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GRID/DATABASE ENABLED GAMESS/QMView. GAMESS workflow via xml/java GAMESS directly outputs data to XML file via Castor “marshalling” QMView reads in XML DATA via Castor “unmarshalling” - PowerPoint PPT Presentation
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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