GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid 2009-04-03: Napoli ENEA Grid e CRESCO in GRISU: uno strumento per la scienza dei materiali

GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid2009-04-03: Napoli

ENEA Grid e CRESCO in GRISU’: uno strumento per la scienza dei materiali

Presentazione: S. Raia(1), S. Migliori(1)

Collaborazioni : M. Celino(1), M. Gusso(1), P. Morvillo(1), A. Marabotti(2), L. Cavallo(3), F. Ragone(3). (1): ENEA: Sede/Portici/Casaccia/Brindisi (2): ISA CNR Avellino (3): UNISA: Salerno

Outline:• ENEA Grid / Cresco infrastructures• Computational Capability• Some examples of Material Science Codes running on ENEA

ENEA Grid infrastructures [1]ENEA

-12 research centers in Italy -A Central Computer and Network Service (INFO)- 6 Computer Centres: Casaccia, Frascati, Bologna,Trisaia, Portici, Brindisi- Multiplatform resources for serial & parallel computation and graphical post-processing.

- Others computer resources in ENEA: departments & individuals

Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | 2009-04-03: Napoli

Main features:- Access from any kind of connection- Sharing data in world wide areas (geographical file system AFS) - Access to the data from any kind of digital device client - Running any kind of programs - Access to National and International GRIDS

ENEA Grid infrastructures [2]

For each computational site, ENEA manages Local Networks (LAN) whereas the computational centres (WAN) are interconnected via “Consortium GARR” Network


O.S. #CPU/Core Gflops …where

AIX >300 3000 Frascati(258), Bologna(24), Portici(18),Brindisi(2)

Linux x86 32/64 >3000 25000 Frascati(140), Casaccia(54), Portici(2700),Trisaia(20), Brindisi(84)

Linux IA64 (Altix) 64 300 Casaccia

IRIX 26 40Frascati(8), Casaccia(4),

Portici(1),Trisaia(8), Brindisi(1), Bologna(5)

Solaris 8 10 Trisaia(4), Casaccia(2), Bologna(2)

Windows 32/64 46 100 Frascati(4), Portici(34),Trisaia(4), Brindisi(4)

Mac OS X 14 60 Frascati(1), Trisaia(13)

ENEA Grid computatonal resources [3]


ENEA-GRIDwww.afs.enea.it/project/eneagrid

Data archivesColleagues & 3D

Softwarecatalogs

ComputersApplication

Fabric

Connectivity

Resource

Collective

User

ENEA Grid Architecture & resources integration [4]

*A choice of mature components for reliability and easiness of support and maintenance:

Distributed File System: AFSJob and resources manager: LSF MulticlusterUnified GUI access: Java and Citrix TechnologiesQuality monitoring system: PatrolLicence Servers


* Integration with department and individual resources Distributed File System: AFS Licence pool sharing

* Possible integration with other institutions

Portici LAN

Interconnessione InfiniBand4XDDR SERVER GPFS

4 Nodi IBM 3650

IBFC

Sistema Dischi ad alta velocità

2 GByte/s160 TByte

IBM/DDN 9550

Sistema backup300 TByte

IBM Tape Library TS3500 con 4 drive

SERVER BACKUP3 Nodi IBM 3650

FCIB

GARR(WAN)

Sezione 1(Grande Memoria)

42 Nodi SMP IBM x3850-M2 con 4 Xeon Quad-Core Tigerton E7330 (32/64 GByte RAM 2.4GHz/ 1066MHz/6MB L2) per un totale di 672 core Intel Tigerton

Sezione 3(Speciale)

4 Nodi blades IBM QS21 con 2 Cell BE Processors 3.2 Ghz each.6 Nodi IBM x3755, 8 Core AMD 8222 con una scheda FPGA VIRTEX54 Nodi IBM x 3755, 8 core AMD 8222 con schede NVIDIA Quadro FX 4500 X2 4 Nodi windows 8 core 16 Byte RAM

Doppia Intercconnessione a 1 Gbit1 Rete a 1 Gbit di gestione

Sezione 2(Alto Parallelismo)

256 Nodi blades IBM HS21 con 2 Xeon Quad-Core Clovertown E5345 (2.33GHz/1333MHz/8MB L2), 16 GB RAM per un totale di 2048 core Intel Clovertown

4x10 Gbits

2000 Mbits

35 Nodi di ServizioServer di :

•Front-end•insallazione•AFS•…

CRESCO (Portici site) computational resources [5]


• Multicores Platforms (Cresco Linux, sp AIX) : 8, 16, 32, 48 smp nodes • GPFS / Infiniband for high parallelism codes • Hybrid Parallelism (Cresco smp nodes with IB interconnections)• Distributed parallel Jobs across WAN or heterogeneous platforms (Parallel Jobs arrays (AFS ‘sysname’ mechanism))• Nvidia / Cell processor / FPGA accelerators (…next)

Some Codes running in ENEA env.:CPMD

Gromacs Pc Gamess

Gaussian…. …. others: Abinit, Amber, cp2k, etc …

ENEA Grid / Cresco Capability for Material Science codes:


Gromacs on ENEA Grid (CRESCO)Protein in a box of water at ISA CNR, Avellino: A. Marabotti


GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but it can be used also for research on non-biological systems, e.g. polymers.

