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National Center for Supercomputing Applications
Production Cyberenvironment for a
A Computational Chemistry Grid
PRAGMA13, NCSA
26 Sep 07
Sudhakar PamidighantamNCSA, University of Illinois at
National Center for Supercomputing Applications
Acknowledgements
National Center for Supercomputing Applications
Outline
• Historical Background Grid Computational Chemistry
• Production Environments• Current Status Web Services • Usage (Grid and Science
Achievements)• Brief Demo • Future
National Center for Supercomputing Applications
MotivationSoftware - Reasonably Mature and easy to use to address
chemists questions of interest
Community of Users - Need and capable of using the software Some are non traditional computational chemists
Resources - Various in capacity and capability
National Center for Supercomputing Applications
Background
Qauntum Chemistry Remote Job Monitor( Quantum Chemistry Workbench)1998, NCSA
Chemviz1999-2001, NSF (USA)http://chemviz.ncsa.uiuc.edu
TechnologiesWeb Based Client Server ModelsVisual InterfacesDistributed computing (Condor)
National Center for Supercomputing Applications
GridChem
NCSA Alliance was commissioned 1998
Diverse HPC systems deployed
both at NCSA and Alliance Partner Sites
Batch schedulers different at sites
Policies favored different classes and modes of
use at different sites/HPC systems
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Extended TeraGrid Facility
www.teragrid.org
National Center for Supercomputing Applications
NSF Petascale Road Map• Track I Scheme Multi petaflop single site system to be
deployed by 2010 Several Consortia Competing (Now under review)
• Track 2 Sub petaflop systems Several to be deployed until Track 1 is online
First one will be at TACC ( 450 TFlops) Available Fall 2007( 50 000 Processors/Cores)
NCSA is deploying a 110 TFlops in April 2007(10000 Processors/cores)
Second subpetaflops systems being reviewed
National Center for Supercomputing Applications
Grid and GridlockAlliance lead to Physical Grid
Grid lead to TeraGrid
Homogenous Grid with predefined fixed software and system stack was planned (Teragrid) but it was difficult to keep it homogenous
Local preferences and diversity leads to heterogeneous grids now! (Operating Systems, Schedulers, Policies, Software and Services)
Openness and standards that lead interoperability are critical for successful services
National Center for Supercomputing Applications
Current Grid Status
Grid Hardware
Middleware
Scientific Applications
InterfacesInterfaces
National Center for Supercomputing Applications
User Community
Chemistry and Computational Biology
User BaseSep 03 – Oct 04
NRAC AAB Small Allocations
-------------------------------------------------------------
#PIs 26 23 64
#SUs 5,953,100 1,374,100 640,000
National Center for Supercomputing Applications
National Center for Supercomputing Applications
Some User Issues Addressed by the new Services
• New systems meant learning new commands• Porting Codes• Learning new job submissions and monitoring
protocols• New proposals for time (time for new
proposals)• Computational modeling became more popular
and number of users increased (User Management)
• Batch queues are longer / waiting increased• Finding resources where to compute
complicated - probably multiple distributed sites
• Multiple proposals/allocations/logins• Authentication and Data Security • Data management
National Center for Supercomputing Applications
Computational Chemistry Grid
This is a Virtual Organization
Integrated Cyber Infrastructure for Computational Chemistry
Integrates Applications, Middleware, HPC
resources, Scheduling and Data
management
Allocations, User services and Training
National Center for Supercomputing Applications
Resources
System (Site) Procs Avail
Total CPU Hours/Year
Status
Intel Cluster (OSC) 36 315,000 SMP and Cluster nodes
HP Integrity Superdome (UKy)
33 290,000 TB Replaced with an SMP/ Cluster nodes
IA32 Linux Cluster (NCSA)
64 560,000 Allocated
Intel Cluster (LSU) 1024 1,000,000 Allocated
IBM Power4 (TACC) 16 140,000 Allocated
Teragrid (Multiple Institutions)
2-10000 250,000 New Allocations Expected
The initial Acesss Grid Testbed Nodes (38) and Condor SGI resources (NCSA, 512 nodes) have been retired this year.
