on the development of an a priori grid enabled molecular simulator
DESCRIPTION
On the development of an a priori Grid enabled molecular simulator. EGEE User Forum – March 1-3, 2006 Geneva, CH Antonio Laganà 1 , Osvaldo Gervasi 2 1 Dept. of Chemistry, University of Perugia 2 Dept. of Math. & Computer Science, University of Perugia. FACTS. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/1.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
On the development of an a priori Grid enabled molecular simulator
EGEE User Forum – March 1-3, 2006
Geneva, CH
Antonio Laganà1, Osvaldo Gervasi2
1 Dept. of Chemistry, University of Perugia2 Dept. of Math. & Computer Science, University of Perugia
![Page 2: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/2.jpg)
2
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
FACTS
COMPCHEM is a virtual organization (VO) of Chemists and Molecular Scientists having the mission of developing cooperative computational tools for complex a priori realistic simulations
GEMS is the Grid Enabled Molecular Simulator meant to be made of all the components needed to implement on the Grid a priori molecular simulations
A prototype demo (GEMS.0) has been already implemented on the production grid of EGEE
![Page 3: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/3.jpg)
3
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
COMPUTATIONAL MOLECULAR SCIENCE• The starting point GEMS.0• Theoretical and computational know how • A workflow for distributed running
COMPUTER SCIENCE AND ORGANISATION• The need for a production grid infrastructure• The definition of operational modalities• A mechanism to reward cooperation
SUMMARY
![Page 4: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/4.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
FROM WHERE DOES THE GRID ENABLED MOLECULAR SIMULATOR (GEMS) COME ?
![Page 5: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/5.jpg)
5
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
THE CHEMISTRY AND MOLECULAR SCIENCE METALABORATORIES
• A Cost-Chemistry Action (D23) • Called METACHEM (Metalaboratories for
complex computational applications in Chemistry)
• Started in the year 1999 (ended 2005)• Having the goal of establishing the
Metalaboratories (clusters of geographically distributed laboratories sharing expertise, hardware and software on the net) for Chemistry and Molecular Science complex computational simulations
![Page 6: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/6.jpg)
6
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
Metachem: Metalaboratories for Complex Computational Applications in Chemistry
MURQM: Multireference Quantum Chemical Methods
DIRAC: Four Component Relativistic Quantum Chemical Calculations
SIMBEX: Simulation of Molecular Beam Experiments
![Page 7: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/7.jpg)
7
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
Metachem: Metalaboratories for Complex Computational Applications in Chemistry
DYSTS: Dynamics and Spectroscopy of Systems : Relevant to Environment and Applied ChemistryMURQM: Multireference Quantum Chemical Methods
ELCHEM: E-learning Technologies for Chemistry
ICAB: Integration of Codes for Ab Initio
Methods
![Page 8: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/8.jpg)
8
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
EU GRID for Chemistry: D23 COST action
Simbex
Murqm
Dirac
Elchem
Dysts
Comovit
Icab
![Page 9: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/9.jpg)
9
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
PARTNER GROUPS FROM NATIONAL PROJECTS
1 Isr, Pl, Sk, Nl, Ch
2 Cz, Fr, Dk, A, Sw, No
3 Hu
4 Gr
5 E
6 D, Uk,
9 I
![Page 10: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/10.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
SIMBEX: a research/educational tool for the simulation of elementary chemical reaction
•High interactivity
•Advanced visualization
•In deep insight into the chemical mechansm
![Page 11: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/11.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
THE STARTING POINT: GEMS.0
![Page 12: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/12.jpg)
12
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
GEMS.0
Interaction
Observables
Dynamics
The solution
The problem
![Page 13: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/13.jpg)
13
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The INTERACTION module
INTERACTION
DYNAMICS
Is therea suitable LEPS
Pes?
Import thePES parameters
NO
YES
START
![Page 14: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/14.jpg)
14
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The DYNAMICS module
DYNAMICS
OBSERVABLES
Are quantumdynamics
calculationsInappro-priate?
NO
YES
TRAJ: application
using classical trajectory
calculations(atom-diatom)
![Page 15: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/15.jpg)
15
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The OBSERVABLES module
OBSERVABLESNO
YES
Is the observable
a state-to-stateone?
DISTRIBUTIONS: VMfor scalar and vectorproduct distributions,
and state-to-state crosssections
Do calculated
and measuredproperties
agree?
END:EXTEND THE
CALCULATIONTO OTHER
PROPERTIES
YES NO END:TRY WITHANOTHER SURFACE
![Page 16: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/16.jpg)
16
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
THE ANGULAR DISTRIBUTION VIR-TUAL MONITORS FOR ATOM DIATOMSH+ICl→H+ICl
H+ICl→HI+Cl
H+ICl→HCl+I
![Page 17: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/17.jpg)
17
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The GRIDified TRAJ kernel
TRAJ
return
Iterate over initial conditionsthe integration of individualtrajectories (ABCTRAJ, etc.)
Define quantities of generaluse
![Page 18: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/18.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
FROM WHERE DOES THE COMPUTATIONAL KNOW HOW COME FROM?
