1) GAMESS workflow via xml/java2) GAMESS directly outputs data to XML file via Castor

“marshalling”3) QMView reads in XML DATA via Castor

“unmarshalling”4) One GAMESS run creates initial XML data document,

pltorb reads in XML data to produce orbitals, then produces new XML document containing all original data plus MO data grids

GRID/DATABASE ENABLED GAMESS/QMView

GAMESS DATA FLOW AND ANALYSISConventional Iterative Workflow.Cut and paste new input files.Data stored as flat files

Evolving Iterative WorkflowGamess writes out XML document based on a schema.Filters create new input.Data is stored in a database for queries.QMView reads data either from XML documentor the database

----- RESULTS FROM SUCCESSFUL RHF GEOMETRY SEARCH ---------- COORDS, ORBS, GRADIENT, AND APPROX. HESSIAN -----

COORDINATES OF SYMMETRY UNIQUE ATOMS (ANGS)

ATOM CHARGE X Y Z

------------------------------------------------------------

C 6.0 0.0000000000 0.0000000000 -0.1584868129

H 1.0 0.8569373922 0.0000000000 0.5695730947

CREATING GAMESS XML DOCUMENTS

public ATOM_POSITION[] getATOM_POSITION(){int size = _ATOM_POSITIONList.size();ATOM_POSITION[] mArray = new ATOM_POSITION[size];for (int index = 0; index < size; index++) {mArray[index] = (ATOM_POSITION) _ATOM_POSITIONList.elementAt(index);return mArray;}

2) Create JAVA classes corresponding to XML elements with the CASTOR (exolab.org) SourceGenerator. Each class contains methods for setting and retrieving data:

1) Start with GAMESS SCHEMA (gamess.xsd) http://www.sdsc.edu/~jpg/nmi/newgamess.xsd

public void addATOM_POSITION(ATOM_POSITION vATOM_POSITION)throws java.lang.IndexOutOfBoundsException{_ATOM_POSITIONList.addElement(vATOM_POSITION);}

Add an ATOM_POSITION element

Retrieve an array of ATOM_POSITION elements

CREATING GAMESS XML DOCUMENTS (continued)_

3) Link JAVA code to GAMESS via JNI (JAVA NATIVE INTERFACE). Write out required data to GAMESS java class.Marshall java data to an xml document

GAMESS(FORTRAN)

C GAMESS/XML LIBRARY

GAMESS JAVA class

XML exam01.xml

C library linked in gamess

executableCall java via JNI

“marshall” XML document

-

<ATOM_POSITIONATOM_NUMBER="1“> <ATOM_NAME>C</ATOM_NAME>   <ATOMIC_NUMBER>6.000000</ATOMIC_NUMBER> <XCOORD>0.000000</XCOORD>   <YCOORD>0.000000</YCOORD>   <ZCOORD>-0.089912</ZCOORD>   </ATOM_POSITION>- <ATOM_POSITION>

GAMESS WORKFLOW EXAMPLE(Calculate Molecular Orbitals,Calculate Molecular Orbital Grid,Visualize Molecular Orbital Surfaces)

-

GAMESS

Conventional OUTPUT FILES

Current Method $VEC 1 1 9.83982504E-01 6.1548973b5E-02 0.00000000E+00 0.00000000E+00 1.16964453E-02 1 2-1.55605505E-02-1.55605505E-02 2 1-2.42704529E-01 6.50084869E-01 0.00000000E+00 0.00000000E+00 1.75598849E-01 2 2 2.81180939E-01 2.81180939E-01

Make MO coeff. file and coordinate /atomic basis file

PLTORB3D

MDM MO Grid File

Store conventional files

QMView

“Retrieve” results

GAMESS WORKFLOW EXAMPLE(Calculate Molecular Orbitals,Calculate Molecular Orbital Grid,Visualize Molecular Orbital Surfaces)

GAMESS

New Method (under development)

XML Data File

MO Grid data added to original GAMESS XML doc

Java/Castorinterface

<?xml version="1.0" ?> - <GAMESS xmlns="http://www.sdsc.edu" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.sdsc.edu G:\nmi\newgamess.xsd">- <IN>  <RUN_TITLE>"Methylene."</RUN_TITLE>

<xs:element name="PROPERTIES" minOccurs="0">- <xs:complexType>- <xs:sequence> 

<<xs:element name="VOLUME_GRID" minOccurs="0" maxOccurs="unbounded">- <xs:complexType>

QMView reads volume data from XML file via java/jni

PLTORB3D reads MO, coord and AO basis from

XML file

Data stores in database,and

transmitted as JAVA objects

1) Establish workflow between GAMESS (QM) and APBS (classical charge distribution)

2) Connect GAMESS to APBS3) Create a workflow to achieve self consistent solution to

large (classical) macromolecule/small ligand (QM) molecule system

GAMESS/APBS

GAMESS/APBS

Workflow

GAMESS CALC APBS CALC

totalGAMESS

APBS

Iterate to Self-Consistency

Charges calculated with chelpg, PARSE radii, Ligand Coordinates from GAMESS

QMView

A

D

B

C

A

D

BC

E

Select structure and ligand

Remove the macromolecule

Protonate

1) Facilitating running GAMESS Jobs on the Grid Via the Gridport Tool Kit

2) Enabling Data Storage, Retrieval and Querying via XML documents generated directly from GAMESS

3) In the near future: an integrated workflow service

GRID ENABLED GAMESS AND APBS

Web ServerUser authentification, File transer, and remote procedureCalls via globus facilitated via theGridport Toolkit

SRBStore data and job status. Users given accounts via the portal

Download output dataUpload input data

SDSC/NBCR PORTALS

Globus call for copying packed script. Globus call for execution of packed script.

Remote Computational Platforms

1) Unpack scripts2) Copy data from SRB 3) Submit Job to Queue4) Store current Job status on SRB5) Store job output on SRB(GSI Authentification used for SRB file Transfers)Users have accounts orJobs are run via a master account

Workstation

First efforts: web servicesfor each separate program. Similar portals, identical

visualization server

APBS Electrostatic Force Field Calculation

GAMESS QM

Calculation

Grid PortalServices Broker

Select remote service

Globus SSH SCP SRB

HARDWARE

Grid Portal Web Server

gridport.npaci.edu

QMView Server

QMView Server

1) Runs on server independent of client platform

2) All capabilities of interactive QMView

3) Can read APBS and GAMESS files, and XML files put out by GAMESS and eventually APBS

4) Puts out images

5) Could be configured to put out

a) Animations

b) XML files for:

i. SVG

ii. JAVA3D based browsers

Future General Scientific Workflow

•Application schemas define general scientific applications in terms of what platforms are supported and what are its inputs and outputs. It is independent of a runtime platform. Each application constitutes a “node”.

•A node “graph” defines how different applications, including simulations, analysis and input/output filters connect.

•File schema defines where input files can be found and show they can be retrieved*

*XMLSpy representation of schema

Specify applications that are to be connected, input files and platforms.

Instance of a Scientific Workflow

When input data is combined with a workflow and its application definitions, and platforms are chosen, a job is instantiated*.

*XMLSpy representation of schema

Grind Away