National Center for Supercomputing Applications
Other Resources
Extant HPC resources at various
Supercomputer Centers (Interoperable)
Optionally Other Grids and Hubs/local/personal
resources
These may require existing
allocations/Authorization
National Center for Supercomputing Applications
National Center for Supercomputing Applications
Grid Middleware Proxy Server
GridChem System
user user useruser user
PPortal Clientortal Client
Grid ServicesGrid Services
GridGrid
applicationapplicationapplicationapplication
Mass Storage
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0438312
National Center for Supercomputing Applications
Applications
• GridChem supports some apps already– Gaussian, GAMESS, NWChem, Molpro, ADF,QMCPack,
Amber
• Schedule of integration of additional software– ACES-3– Crystal– Q-Chem– Wein2K– MCCCS Towhee – Others...
National Center for Supercomputing Applications
GridChem User ServicesAllocation Request
https://www.gridchem.org/allocations/comm_form.php
National Center for Supercomputing Applications
GridChem User ServicesConsulting Ticketing System
User View
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GridChem User ServicesConsulting Ticketing System
https://www.gridchem.org/consult/Consultants View
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Gridchem Middleware Service (GMS)
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GrdiChem Web ServicesQuick Primer
XML is used to tag the data, SOAP is used to transfer the data, WSDL is used for describing the services available and UDDI is used for listing what services are available.
Web Services is different from Web Page Systems or Web Servers:There is no GUI
Web Services Share business logic, data & processes through APIs with each other (not with user)
Web Services describe Standard way of interacting with “web based” applications
A client program connecting to a web service can read the WSDL to determine what functions are available on the server. Any special datatypes used are embedded in the WSDL file in the form of XML Schema. Universal Description, Discovery, and Integration. WSRF Standards Compliant.
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GridChem Web Services Client Objects Database Interaction
WSResources
DTO
Objects Hibernate
Databasehb.xml
Client
DTO (Data Transfer Object)Serialize transfer through XML
DAO (Data Access Object) How to get the DB objectshb.xml (Hibernate Data Map)
describes obj/column data mapping
BusinessModel
DAO
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GridChem Data Models
Users Projects Resources
UserProjectResource
SoftwareResources
ComputeResources
NetworkResources
StorageResources
Resources
resoruceIDTypehostNameIPAddresssiteID
userIDprojectIDresourceIDloginNameSUsLocalUserUsed
JobsjobIDjobNameuserIDprojIDsoftIDcost
Users Resources
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Computational Chemistry Resource
National Center for Supercomputing Applications
GMS_WS Use Cases
• Authentication
• Job Submission
• Resource Monitoring
• Job Monitoring
• File Retrieval
• …
http://www.gridchem.org:8668/space/GMS/usecase
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• GetResourceProperty• SetTerminationTime • Destroy• Create • Login • LoadVO • RetrieveFiles • LoadFiles • DeleteFiles • LoadParentFiles • RefreshFiles • MakeDirectory • SubmitJob • SubmitMultipleJobs • PredictJobStartTime • KillJob • HideJob • UnhideJob • UnhideJobs • DeleteJob • FindJobs • GetJobStatus • RetrieveJobOutput • RetrieveNextDataBlock • StopFileAction • GetUserPreferences • PutUserPreferences
GridChem Web Services Operations
National Center for Supercomputing Applications
GMS_WS Authentication
• WSDL (Web Service Definition Language) is a language for describing how to interface with XML-based services. It describes network services as a pair of endpoints operating on messages with either document-oriented or procedure-oriented information.
• The service interface is called the port type • WSDL FILE: <?xml version="1.0" encoding="UTF-8"?> <definitions name=“GMS"
targetNamespace=http://www.gridchem.org/gms " xmlns="http://schemas.xmlsoap.org/wsdl/" …
http://www.gridchem.org:8668/space/GMS/usecase
Contact GMSCreates Session, Session RP and EPRSends EPR ( Like a Cookie, but more than that)
Login Request(username:passwd)
Validates, Loads UserProjectsSends acknowledgement
Retrieve UserProjects(GetResourceProperty Port Type [PT])
GridChem Client GMS
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GMS_WS Authenticationhttp://www.gridchem.org:8668/space/GMS/usecase
Selects projectLoadVO port type(w. MAC address)
Verifies user/project/MACaddrLoad UserResources RP
Retrieve UserResources[as userVO/ Profile](GetResourceProperty port Type PT)
GridChem Client GMS
Validates, Loads UserProjectsSends acknowledgement
Sends acknowledgement
National Center for Supercomputing Applications
GMS_WS Job Submission
Create Job objectPredictJobStartTime PT + JobDTO
JobStart Prediction RP
PT = portType RP = Resource PropertiesDTO = Data Transfer Object
Completion:Email from batch systemto GMS servercron@GMS DB
SubmissionCoGKitGAT“gsi-ssh”
If decision OK,SubmitJob PT + JobDTO
Create Job objectAPI—SubmitStore Job Object
Send Acknowledgement
Need to check to make sure allocation-time is available.
