CPU’s of more sites to • Are these all available? add No, unfortunately not - Shared with other web portals and other VO’s - Pooled in different queues - Sites not always up www.gromacs.org

  3. GROMACS on the Grid: basics • Ported GROMACS version: 4.5.3 with rotational constraint support • Installed on 16 sites supporting the eNMR Virtual Organization Always in search • Together they support ~47500 CPU’s of more sites to • Are these all available? add No, unfortunately not ✓ - GROMACS on the Grid IS NOT HPC for single simulations Shared with other web portals and other VO’s - Pooled in different queues ✓ GROMACS on the Grid IS HPC for parametric simulations - Sites not always up www.gromacs.org

  4. GROMACS on the Grid: how to use it 1 Use the WeNMR GROMACS web portal to submit MD projects starting from a structure file or from your own pre-configured simulation system. 2 launch your own MD jobs on the WeNMR Grid infrastructure using for instance the Miramare Interoperable Lite UI (MILU) www.wenmr.eu/wenmr/quick-glite-how-wenmr-users

  5. Access to WeNMR portals via the VRC Your profile • Login to the VRC (signup for an account, its free) • Request a x.509 grid certificate and membership of the eNMR VO • Subscribe to the GROMACS web portal on your “My Services” page www.wenmr.eu

  6. Access to WeNMR portals via the VRC Your profile • Login to the VRC (signup for an account, its free) • Request a x.509 grid certificate and membership of the eNMR VO • Subscribe to the GROMACS web portal on your “My Services” page www.wenmr.eu

  7. GROMACS on the WeNMR VRC Added benefits ★ Help Center ★ Documentation ★ Tutorials www.wenmr.eu

  8. The GROMACS web portal: two interfaces 1 Start the simulation using a PDB or Gromacs structure file 2 Start the simulation using a preconfigured Gromacs binary run input file (.tpr) 1 2 http://haddock.science.uu.nl/enm/services/GROMACS

  9. The GROMACS web portal: start with a structure file 1 Starting a Grid MD project from a structure file and a set of basic parameters

  10. The GROMACS web portal: start with a structure file 1 Upload Structure file 1 ★ .pdb or .gro file ★ NMR ensembles accepted, 1st model used ★ ATOM and HETATM type check ★ <= 1200 residues

  11. The GROMACS web portal: start with a structure file 2 Optional parameters ★ Simulation time in ns. 2 ★ Output resolution ns. ★ Forcefield type ★ Solvent model, default for FF or: SPC, TIP3P, TIP4P ★ Electrostatics: cut-off/reaction field, PME

  12. The GROMACS web portal: start with a structure file 3 Advanced parameters ★ Salt concentration (mol/l) ★ Temperature and pressure ★ Minimal distance between periodic images ★ Seed for velocity distribution ★ Perform basic analysis 3 ★ Create NDLP simulation box ★ Roto-translational constraints ★ Virtual sites

  13. The GROMACS web portal: what happens behind the scenes Local Grid gmx45setup.sh - Topology generation - Energy minimization in vacuum Project setup - Optimizing simulation box (squeez) - Solvation and addition of ions - Minimize solvated system, position restraint MD - Temperature/Pressure coupling - Production Simulation JDL - MD production run in parts gmx45md.sh Project execution JDL post processing Finished Project m.vandijk1@uu.nl

  14. The GROMACS web portal: start from a .tpr file 2 Starting a Grid MD project from a preconfigured simulation system

  15. The GROMACS web portal: start from a .tpr file Upload preconfigured 1 simulation system ★ Upload valid .tpr file ★ Upload option checkpoint file (.cpt) ★ Simulation time in ns 1 ★ Perform basic analysis

  16. The GROMACS web portal: what happens behind the scenes Local Grid gmx45setup.sh - Topology generation - Energy minimization in vacuum Project setup - Optimizing simulation box (squeez) - Solvation and addition of ions - Minimize solvated system, position restraint MD - Temperature/Pressure coupling - Production Simulation JDL - MD production run in parts gmx45md.sh Project execution JDL post processing Finished Project m.vandijk1@uu.nl

  17. The GROMACS web portal: progress and results page ★ A GROMACS project can consist of several jobs (simulation parts) ★ Simulation parts can be combined and analysed at any time ★ A simulation can be extended ★ Manually revive a stuck job http://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server

  18. The GROMACS web portal: doing it manually 3 Interact directly with the WeNMR Grid infrastructure using your own scripts

  19. The GROMACS web portal: setup of a JDL file JobType = "Normal"; Requirements = (other.GlueCEPolicyMaxWallClockTime >= 300 && other.GlueCEPolicyMaxCPUTime >= 1800 && Member("VO-enmr.eu-GROMACS4.5.3-rtc-r2",other.GlueHostApplicationSoftwareRunTimeEnvironment)); Rank = ( other.GlueCEStateFreeJobSlots > 100 ? other.GlueCEStateFreeJobSlots : other.GlueCEStateWaitingJobs == 0 ? other.GlueCEStateFreeJobSlots * 100 / (other.GlueCEInfoTotalCPUs + 1) : (-other.GlueCEStateWaitingJobs * 4 / ( other.GlueCEStateRunningJobs + 1 )) - 1 ); FuzzyRank = false; CPUNumber = 6; SMPGranularity = 6; RetryCount = 0; ShallowRetryCount = 3; Executable = "gmx45setup.sh"; Arguments = "-salt 0.1539976 -D 2.25 -maxh 18000 -f project.pdb -at 0.05 -np 6 -ff charmm27 -elec default -T 300.0 -P 1.0 -time 1.0 -archive project.tgz"; StdOutput = "project.stdout"; StdError = "project.stderr"; InputSandbox = {"gmx45setup.sh", "project.pdb"}; OutputSandbox = {"project.stdout","project.stderr","project.tgz"}; http://www.wenmr.eu/wenmr/gromacs-grid

  20. The GROMACS web portal: communicate with the grid ★ Prerequisites: valid Grid x.509 certificate and membership of the eNMR VO; a UI to access the grid such as MILU ★ Create a certificate proxy: voms-proxy-init -voms wenmr.eu ★ Check availability of resources: glite-wms-job-list-match -a gmx.jdl ★ Submit your job: glite-wms-job-submit -a -o gmx.id gmx.jdl ★ Obtain the status of your job: glite-job-status -i gmx.id ★ Retrieve results: glite-wms-job-output --noint -i gmx.id --dir gmx.out http://www.wenmr.eu/wenmr/gromacs-grid

  21. THANK YOU ..... QUESTIONS? m.vandijk1@uu.nl

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