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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.

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Presentation on theme: "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."— Presentation transcript:

1 GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid : 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

2 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 | : Napoli

3 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 Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli

4 O.S.#CPU/CoreGflops…where AIX> Frascati(258), Bologna(24), Portici(18),Brindisi(2) Linux x86 32/64> Frascati(140), Casaccia(54), Portici(2700),Trisaia(20), Brindisi(84) Linux IA64 (Altix)64300 Casaccia IRIX 2640 Frascati(8), Casaccia(4), Portici(1),Trisaia(8), Brindisi(1), Bologna(5) Solaris 810Trisaia(4), Casaccia(2), Bologna(2) Windows 32/ Frascati(4), Portici(34),Trisaia(4), Brindisi(4) Mac OS X1460Frascati(1), Trisaia(13) ENEA Grid computatonal resources [3] Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli

5 ENEA-GRID Data archives Colleagues & 3D Software catalogs Computers Application 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: AFS Job and resources manager: LSF Multicluster Unified GUI access: Java and Citrix Technologies Quality monitoring system: Patrol Licence Servers Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli * Integration with department and individual resources Distributed File System: AFS Licence pool sharing * Possible integration with other institutions

6 Portici LAN Interconnessione InfiniBand 4XDDR SERVER GPFS 4 Nodi IBM 3650 IB FC Sistema Dischi ad alta velocità 2 GByte/s 160 TByte IBM/DDN 9550 Sistema backup 300 TByte IBM Tape Library TS3500 con 4 drive SERVER BACKUP 3 Nodi IBM 3650 FC IB 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 VIRTEX5 4 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 Gbit 1 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 Servizio Server di : Front-end insallazione AFS … CRESCO (Portici site) computational resources [5] Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli

7 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: Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli

8 Gromacs on ENEA Grid (CRESCO) Protein in a box of water at ISA CNR, Avellino: A. Marabotti Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli 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 ns Simulation 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 atoms Timescale of simulation: 40 ns Time required: 24 h (on 8 cores smp Intel Xeon)

9 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). 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. Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli modello TDDFT B3LYP/6-311G* N. cores (MPI procs)Elapsed Time ( min.)

10 1) Static DFT calculations (Gaussian) Working in shared memory with 8 cores maximum/job Usually 10 jobs/day Speedup ~4-5 2) Dynamic DFT simulation (cp2k) (Car-Parrinello MD) working with MPI, the code scales well up to 64 cores Usually 1-2 jobs max/day Speedup excellent (~60) Structural Bioinformatics (rosettacommons) Simulating Antibody/Antigen recognition through docking simulations. Typical embarrassingly parallel problem. No limits to the speedup, 1 core per job. Using ENEA Grid technologies: we have run tipically up to 500 jobs/day With 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 Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli Olefin Metathesis, the Nobel 2005 Reaction

11 Multiscale Modeling Parallel Code Development at University of Salerno: Dr. Giuseppe Milano Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli Coarse-Grain Models of Biomembranes The 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

12 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 GROUPS Iterations / sec : :1NO : :2NO : :4NO It is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli

13 Conclusions … References in ENEA and collaborations … CRESCO Project/ENEA Grid: S. Migliori, ENEA Roma, S. Raia, ENEA C.R. Portici, M.Celino, ENEA C.R. Casaccia, Risultati sui codici qui descritti: Cpmd: S. Raia, M. Gusso Celino Gromacs: A. Marabotti, ISA CNR, Avellino, Gaussian, RosettaCommons: L. Cavallo, Università di Salerno, Pc Gamess: P. Morvillo, ENEA C.R. Portici, 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 Salvatore Raia | GRISU' Open Day su Scienza ed Ingegneria dei Materiali e Grid | : Napoli


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