GC Client GMS
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GMS_WS Monitoring
Parse XML,Display
PT = portType RP = Resource PropertiesDTO = Data Transfer ObjectDB = Data Base
cron@GMS servercron@HPC ServersJob Launcher NotificationsVO Admin emailparses email DB(status + cost)
Request for Job,Resource StatusAlloc. Balance
UserResource RP Updated from DB
GC Client GMS Resources/Kits/DB
Send info
Discover Applications (Software Resources)
Monitor System
Monitor Queues
National Center for Supercomputing Applications
GMS_WS Job Status
Job Status jobDTO.status Job Launcher
Status Update
Estimate Start time
Scheduler emails/
notifications
Notifications: Client, email, IM
GC Client GMS Resources/Kits/DB
National Center for Supercomputing Applications
GMS_WS File Retrieval (MSS)
GetResourceProperty PTFileDTO(?)LoadFile PT(project folder+job)
Validates projectfolder owned by user.Send new listing
PT = portType RP = Resource PropertiesDTO = Data Transfer ObjectMSS = Mass Storage System
Job Completion:Send Output to MSS
LoadFile PT MSS queryUserFiles RP +FileDTO object
Retrieve Root Dir. Listing on MSS withCoGKit orGAT or“gsi-ssh”
API file requestStore locallyCreate FileDTOLoad into UserData RP
RetrieveFiles PT(+file rel.path)
Retrieve file:CoGKit orGAT or“gsi-ssh”
GetResourceProperty PT
GC Client GMS Resources/Kits/DB
National Center for Supercomputing Applications
GMS_WS File Retrieval
PT = portType RP = Resource PropertiesDTO = Data Transfer ObjectMSS = Mass Storage System
Create FileDTO (?)Load into UserData RP
RetrieveJobOutput PT(+JobDTO)
Job Record fromDB.Running: from ResourceComplete: from MSS
Retrieve file:CoGKit orGAT or“gsiftp”
GetResourceProperty PT
GC Client GMS Resources/Kits/DB
National Center for Supercomputing Applications
GridChem Web ServicesWSRF (Web Services Resource Framework) Compliant
WSRF Specifications:WS-ResourceProperties (WSRF-RP) WS-ResourceLifetime (WSRF-RL) WS-ServiceGroup (WSRF-SG) WS-BaseFaults (WSRF-BF)
%ps -aux | grep ws/usr/java/jdk1.5.0_05/bin/java \-Dlog4j.configuration=container-log4j.properties \-DGLOBUS_LOCATION=/usr/local/globus \-Djava.endorsed.dirs=/usr/local/globus/endorsed \-DGLOBUS_HOSTNAME=derrick.tacc.utexas.edu \-DGLOBUS_TCP_PORT_RANGE=62500,64500 \-Djava.security.egd=/dev/urandom \-classpath /usr/local/globus/lib/bootstrap.jar: /usr/local/globus/lib/cog-url.jar: /usr/local/globus/lib/axis-url.jar org.globus.bootstrap.Bootstrap org.globus.wsrf.container.ServiceContainer -nosec
Logging ConfigurationWhere to find Globus
Where to get random seedfor encryption key generation
Classpath (required jars)
National Center for Supercomputing Applications
GridChem Software OrganizationOpen Source Distribution
• CVS for GridChem
National Center for Supercomputing Applications
• Package:org.gridchem.service.gms
GMS_WS
National Center for Supercomputing Applications
GMS_WS
+
Should these each be a separate package?
National Center for Supercomputing Applications
model
dto
credential
job
notification
file file.taskjob.task
user
exceptions
resource
persistence
synchquery
test
util
dao
gpir
cryptenumeratorsgatproxy
GMS_WS
client
audit
gms Classes for WSRF service implementation (PT)Cmd line tests to mimic client requestsData Access Obj – queries DB via persistent classes (hibernate)Data Transfer Obj – (job,File,Hardware,Software,User) XMLHow to handle errors (exceptions)CCG Service business mode (how to interact)Contains user’s credentials for job sub. file browsing,…“Oversees correct” handling of user data (get/putfile).Define Job & util & enumerations (SubmitTask, KillTask,…)
CCGResource&Util, Synched by GPIR, abstract classesNetworkRes., ComputeRes., SoftwareRes., StorageRes., VisualizationRes.
