www.hp-see.eu

HP-SEEHigh-Performance Computing Infrastructure for

South East Europe’s Research Communities 2nd HellasHPC Workshop, Athens, October 2010

Ioannis LiabotisProject Technical Coordinator

GRNETiliaboti at grnet dot gr

The HP-SEE initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no. 261499

HP-SEE

Contract n°: RI-261499 Project type: CP & CSA Call: INFRA-2010-1.2.3: VRCs Start date: 01/09/2010 Duration: 24 months Total budget: 3 885 196 € Funding from the EC: 2 100 000 € Total funded effort, PMs: 539.5 Web site: www.hp-see.eu

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HP-SEE Partnership

Contractors (14)

Third Party / JRU mechanism usedassociate universities / research centres

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Context: the Timeline

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SEE eInfrastructure activities – past 6 years

SEEREN1/2: regional inter-NREN connectivity and GEANT links [DGINFSO] BSI: Southern Caucasus links [DGINFSO] SEELIGHT: lambda facility in SEE [Greek HiperB] Result: sustainable national & regional networks, most countries in GEANT

SEEGRID1/2: regional Grid infrastructure, building NGIs and user communities SEE-GRID-SCI: eInfrastructure for large-scale environmental science user communities:

meteorology, seismology, environmental protection. Inclusion of Caucasus. [DGINFSO] Result: sustainable national Grids, all countries within European Grid Initiative

HP-SEE: regional HPC interconnection and 2nd generation Caucasus link Expected result: sustainable national HPC centers, long-term sustainable (hierarchical)

model in collaboration with PRACE and DEISA

SEERA-EI: regional programme managers collaboration towards common eInfrastructure vision, strategy and regional funds [DGRTD]

Result: ensuring long-term national-level funds and regional funds to complement EC funds

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Context: the Model:Converged communication & service infrastructure for South-East Europe

SEE-LIGHT & BSI & GEANT

Comp physics,Comp chem, Life sciences

Seismology, Meteorology, Environment

HP-SEE

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HP-SEE Project Objectives

Objective 1 – Empowering multi-disciplinary virtual research communities

Objective 2 – Deploying integrated infrastructure for virtual research communities Including a GEANT link to Southern Caucasus

Objective 3 – Policy development and stimulating regional inclusion in pan-European HPC trends

Objective 4 – Strengthening the regional and national human network

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Work Organization - PERT

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Existing infrastructure – Blue Gene/P

IBM Blue Gene/P –two racks, 2048 PowerPC 450processors (32 bits, 850 MHz), a total of 8192 cores;

Double-precision, dual pipe floating-point acceleration on each core;

A total of 4 TB random access memory; 16 I/O nodes currently connected via

fibre optics to 10 Gb/s Ethernet switch; Theoretical peak performance: Rpeak=

27.85 Tflops; Energy efficiency: 371.67 MFlops/W:

Green top 10 Application software:

GotoBLAS GAMMES NAMD CPMD LAMMPS GROMACS OpenAtom

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Existing infrastructure – BGHPC Cluster at IICT-BAS

HP Cluster Platform Express 7000 enclosures with 36 blades BL 280c with dual Intel Xeon X5560 @ 2.8Ghz (total 576 cores), 24 GB RAM per blade

8 controlling nodes HP DL 380 G6 with dual Intel X5560 @ 2.8 Ghz, 32 GB RAM

Non-blocking DDR Interconnection via Voltaire Grid director 2004

Two SAN switches for redundant access MSA2312fc with 48 TB storage, Lustre filesystem More than 92% efficiency on LINPACK (>3 TFlops,

peak performance 3.2TFlops) SL 5, gLite, torque+maui, eucalyptus walrus Software: MPICH, MPICH2,OPENMPI, Maple, GROMACS, FFTW, Elmer, BLAS, LAPACK Middleware of choice for HPC: openssh

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HPC infrastructure – HU

SUN Fire supercomputer cluster run by the National Information Infrastructure Development Institute (NIIF);

The resource currently consists of two SUN Fire (SMP) machines totaling to 216 cores providing 0.6 Tflop/s computational power as well as 20 Tbytes of primary and 40 Tbytes of secondary storage facilities in total.

Planned: NIIF has managed to establish funding to improve the current compute power and

to increase the data storage capacity up to 30 Tflop/s and 0.5 Pbyte. The current central SMP infrastructure will also have been gradually upgraded.

