user-friendly metaworkflows in quantum chemistry

User-‐friendly metaworkflows in quantum chemistry

Alexander Hoffmann, Sonja Herres-‐Pawlis, Sandra Gesing, Luis de la Garza, Jens Krüger, and Richard Grunzke

[email protected]

Science Gateway InsKtute Workshop

September 27, 2013, Indianapolis, Indiana

Sandra Gesing

MoKvaKon

2 User-‐friendly metaworkflows in quantum chemistry

•  Excellent simulaKon codes available

•  Huge amount of computaKonal resources

•  Time consuming access even for experienced users

•  Impassable obstacle for beginners

Sandra Gesing

Aims of MoSGrid


Molecular SimulaKon Grid •  Enabling easier access to DCIs •  Allowing inexperienced scienKsts to run molecular simulaKons on DCIs

•  Offering an intuiKve user interface (gateway) •  Enabling easy access to workflows and data repositories

Sandra Gesing

MoSGrid in a Nutshell


XtreemFS

Distributed File

System

Portal WS-‐PGRADE

Liferay

DCIs UNICORE 6

Result

Coordinates(xyz/pdb)

Multiplicity/Charge Job Type #CPU/

Memory

Job Creation

input.gjf

g09

gaussian.log

User-Input

Portal

GridRessource

Recipe Structure Result

High-‐level middleware service level

gUSE

Workflow

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Data Repository


•  Repository consists of data and metadata storage •  MSML (Molecular SimulaKon Mark-‐up Language) •  Subset and extension of CML (Chemical Mark-‐up Language)

•  Unified data representaKon for molecules, macromolecules and recipes

•  Parsers and adapters used for conversions to and from MSML Repository convert

from MSML convert to MSML

and index

Sandra Gesing

Use of Workflows in Domains


•  Quantum Chemical CalculaKons •  Based on approximated soluKons of the Schrödinger equaKon •  Average scalability •  Gaussian, NWChem, …

•  Molecular Dynamics •  based on forcefields describing molecular interacKons •  Good scalability •  Gromacs, NWChem, MD-‐eSBM-‐Tools…

•  Docking •  Based on simplified forcefields •  Excellent scalability •  CADDSuite, FlexX, Autodock Vina…

Sandra Gesing

Basic Workflow


Job DefiniKon

ApplicaKon Input

ExecuKon

Meta-‐ processing

Job Submission

ApplicaKon Output

Output

Portal User-‐ Input

Grid Resource

Post processing

Visualizaton

Sandra Gesing

The QC Portlet @ Mosgrid.de


•  Specialised interface for quantum chemistry sojware

•  Basic workflows •  Easy GeneraKon or Uploading of Input Files •  Parsing of result files

Sandra Gesing



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Example: Parameter Sweep


•  Input

–  Molecular structure –  Parameter –  Parameter range

•  First step –  AutomaKc generaKon of input files

•  Second step –  Submission into the grid

•  Third step –  Plomng of obtained energies against the chosen parameter

QC code

Converter •  Parameter Sweep

–  Scan of a potenKal energy surface (PES)

–  Change of one parameters crucial for theoreKcal analysis

–  ReacKon path analysis

–  Pre-‐defined steps

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File) Input file

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File) Output file

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File) Result plot

Postprocessor

PES file Parameter range

Sandra Gesing

Example: High-‐Throughput


•  Input –  X-‐ray data

•  First step –  Conversion into mol file

•  Second step –  Conversion into job file with pre-‐defined job parameters (funcKonal, basis set)

•  Third step –  Submission into the grid QC code

Converter

– NaKve X-‐ray format needs to be converted into a computaKonal readable mol file.

– Time-‐consuming process of manual conversion can be transferred into the portlet.