User (has attributes – Preference/Address)DB operations (CRUD), OR Maps, pool mgmt,DB session,Classes that communicate with other web services
Periodically update DB with GPIR info (GPIR calls)JUnit service test (gms.properties): authen. VO retrieval, Res.Query,Synch, Job Mgmt, File Mgmt, NotificationContains utility and singleton classes for the service.Encryption of login passwordMapping from GMS_WS enumeration classes DBGAT util classes: GATContext & GAT Preferences generationClasses deal with CoGKit configuration.
Autonomous notification via email, IM, textmesg.
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GMS_WS external jars
• Testing• For XML Parsing
• “Java” Document Object Model – Lightweight– Reading/Writing XML Docs– Complements SAX (parser) & DOM– Uses Collections**
National Center for Supercomputing Applications
GridChem Resources Monitoring
http://portal.gridchem.org:8080/gridsphere/gridsphere?cid=home
National Center for Supercomputing Applications
GridChem Resources
New Computing Systems System Capacity (Cpus/Cores) Capability
Mercury(NCSA) 1774 Small/Large Parallel Runs
Abe(NCSA) 9600 Massively Parallel Runs
DataStar(SDSC) 2368 SharedMemory Large Runs
Bluegene/L(SDSC) 3456 Cluster Large Parallel Runs
TeragridCluster(SDSC) 564 Small/Large Parallel Runs
BigRed(IU) 1024 SharedMemory Small/Large Runs
BCX (UKy) 1360 Shared/Distributed Memory small/Large Parallel Runs
National Center for Supercomputing Applications
Application Software ResourcesCurrently Supported
Suite Version Location
Gaussian 03 C.02/D.01 Many Platforms
MolPro 2006.1 NCSA
NWChem 5.0/4.7 Many Platforms
Gamess Jan 06 Many Platforms
Amber 8.0 Many Paltforms
QMCPack 2.0 NCSA
National Center for Supercomputing Applications
GridChem Software ResourcesNew Applications
Integration Underway
• ADF Amsterdam Density Functional Theory• Wien2K Linearized Augemented Plain wave (DFT)• CPMD Car Parinello Molecular Dynamics • QChem Molecular Energetics (Quantum Chemistry)• Aces3 Parallel Coupled Cluster Quantum Chemistry• Gromacs Nano/Bio Simulations (Molecular Dynamics)
• NAMD Molecular Dynamics• DMol3 Periodic Molecular Systems ( Quantum Chemistry)• Castep Quantum Chemistry • MCCCS-Towhee Molecular Confirmation Sampling (Monte Carlo)• Crystal98/06 Crystal Optimizations (Quantum Chemistry)• ….
National Center for Supercomputing Applications
GridChem User Services• Allocationhttps://www.gridchem.org/allocations/index.shtmlCommunity and External Registration Reviews, PI Registration and Access Creation Community User Norms Established
• Consulting/User Serviceshttps://www.gridchem.org/consultTicket tracking, Allocation Management
• Documentation, Training and Outreachhttps://www.gridchem.org/doc_train/index.shtmlFAQ Extraction, Tutorials, Dissemination
Help is integrated into the GridChem client
National Center for Supercomputing Applications
Users and Usage
• 242 Users under 128 Projects
Include Academic PIs, two graduate classes
And about 15 training users
More than a 442000 CPU Wallhours since Jan 06
More than 10000 Jobs processed
National Center for Supercomputing Applications
Science Enabled
• Azide Reactions for Controlling Clean Silicon Surface Chemistry: Benzylazide on Si(100)-2 x 1Semyon Bocharov et al..J. Am. Chem. Soc., 128 (29), 9300 -9301, 2006
• Chemistry of Diffusion Barrier Film Formation: Adsorption and Dissociation of Tetrakis(dimethylamino)titanium on Si(100)-2 × 1 Rodriguez-Reyes, J. C. F.; Teplyakov, A. V.J. Phys. Chem. C.; 2007; 111(12); 4800-4808.
• Computational Studies of [2+2] and [4+2] Pericyclic Reactions between Phosphinoboranes and Alkenes. Steric and Electronic Effects in Identifying a Reactive Phosphinoborane that Should Avoid Dimerization Thomas M. Gilbert* and Steven M. Bachrach Organometallics, 26 (10), 2672 -2678, 2007.
