GRID/DATABASE ENABLED GAMESS/QMView

1. 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” • 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

2. GAMESS DATA FLOW AND ANALYSIS Conventional Iterative Workflow. Cut and paste new input files.Data stored as flat files ----- 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 Evolving Iterative Workflow Gamess 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 document or the database

3. CREATING GAMESS XML DOCUMENTS • Start with GAMESS SCHEMA (gamess.xsd) http://www.sdsc.edu/~jpg/nmi/newgamess.xsd • Create JAVA classes corresponding to XML elements with the CASTOR (exolab.org) SourceGenerator. Each class contains methods for setting and retrieving data: public void addATOM_POSITION(ATOM_POSITION vATOM_POSITION) throws java.lang.IndexOutOfBoundsException { _ATOM_POSITIONList.addElement(vATOM_POSITION); } Add an ATOM_POSITION element 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; } Retrieve an array of ATOM_POSITION elements

4. - - - 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 C GAMESS/XML LIBRARY GAMESS (FORTRAN) C library linked in gamess executable Call java via JNI <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 JAVA class XML exam01.xml - “marshall” XML document

5. GAMESS WORKFLOW EXAMPLE (Calculate Molecular Orbitals,Calculate Molecular Orbital Grid,Visualize Molecular Orbital Surfaces) QMView Store conventional 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 Conventional OUTPUT FILES PLTORB3D MDM MO Grid File GAMESS - “Retrieve” results

6. GAMESS WORKFLOW EXAMPLE (Calculate Molecular Orbitals,Calculate Molecular Orbital Grid,Visualize Molecular Orbital Surfaces) New Method (under development) <?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> XML Data File Java/Castor interface PLTORB3D reads MO, coord and AO basis from XML file GAMESS MO Grid data added to original GAMESS XML doc QMView reads volume data from XML file via java/jni <xs:element name="PROPERTIES" minOccurs="0">- <xs:complexType>- <xs:sequence> <<xs:element name="VOLUME_GRID" minOccurs="0" maxOccurs="unbounded">- <xs:complexType> Data stores in database,and transmitted as JAVA objects

7. GAMESS/APBS • Establish workflow between GAMESS (QM) and APBS (classical charge distribution) • Connect GAMESS to APBS • Create a workflow to achieve self consistent solution to large (classical) macromolecule/small ligand (QM) molecule system

8. GAMESS/APBS Workflow Charges calculated with chelpg, PARSE radii, Ligand Coordinates from GAMESS GAMESS CALC APBS CALC Iterate to Self-Consistency H = H + H APBS GAMESS total

9. QMView

10. A B D C

11. A B C D E

12. Select structure and ligand Remove the macromolecule Protonate

14. GRID ENABLED GAMESS AND APBS • Facilitating running GAMESS Jobs on the Grid Via the Gridport Tool Kit • Enabling Data Storage, Retrieval and Querying via XML documents generated directly from GAMESS • In the near future: an integrated workflow service

15. SDSC/NBCR PORTALS Remote Computational Platforms Workstation Download output data Upload input data Web Server User authentification, File transer, and remote procedure Calls via globus facilitated via the Gridport Toolkit • Unpack scripts • Copy data from SRB • Submit Job to Queue • Store current Job • status on SRB • Store job output on • SRB • (GSI Authentification used • for SRB file Transfers) • Users have accounts or • Jobs are run via a master • account Globus call for copying packed script. Globus call for execution of packed script. SRB Store data and job status. Users given accounts via the portal

16. GAMESS QM Calculation First efforts: web services for each separate program. Similar portals, identical visualization server APBS Electrostatic Force Field Calculation Grid Portal Web Server gridport.npaci.edu Grid Portal Services Broker Select remote service Globus SRB SSH SCP HARDWARE QMView Server

17. QMView Server • Runs on server independent of client platform • All capabilities of interactive QMView • Can read APBS and GAMESS files, and XML files put out by GAMESS and eventually APBS • Puts out images • Could be configured to put out • Animations • XML files for: • SVG • JAVA3D based browsers

18. Future General Scientific Workflow • 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* Specify applications that are to be connected, input files and platforms. • 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”. *XMLSpy representation of schema

19. Instance of a Scientific Workflow Grind Away When input data is combined with a workflow and its application definitions, and platforms are chosen, a job is instantiated*. *XMLSpy representation of schema