![Page 19: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/19.jpg)
19
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
NATIONAL PROJECTS
• GRID.it
• UNICORE
• NORDUGRID
![Page 20: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/20.jpg)
20
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
GRID.IT
The Italian GRID project
CNR, INFN, CNIT, ASI, Universities
Enabling platforms for high performance computational Grids oriented to scalable virtual organizations
![Page 21: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/21.jpg)
21
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
High perfor-mance nets
GARR Fiber optics
Portals Security Communications
Resource Management MonitoringMiddleware
HP Components Problem Solving
Libraries Cost models
Program-Ming tools
Applications
Astrophysics Bioinformatics Earth observation
Geophysics Computational Chemistry
![Page 22: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/22.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
WHERE WE GO
![Page 23: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/23.jpg)
23
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
A priori molecular simulator
Service request
Interaction
Observables
Service delivery
Dynamics
YES
NO Is validation passed?
![Page 24: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/24.jpg)
24
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The INTERACTION module
INTERACTION
DYNAMICS
Is therea suitable Pes?
Are ab initiocalculationsavailable?
Are ab initiocalculations
feasible?
CALL SUPSIMCALL FITTING Import the
PES routine
NO NO NO
YES YES YES
Take force fielddata and
procedures from relateddatabases
START
![Page 25: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/25.jpg)
25
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The SUPSIM module (atom-diatom)
SUPSIM
return
Iterate over the systemgeometries geometries
the call of ab initio suitesof codes (GAMESS, etc)
Define the characteristics of the ab initio calculation, the coordinates used and the
Variable’s intervals
![Page 26: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/26.jpg)
26
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The FITTING module (atom-diatom)
FITTING
Return
Are asym-ptotic values
accurate?
Are remai-ning valuesinaccurate?
Do ab initiovalues have the
proper sym-metry?
Enforce the propersymmetry
Application using fitting programs to
generate a PESroutine
Modify asym-ptotic values
NO NONO
Modify short andlong range values
YES YESYES
![Page 27: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/27.jpg)
27
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The DYNAMICS module
DYNAMICS
OBSERVABLES
Are quantumdynamics
calculationsInappro-priate?
Is the calculation
single initial state?
NO NO
YES YES
TI: application carrying out
time-independentquantum
calculations(atom-diatom)
TD: application carrying out time-
dependent quantumcalculations
(atom-diatom)
TRAJ: application
using classical trajectory
calculations(atom-diatom)(polyatomic)
(many-bodies)
![Page 28: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/28.jpg)
28
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The TD QM module (atom-diatom)
TD
return
•Iterate over initial conditions•the integration over time•propagation (RWAVEPR, etc.)
Define quantities of generaluse
![Page 29: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/29.jpg)
29
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The TI QM module (atom-diatom)
TI
return
Iterate over total energy value the integration of scattering
equations
Define quantities of generaluse including the integration
bed
Iterate over the reaction coor-dinate to build the interaction
matrix
Broadcast coupling matrix
![Page 30: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/30.jpg)
30
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The OBSERVABLES module
OBSERVABLESNO NO
YES YES
Is the observable
a state-to-stateone?
Is theobservable
a state specificonee?
RATE: virtual monitor (VM)
for thermal ratecoefficients
CROSS: VM for statespecific cross sections,
rate constants and maps of
product intensity
DISTRIBUTIONS: VMfor scalar and vectorproduct distributions,
and state-to-state crosssections
Do calculated
and measuredproperties
agree?END
YES
INTERACTION
NO
Beam VM for Intensity in the
Lab frame
![Page 31: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/31.jpg)
Enabling Grids for E-sciencE
www.eu-egee.org
University of Perugia
COMPUTER SCIENCE AND ORGANISATION
![Page 32: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/32.jpg)
32
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
The PG hardware configuration
Access to Grid
![Page 33: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/33.jpg)
33
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
PRACTICAL GOALS
Perform extended computational campaigns for systems relevant to scientific and technological applications
Develop grid tools: middleware, workflow mana-gers, problem solving environments and coordi-nation languages for distributed heterogeneous environments
Specialize in some specific applications
![Page 34: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/34.jpg)
34
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
NEXT STEPS
Generalize GEMS to more complex research
purposes using a web service approach
Diffuse the membership among the members of the Computational Molecular Science community
Open the VO to non EU scientists
![Page 35: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/35.jpg)
35
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
Conditions
1. sign the consortium agreement 2. provide in due time requested information 3. (negotiable) implement locally at least a 4 node
cluster exposed outside the local firewall to the Grid (perform development on unexposed machines)
4. implement one stable code or suite of codes. This will be first only for personal use and later-on open for shared use in a coordinated way
5. (for labs of point 3) designate a person taking care of the local machines, ensuring real time Grid connections and implementation of necessary middleware
6. accept the credit policy (in progress)
![Page 36: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/36.jpg)
36
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
![Page 37: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/37.jpg)
37
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
wavepacket scalar pseudocode
Read input data: v, j, k, masses…Perform preliminary calculationsLoop on J
Loop on tLoop on Λ Perform time-step propagation
Perform the asympotic analysis Calculate C(t) coefficients and update the fixed-J S matrix
End loop on Λ End loop on t
End loop on J
![Page 38: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/38.jpg)
38
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
Coarse grain Master-worker parallel Model
J=0,Nmaster
J=0 Λ=0 J=N Λ=0 J=N Λ=1 … J=N Λ=Nslave
master Collect
J=1 Λ=0 J=1 Λ=1 J=N-1 Λ=0 … J=N-1 Λ=N-1slave
master Collect
…
END
![Page 39: On the development of an a priori Grid enabled molecular simulator](https://reader035.vdocuments.mx/reader035/viewer/2022081603/568145b7550346895db2beeb/html5/thumbnails/39.jpg)
39
Enabling Grids for E-sciencE
University of Perugia GEMS and CompChem VO status
Fine grain DVR: MPI vs ASSIST