National Center for Supercomputing Applications
Science Enabled• Chemical Reactivity of the Biradicaloid (HO...ONO) Singlet
States of Peroxynitrous Acid. The Oxidation of Hydrocarbons, Sulfides, and Selenides. Bach, R. D et al. J. Am. Chem. Soc. 2005, 127, 3140-3155.
• The "Somersault" Mechanism for the P-450 Hydroxylation of Hydrocarbons. The Intervention of Transient Inverted Metastable Hydroperoxides. Bach, R. D.; Dmitrenko, O. J. Am. Chem. Soc. 2006, 128(5), 1474-1488.
• The Effect of Carbonyl Substitution on the Strain Energy of Small Ring Compounds and their Six-member Ring Reference Compounds Bach, R. D.; Dmitrenko, O. J. Am. Chem. Soc. 2006,128(14), 4598.
National Center for Supercomputing Applications
GridChem Client Download Statistics
http://download.gridchem.org/usage/
National Center for Supercomputing Applications
Distribution of GridChem User Community
National Center for Supercomputing Applications
Job Distribution
Job Distribution by Time
0
50
100
150
200
250
300
350
100
300
500
700
900
1100
1300
1500
1700
1900
2100
2300
2500
2700
2900
Wall Clock x CPUs (~SUs)
Num
ber o
f Job
s
Job Distribution by Time
0
20
40
60
80
100
120
140
2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50
Wall Clock Time x CPUs (~SUs)Nu
mber
of Jo
bs
National Center for Supercomputing Applications
System Wide UsageHPC System Usage (SUs)
Tungsten(NCSA) 5507
Copper(NCSA) 86484
CCGcluster(NCSA) 55709
Condor(NCSA) 30
SDX(UKy) 116143
CCGCluster(UKy) .5
Longhorn(TACC) 54
CCGCluster(OSC) 62000
TGCluster(OSC) 36936
Cobalt(NCSA) 2485
Champion(TACC) 11
Mike4 (LSU) 14537
National Center for Supercomputing Applications
GridChem Client Enhancements
• New Molecular Editor
JMolEditor (ANU) Integration
• VMD Is integrated
• Nanotube Generator (Tubegen) Will be available
• Gamess Graphical User Interphase
National Center for Supercomputing Applications
Java Molecular Editor• JMolEditorThree Dimensional Visual with Java 3D
Intuitive Molecule ManipulationInteractive Bond, Angle and Dihedral Settings
A Gaussian input generator Interface
National Center for Supercomputing Applications
Nanotube Generator:Tubegen
Courtesy: Doren Research Group at the University of Delaware Crystal Cell Types
Output Formats
National Center for Supercomputing Applications
GridChem Gamess GUI
National Center for Supercomputing Applications
GridChem Post Processing• IR/Raman Spectra now accessible from G03, MolPro,
NWChem and Gamess Suites
VCD/ROA To be Included
National Center for Supercomputing Applications
GridChem Post Processing
• Normal Mode Viewing in 3D VRML
• Other Spectra With MO Integration
NMR
Electronic Spectra
National Center for Supercomputing Applications
GridChem UsabilityDynamic Information
National Center for Supercomputing Applications
GridChem Usability
• Information on Potential Start and End Time for a given set of Job parameters
• Automated Resource Selection • Possible Job Migration In case of
dropped nodes or incomplete job• Monitoring Multiple Jobs • Automated Monitoring Job Output
National Center for Supercomputing Applications
• Implementation of GRMS resource management Service http://www.gridlab.org/WorkPackages/wp-9
• Moving toward Service based job submission eliminating gateway interfaces
• Infrastructure for multiple input files for single application
• Infrastructure for multiple inputs in High Throughput processing
• Integrated workflow for multi scale coupled modeling
• Meta-scheduling for High Throughput Processing Match Making, Round-robin scheduling, Preferred Host Set usage
GridChem Middleware InfrastructureImplementation Currently underway
National Center for Supercomputing Applications
GridChem In New CollaborationsResource Providers
• New Resource Providers Open Science Grid Initially for Bio-related applications (open
source preferably)
• PRAGMA Partner sites University of Hyderabad
• ORNL (Could be via TeraGrid)
• International Partners KISTI, APAC, Daresbury Labs
National Center for Supercomputing Applications
Scientific Collaborations
• GridChem Extension to Molecular Sciences (Bio, Nano, Geo and Materials Sciences) (NSF Proposal)
• Parameter Sweep for Potential Energy Hyper Surfaces (Faculty Fellows, NCSA)
• Automated Parameterization of Force fields (NSF Proposal)
• Ab initio Molecular Dynamics (Faculty Fellows, NCSA)
• Education (CI-TEAM) (NSF Proposals)
• Multi-Scale Modeling (IACAT, UIUC)