Dimeric protein + water + ions: ~77000 atoms. Timescale of simulation: 5 nsSimulation made on 16 cores on Cresco1, Time required: 40 h.Same simulation on cluster dual-core AMD Opteron (Gbit Eth): 10 gg. no scaling beyond 2 cores

Peptide + water + ions: ~2500 atomsTimescale of simulation: 40 nsTime required: 24 h (on 8 cores smp Intel Xeon)

PC GAMESS / Firefly ENEA-Grid(CRESCO) absorption spectrum of molecules at C.R. ENEA Portici: P. Morvillo

PC GAMESS/Firefly: computational Chemistry code for ab initio and DFT calculations. Developed for high performance calculation on Intel processors (x86, AMD64, and EM64T).

http://classic.chem.msu.su/gran/gamess/index.html

Used on CRESCO for studying electronic proprieties and absorption spectrum of molecules in the photovoltaic field.

On Cresco: Performances improvement of 370% (16 cores) compared to runs on PC Desktop quad core.


modello TDDFT B3LYP/6-311G*

N. cores (MPI procs) Elapsed Time ( min.)

16 313.7

32 200.2

48 142.7

64 125.1

80 114.0

96 103.1

112 93.9

128 90.0

1) Static DFT calculations (Gaussian)Working in shared memorywith 8 cores maximum/jobUsually 10 jobs/daySpeedup ~4-5

2) Dynamic DFT simulation (cp2k)(Car-Parrinello MD)working with MPI, the codescales well up to 64 coresUsually 1-2 jobs max/daySpeedup excellent (~60)

Structural Bioinformatics (rosettacommons)Simulating Antibody/Antigenrecognition through docking simulations.

Typical embarrassingly parallelproblem. No limits to the speedup, 1 core per job.Using ENEA Grid technologies: we have run tipically up to 500 jobs/dayWith speedup excellent (500) and efficiency 100%

Gaussian/cp2k/RosettaDock on ENEA-Grid(CRESCO)Chemical Reactivity at the University of Salerno. Dipartimento di Chimica: Prof. Cavallo


Olefin Metathesis, the Nobel 2005 Reaction

Multiscale Modeling Parallel Code Development at University of Salerno: Dr. Giuseppe Milano


Coarse-Grain Models of BiomembranesThe understanding of interactions of biocompatible block polymers with biological interfaces has important technological applications in industry and in medicine

Ancillary Programs -MC charge-Back Mapping

Molecular Dynamics Simulator (OCCAM) -Iterative Boltzmann Inversion-Hybrid Particle Field MD-Hybrid Monte Carlo-Gran Canonical Montecarlo

Methods: Hybrid Particle Field Molecular Dynamics Highly Parallelizable Method

Program: OCCAM 3.0 developed at University of Salerno

CPMD: Car-Parrinello Molecular Dynamics on ENEA-Grid(CRESCO)Supercell crystalline systems Benchmark at ENEA C.R. Portici: S. Raia

Extented tests in order to: 1- Scaling performances up to 1024 cores 2- Exploiting Dual-level Parallelism 3- Outer loop parallelization: TASKSGROUPS

Total tasks MPI : Threads TASKS

GROUPSIterations / sec

1024 1024:1 8 0.0068

1024 1024:1 NO 0.0060

1024 512:2 8 0.0244

1024 512:2 NO 0.0089

1024 256:4 8 0.0253

1024 256:4 NO 0.0131

It is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.


Conclusions …

References in ENEA and collaborations …

CRESCO Project/ENEA Grid: S. Migliori, ENEA Roma, [[email protected]] S. Raia, ENEA C.R. Portici, [[email protected]] M.Celino, ENEA C.R. Casaccia, [[email protected]]Risultati sui codici qui descritti: Cpmd: S. Raia, M. Gusso [[email protected]],M. Celino Gromacs: A. Marabotti, ISA CNR, Avellino, [[email protected]] Gaussian, RosettaCommons: L. Cavallo, Università di Salerno, [[email protected]] Pc Gamess: P. Morvillo, ENEA C.R. Portici, [[email protected]]

• Multicores Platforms (Cresco Linux, sp AIX) : 8, 16, 32, 48 smp nodes • GPFS / Infiniband for high parallelism codes • Hybrid Parallelism• Special sections and multiscale modelling … next


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GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid 2009-04-03: Napoli ENEA Grid e CRESCO in GRISU: uno strumento per la scienza dei materiali