MD ON THE GRID USING THE WENMR GROMACS WEB PORTAL Marc van Dijk - - PowerPoint PPT Presentation

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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

Apr 08, 2023 510 likes •728 views

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

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MD ON THE GRID USING THE WENMR GROMACS WEB PORTAL

Marc van Dijk Utrecht University The Netherlands

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GROMACS on the Grid: basics

  • Ported GROMACS version: 4.5.3 with rotational constraint support
  • Installed on 16 sites supporting the eNMR Virtual Organization
  • Together they support ~47500 CPU’s
  • Are these all available?
  • Shared with other web portals and other VO’s
  • Pooled in different queues
  • Sites not always up

No, unfortunately not Always in search

  • f more sites to

add www.gromacs.org

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SLIDE 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
  • Together they support ~47500 CPU’s
  • Are these all available?
  • Shared with other web portals and other VO’s
  • Pooled in different queues
  • Sites not always up

No, unfortunately not Always in search

  • f more sites to

add

✓

GROMACS on the Grid IS NOT HPC for single simulations

✓

GROMACS on the Grid IS HPC for parametric simulations www.gromacs.org

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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

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  • 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

Access to WeNMR portals via the VRC www.wenmr.eu

Your profile

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SLIDE 6
  • 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

Access to WeNMR portals via the VRC www.wenmr.eu

Your profile

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GROMACS on the WeNMR VRC www.wenmr.eu

★ Help Center ★ Documentation ★ Tutorials

Added benefits

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http://haddock.science.uu.nl/enm/services/GROMACS

The GROMACS web portal: two interfaces

1 2 1 2

Start the simulation using a PDB or Gromacs structure file Start the simulation using a preconfigured Gromacs binary run input file (.tpr)

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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

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The GROMACS web portal: start with a structure file

1

★ .pdb or .gro file ★ NMR ensembles accepted,

1st model used

★ ATOM and HETATM type

check

★ <= 1200 residues

Upload Structure file 1

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The GROMACS web portal: start with a structure file

2

★ Simulation time in ns. ★ Output resolution ns. ★ Forcefield type ★ Solvent model, default for FF

  • r: SPC, TIP3P, TIP4P

★ Electrostatics: cut-off/reaction

field, PME Optional parameters 2

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The GROMACS web portal: start with a structure file

3

★ Salt concentration (mol/l) ★ Temperature and pressure ★ Minimal distance between

periodic images

★ Seed for velocity distribution ★ Perform basic analysis ★ Create NDLP simulation box ★ Roto-translational constraints ★ Virtual sites

Advanced parameters 3

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SLIDE 13

The GROMACS web portal: what happens behind the scenes

  • Topology generation
  • Energy minimization in vacuum
  • Optimizing simulation box (squeez)
  • Solvation and addition of ions
  • Minimize solvated system, position restraint MD
  • Temperature/Pressure coupling
  • Production Simulation

Project execution

JDL

  • MD production run in parts

JDL

gmx45setup.sh gmx45md.sh

Finished Project

Project setup post processing Local Grid m.vandijk1@uu.nl

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The GROMACS web portal: start from a .tpr file

2

Starting a Grid MD project from a preconfigured simulation system

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The GROMACS web portal: start from a .tpr file

1

★ Upload valid .tpr file ★ Upload option checkpoint

file (.cpt)

★ Simulation time in ns ★ Perform basic analysis

Upload preconfigured simulation system 1

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The GROMACS web portal: what happens behind the scenes

  • Topology generation
  • Energy minimization in vacuum
  • Optimizing simulation box (squeez)
  • Solvation and addition of ions
  • Minimize solvated system, position restraint MD
  • Temperature/Pressure coupling
  • Production Simulation

Project execution

JDL

  • MD production run in parts

JDL

gmx45setup.sh gmx45md.sh

Finished Project

Project setup post processing Local Grid m.vandijk1@uu.nl

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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

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SLIDE 18

The GROMACS web portal: doing it manually

3

Interact directly with the WeNMR Grid infrastructure using your own scripts

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http://www.wenmr.eu/wenmr/gromacs-grid

The GROMACS web portal: setup of a JDL file

JobType = "Normal"; Requirements = (other.GlueCEPolicyMaxWallClockTime >= 300 &&

  • ther.GlueCEPolicyMaxCPUTime >= 1800 &&

Member("VO-enmr.eu-GROMACS4.5.3-rtc-r2",other.GlueHostApplicationSoftwareRunTimeEnvironment)); Rank = ( other.GlueCEStateFreeJobSlots > 100 ? other.GlueCEStateFreeJobSlots :

  • ther.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"};

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http://www.wenmr.eu/wenmr/gromacs-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

The GROMACS web portal: communicate with the grid

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m.vandijk1@uu.nl

THANK YOU ..... QUESTIONS?