National Center for Supercomputing Applications
Some New GridChem Infrastructure• Workflow Editors• Coupled Application Execution• Large Scale Computing• Metadata and Archiving • Rich Client Platform Refactorization• Intergrid Interactions
• Open Source Distribution http://cvs.gridchem.org/cvs/
• Open Architecture and Implementation details http://www.gridchem.org/wiki
National Center for Supercomputing Applications
Critical Gateways Issues
• Science Gateways compete with business as usual for the end user research scientist
• No direct access to HPC systems may be possible leading to apparent lack of control for users
• No “End to end solutions” If part of the research needs require old ways
Gateways may be avoided• Learning to use Gateways should provide substantial
added benefit –Cost/Benefit Issues for users• Flexibility to integrate new applications as needed by
community quickly is critical to keep the user community engaged
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Authentication
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Resource Status
National Center for Supercomputing Applications
Job Editor
National Center for Supercomputing Applications
Job Submission
National Center for Supercomputing Applications
Job Monitoring
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Gradient Monitoring
National Center for Supercomputing Applications
Energy Monitoring
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Post Processing
National Center for Supercomputing Applications
Visualization
Molecular Visualization
Electronic Properties
Spectra
Vibrational Modes
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Molecular Visualization
Better molecule representations(Ball and Stick/VDW/MS)
In Nanocad Molecular Editor Third party visualizer integration Chime/VMD
Export Possibilities to others interfaces Deliver standard file formats
(XML,SDF,MSF,Smiles etc…)
National Center for Supercomputing Applications
Eigen Function Visualization
• Molecular Orbital/Fragment Orbital
• MO Density Visualization
• MO Density Properties
• Other functions
Radial distribution functions
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Some example VisualsArginine Gamess/6-31G*Total electronic density
2D - Slices
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Electron Density in 3DInteractive (VRML)
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Orbital 2D DisplaysN2 6-31g* Gamess
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Orbital 3DVRML
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Spectra
• IR/Raman Vibrotational Spectra
• UV Visible Spectra
• Spectra to Normal Modes
• Spectra to Orbitals
National Center for Supercomputing Applications
Possible H-bonds network for P450cam
hydroperoxy intermediate
C
O
H
OH
OO H
Fe3+
O
H
CH3
HO
H
H
N
GLY248 peptide
VAL253 peptide
THR252
2.98Å2.79Å
2.99Å
2.75Å
3.16Å
3.07Å
3.32Å
Suggested:
THR252 accepts an H-bond from the hydroperoxy (Fe(III)-OOH that promotes thesecond protonation on the distal oxygen, leading to the O-O bond cleavage
Nagano, S.; Poulos, T.L. J. Biol. Chem. 2005, 250, p.1668• Auclair, K.; Hu, Z.; Little, D. M.; Ortiz de Montellano, P. R.; Groves, J. T. J. Am.
Chem. Soc. 2002, 124, 6020.
National Center for Supercomputing Applications
The Somersault Isomerization of Model Cpd0
TS
Fe
O
O H
SHFe
O
SH
H
O
E24.8 (24.3) 20.3 kcal/mol
1.447Å
2.226Å
2.408Å
1.869Å116.7
102.0
97.9
1.665Å
2.473Å
1.662Å
97.2
177.9
E = 17.5 (17.8) kcal/mol
EH-bonding = 17.0 kcal/mol
77.0
127.4
97.8
2.437Å
vi=101.5i cm-1
GS MIN
CCCC CC N
C CC
S
C
O
NFeNC
O
CC CN CC CC
CC
CC
C CCN
CC
CN
S
CC Fe
O
CC N
O
CCC N CC C
CC
CC CC
CCC NCC N
S
2.487Å
CFe
1.658Å
C
O
2.186Å
O
NCC N CCC CC CC
vi=93.7i cm-1
Robert Bach and Olga Dmytrenko, 2006
National Center for Supercomputing Applications
Energy Diagram for the Concerted Non-synchronous Hydroxylation of Isobutane
Fe
SH
O
O(H3C)3C
H
H
Fe
SH
O
OH
H(H3C)3C
Fe
SH
O
OH
H(H3C)3C
MIN-26a
Fe
SH
O
OHH
(H3C)3C
SH
O
OH
H
(H3C)3C
Fe
Fe
SH
OH
OH
(H3C)3C
-4.0
-19.2
17.2
-83.7
MIN-24bTS-25
MIN-26b
PRODUCT 28
3.848Å5.5
11.7
TS-27
GS-24a
19.5
Fe
SH
O
(H3C)3COHH
Energy diagram (kcal/mol) for the oxidation of the isobutane with ground state, 24a (GS-8 hydrogen bonded to isobutane). MIN-24b [model oxidant MIN-10 (PorFe(SH)OHO) hydrogen bonded to isobutene] is not necessarily on the reaction pathway.
