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National Center for Supercomputing Applications
GridChem Science Gateway
In Production
National Science Foundation 23 May 2007
Sudhakar PamidighantamNCSA, University of Illinois at Urbana-Champaign
National Center for Supercomputing Applications
Outline
• GridChem: A Brief Overview• Scientific Impact• Resources High End Computing Systems Applications Software• Middleware Infrastructure• Portal/Gateway Client • User Community • Usage• Critical Gateway Issues• Future Plans
National Center for Supercomputing Applications
The Big Picture
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
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
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.
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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
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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
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[4+2] Cycloadditions involving B=P BondsGilbert and Bachrach
Cis-Butadiene Addition
Cyclopentadiene Addition
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GridChem Resources
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
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Application Software ResourcesCurrently Supported
Suite Version LocationGaussian 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
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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)• ….
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Gridchem Middleware Service (GMS)
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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
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GridChem Client Download Statistics
http://download.gridchem.org/usage/
National Center for Supercomputing Applications
Users and Usage• 222 Users Under 168 ProjectsInclude Academic PIs and colleagues,
graduate classes and
training users (typically used in tutorials/workshops/demo sessions etc..)
More than a 380000 CPU Wallhours Delivered since Jan 05 for over 5690 Individual Jobs
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Distribution of GridChem User Community
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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 Usage
HPC 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
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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
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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, Daresbsry Labs
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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)
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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
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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