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File) Mol file

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File) Output file

X-ray (ins File)

X-ray (ins File)

X-ray (ins File)

X-ray (ins File)

X-ray (ins File)

Converter

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File)

X-‐ray (ins File) Input file

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Example: TransiKon State Analysis


•  Zinc complex reacKng with lacKde

135

111

0

Sandra Gesing

Example: TransiKon State Analysis


•  Input –  TransiKon state job file (e.g. QST3 file)

•  First step –  CalculaKon of TS geometry

•  Second step –  Conversion into job files for frequency and IRC calculaKons

•  Third step –  CalculaKon of frequency and reacKon path

QC code

Frequency Output

Converter

Frequency Input file IRC Input file

TS Input file

QC code

TS geometry

QC code

IRC Output

Sandra Gesing

Example: Spectroscopic Analysis


2 4 60.0

4.0x104

8.0x104

1200900 600 300

BP86 PW91 TPSSh B3LYP PBE0 CAM-B3LYP wB97xd BHLYP

E / eV

λ / nm

Structure Time-‐dependent Density FuncKonal Theory

Orbital analysis

Sandra Gesing



Freq Output

TD-DFT Output

Popul. Output

Solvation Output

QM code

Job Creator Job Creator Job Creator Job Creator

QM code QM code QM code

QM code

Output file

Opt Input

Freq input TD-DFT

input Popul. input

Solvation input

Opt WF

Metaworkflow

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Freq WF TD WF Pop WF Solv WF

Opt WF Opt WF

Metaworkflow

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Workflow Interoperability


Freq WF TD WF Pop WF Solv WF

Opt WF

JOB1

JOB2

JOB3 JOB4

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Coarse-‐grained WF Interoperability


Workflow system A

Workflow system B

DCI A WF A

WF B DCI B

Workflow editor B

Workflow editor A

Sandra Gesing

Coarse-‐grained WF Interoperability


WF B DCI B

Workflow system A

Workflow system B

DCI A WF A

WF B DCI B

Workflow editor B

Workflow editor A

Meta WF WF B

Meta WF WF B

Sandra Gesing

Fine-‐grained WF Interoperability


Workflow system A

Workflow system B

DCI A WF A

WF B DCI B

Workflow editor B

Workflow editor A

Sandra Gesing

Fine-‐grained WF Interoperability


Workflow system A

Workflow system B

DCI A WF A

WF B DCI B

Workflow editor B

Workflow editor A

Convert to type A

Sandra Gesing

Workflows in Quantum Chemistry


•  Applica'on at the QC codes implemented in MoSGrid: ü Gaussian ü NWChem

•  Great help for users (via standard recipes in the repository)

•  Possibility to generate own complex workflows •  FacilitaKon of data extracKon and postprocessing •  Meta-‐workflows allow re-‐use of basic workflows!

Sandra Gesing

Sustainability


MoSGrid (ended 31.12.2012) but partners parKcipate in SCI-‐BUS (SCIenKfic gateway Based User Support) •  EU project 01.10.2011 – 30.09.2014 •  Extension of the MoSGrid portal with an interacKve molecule editor based on WebGL and a semanKc search

ER-‐flow (Building an European Research Community through Interoperable Workflows and Data) •  EU project 01.10.2012 – 30.09.2014 •  IntegraKon of applicaKons in SHIWA simulaKon plaqorm •  Study of data exchange between workflow systems •  Community management

Sandra Gesing

Acknowledgements


Berlin, Zuse InsItut •  Thomas Steinke •  Patrick Schäfer

Tübingen, BioinformaIcs •  Oliver Kohlbacher •  Jens Krüger •  Luis de la Garza

Köln, RRZK •  Lars Packschies •  MarKn Kruse

Dresden, ZIH •  Ralf Müller-‐Pfefferkorn •  Richard Grunzke

MTA SZTAKI, Computer and AutomaKon Research InsKtute, Budapest

Centre for Parallel CompuKng, University of Westminster, London

München, LMU •  Sonja Herres-‐Pawlis •  Alexander Hoffmann

Sandra Gesing 26 User-‐friendly metaworkflows in quantum chemistry

[email protected]

user-friendly metaworkflows in quantum chemistry

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