National Center for Supercomputing Applications
Somersault Mechanism Summary for Isobutane Hydroxylation
S
FeIV
O
CH
CH3
CH3H3C
HO
S
FeIV
O
C
HCH3
CH3H3C
O
H
S
FeIV
O
C
H CH3
CH3H3C
O
H
S
FeIV
O
C
H
CH3
CH3H3C
O
H
National Center for Supercomputing Applications
TetrakisDimethylAminoTitanium and its derivatives on Si(100)-2x1 Surface: Diffusion Barrier Thinfilms on Silicon
Rodrigues-Reyes and Teplyakov
National Center for Supercomputing Applications
Benzylazide on Si(100)-2x1 SurfaceDeposition of Aromatic Moieties on Silicon for Lateral Electron
TransferBocharov et al..
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[2+2] Cyclo Additions involving B=P BondsGilbert and Bachrach
Dimerization
Ethyne Addition
Ethene Additions
National Center for Supercomputing Applications
Possible H-bonds network for P450cam
hydroperoxy intermediate
C
O
H
OH
OO H
Fe3+
O
H
CH3
HO
H
H
N
GLY248 peptide
VAL253 peptide
THR252
2.98Å2.79Å
2.99Å
2.75Å
3.16Å
3.07Å
3.32Å
Suggested:
THR252 accepts an H-bond from the hydroperoxy (Fe(III)-OOH that promotes thesecond protonation on the distal oxygen, leading to the O-O bond cleavage
Nagano, S.; Poulos, T.L. J. Biol. Chem. 2005, 250, p.1668• Auclair, K.; Hu, Z.; Little, D. M.; Ortiz de Montellano, P. R.; Groves, J. T. J. Am.
Chem. Soc. 2002, 124, 6020.
National Center for Supercomputing Applications
The Somersault Isomerization of Model Cpd0
TS
Fe
O
O H
SHFe
O
SH
H
O
E24.8 (24.3) 20.3 kcal/mol
1.447Å
2.226Å
2.408Å
1.869Å116.7
102.0
97.9
1.665Å
2.473Å
1.662Å
97.2
177.9
E = 17.5 (17.8) kcal/mol
EH-bonding = 17.0 kcal/mol
77.0
127.4
97.8
2.437Å
vi=101.5i cm-1
GS MIN
CCCC CC N
C CC
S
C
O
NFeNC
O
CC CN CC CC
CC
CC
C CCN
CC
CN
S
CC Fe
O
CC N
O
CCC N CC C
CC
CC CC
CCC NCC N
S
2.487Å
CFe
1.658Å
C
O
2.186Å
O
NCC N CCC CC CC
vi=93.7i cm-1
Robert Bach and Olga Dmytrenko, 2006
National Center for Supercomputing Applications
Energy Diagram for the Concerted Non-synchronous
Hydroxylation of Isobutane
Fe
SH
O
O(H3C)3C
H
H
Fe
SH
O
OH
H(H3C)3C
Fe
SH
O
OH
H(H3C)3C
MIN-26a
Fe
SH
O
OHH
(H3C)3C
SH
O
OH
H
(H3C)3C
Fe
Fe
SH
OH
OH
(H3C)3C
-4.0
-19.2
17.2
-83.7
MIN-24bTS-25
MIN-26b
PRODUCT 28
3.848Å5.5
11.7
TS-27
GS-24a
19.5
Fe
SH
O
(H3C)3COHH
Energy diagram (kcal/mol) for the oxidation of the isobutane with ground state, 24a (GS-8 hydrogen bonded to isobutane). MIN-24b [model oxidant MIN-10 (PorFe(SH)OHO) hydrogen bonded to isobutene] is not necessarily on the reaction pathway.
National Center for Supercomputing Applications
Somersault Mechanism Summary for Isobutane Hydroxylation
S
FeIV
O
CH
CH3
CH3H3C
HO
S
FeIV
O
C
HCH3
CH3H3C
O
H
S
FeIV
O
C
H CH3
CH3H3C
O
H
S
FeIV
O
C
H
CH3
CH3H3C
O
H
National Center for Supercomputing Applications
Unsymmetrical Mo(CO)4 Crown Ethers
National Center for Supercomputing Applications
Dibenzaphosphepin based bis(phosphorous)polyether chelated
Mo(CO)4
National Center for Supercomputing Applications
Crystal Structures
CSD:XAPZAP
cis-(6,6'-((1,1'-Binaphthyl)-2,2'-diylbis(oxy))bis(dibenzo(d,f)(1,3,2)dioxaphosp hepin))-tetracarbonyl-molybdenum(0) C48 H28 Mo1 O10 P2
CSD:DEQDOS
cis-Tetracarbonyl-(P,P'-(6-(2'-oxy-2-biphenyl)-3,6-dioxa-hexanolato)-bis(dibenzo (d,f)(1,3,2)dioxaphosphepine)-P,P')-molybdenum C44
H32 Mo1 O12 P2
National Center for Supercomputing Applications
Starting Structure
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Optimized Structure
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Reference Structure for Comparison
8
7
National Center for Supercomputing Applications
Structural ComparisonsC-C Torsion Angles for the OCH2CH2O Fragments and for the Axially
Chiral Biaryl Groups
Atoms PCMODEL* UFF Ab Initio Amber
C37-C42-C43-C48 -49.9 -26.4 -43.0 -40.4C1-C6-C7-C12 45.4 22.3 -22.3 -72.8C13-C22-C23-C32 75.6 74.7 -85.9 -81.2C32-O-C33-C34 -178.4 -140.8 159.7 -171.2O-C33-C34-O 62.4 -64.5 -87.3 -82.4C33-C34-O-C35 -80.6 -118.9 67.8 64.9C34-O-C35-C36 174.6 118.9 -153.4 60.1O-C35-C36-0 66.2 56.0 64.0 67.3
• *Hariharasarma, et al. Organomet., 1232-1238, 2000.• Ab Initio=B3LYP/3-21G*• Amber9 ff03, GAFF, chloroform, 300K, median over 1ns MD
National Center for Supercomputing Applications
MD OCH2CH2O Structure
8
7
National Center for Supercomputing Applications
MD Biaryl Structure
National Center for Supercomputing Applications
1H NMR Chemical Shift ComparisonFor Aromatic Protons
Reference 32ppm (from TMS B3LYP/6-31g*)
Atom Exp. Abinitio Atom Exp. AbinitioH2 7.025 5.6 H25 6.578 5.7H3 7.026 5.8 H26 6.737 5.9H4 7.049 5.9 H27 7.018 6.1H5 7.181 6.0 H28 7.623 6.5
H8 7.110 6.1 H30 7.790 6.7H9 6.890 6.0 H31 7.289 6.9H10 6.721 6.0H11 6.237 5.7 H38 7.327 6.2
H39 7.274 6.1H14 7.925 5.8 H40 7.169 6.0H15 7.808 6.3 H41 7.350 6.3
H17 7.741 6.0 H44 7.360 6.1H18 7.254 5.6 H45 7.160 5.9H19 7.091 5.1 H46 7.176 6.0H20 6.989 4.6 H47 7.060 7.0
National Center for Supercomputing Applications
Third Year Plans• Post Processing Spectra and related entities• New Application SupportAces3, Dmol3, Vasp,…..• Expansion of ResourcesTeragrid, OSG, Pragma Systems and New
resources at Partner Sites• Extension PlanTwo Proposals in review for Extension
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Future Plans
• Preparations for Petaflop computingHigh throughput massively parallel applications
• Complex workflows for integrating multiple interdependent applications
Multiscale Computing
• Archiving and annotating data for future useOpen Data initiatives by NIH and NSF
National Center for Supercomputing Applications
Acknowledgments
• Rion Dooley, TACC Middleware Infrastructure
• Stelios Kyriacou, OSC Middleware Scripts
• Chona Guiang, TACC Databases and Applications
• Kent Milfeld, TACC Database Integration • Kailash Kotwani, NCSA, Applications and Middleware
• Scott Brozell, OSC, Applications and Testing
• Michael Sheetz, UKy, Application Interfaces
• Vikram Gazula, UKy, Server Administration
• Tom Roney, NCSA, Server and Database Maintenance