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HPC infrastructure – RO

The computing centers at IFIN-HH and UPB: IBM BladeCenter Cluster at IFIN-HH, with an HPL benchmark Rpeak of 4

TFLOPS, contains both IBM PowerXCell 8i and AMD Opteron 2356 processors, counting a total of 368 cores and 592 GB RAM, using Infiniband 4X 10Gbps technology;

The Biocomputing cluster, with Rpeak=2,7 TFLOPS, is based on Intel Xeon E5430 (Quad-Core) processors and Myrinet 2000 2Gbps technology.

Application software: NAMD, CHARMM, VASP, ATLAS, GotoBLAS, FFTW, GAUSSIAN, Turbomole, Matlab,

etc.

Planned: The total HPC processing power is expected to double next year. GPU cluster at ISS will reach a processing power of 100 TFLOPS. Ministry of Communications and Information Society recently started a

project for the creation of a National Center of Supercomputing. The center will host, beginning with 2010, a BlueGene supercomputer.

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Planned infrastructure

Serbia joined the PRACE initiative in December 2008, represented by IPB. Institute of Physics Belgrade (IPB) as a coordinating institution for all HPC activities.

IPB has focused HPC activities on establishment of the Blue Danube National Supercomputing and Data Storage Facility, in collaboration with the Ministry of Science and Technological Development of the Republic of Serbia.

Serbian government will invest 10 million Euro in a 7-year period. The hardware is planned to be purchased in several phases.

In Greece, GRNET is currently coordinating the nascent Greek HPC initiative, and pilot project for HPC user communities’ assessment in the country.

The overall goal is to acquire a machine in the range of 100 TFlops Rmax performance according to the Linpack benchmark.

The detailed specification of the supercomputer will derive from the particular requirements from the Greek user community that will benefit from this investment.

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Introduction to VRCs

Comp. Physics6 countries, 8 apps.

Comp. Chemistry6 countries, 7 apps.

Life Sciences5 countries, 7 apps.

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Description of Computational Physics

applicationsCountry Application Name Domains

# of candidate

appls.

Albania Computational Resources for Lattice QCD HE&P Phys. 1

Bulgaria

Computer Simulation of Complex Gas Flows in Micro-sized Channels and

Domains

Fluid dynamics, micro-devices mod.

2

Simulation of Electron TransportCond. Matter,

nanoelectronicsMoldova Adaptive Mesh Refinement General purpose 1FYR Macedonia

Study of atomic collisions of highly charged ions in plasma Plasma Phys. 1

Romania

Dissemination, Developing and Deploying of Graphics Processing Unit

HE&P Phys., Electro-magn., Astrophys.

2

Feature Extraction from Satellite Images Using a Hybrid Computing Architecture Geophysics, Meteorology 2

SerbiaNumerical study of ultra-cold quantum

gasesCond. Matter, Atomic

Phys.1

TOTAL 8 10HellasHPC 2nd Workshop, Athens, 22 Oct 2010 15

Description of Computational Chemistry

applicationsCountry Application Name Domains

# of candidate

appls.Bosnia-Herzegovina

Design of a chemical reactors, burners, boilers or furnaces CFD 1

Bulgaria

Principal Component Analysis of the Conformational Interconversions in large-

ring Cyclodextrins Quantum Chem

2Molecular design of platinum group metal complexes as potential non-classical

cisplatin analogues Quantum Chem.

GreeceDesign of fullerene and metal-diothiolene-based materials for photonic applications

Quantum Chem., Cond. Matter Phys

1

FYR Macedonia

Quantum Mechanical Computer Simulation of Condensed Phases

Quantum Chem., Cond. Matter Phys

1

Romania Simulation and modelling of biomolecules. Biophys., Biochem. 1

SerbiaMolecular-orbital simulations of chemical

reactions Quantum Chem. 1

TOTAL 7 7HellasHPC 2nd Workshop, Athens, 22 Oct 2010 16

Description of Life Sciences applications

Country Application Name Domains# of

candidate appls.

ArmeniaSimulations for Biological Model Membranes

and Surfactant Systems Biophys., Biochem. 1

Greece

Network models of short and long term memory .

2Searching for novel miRNA genes and their

targets Genomics

GeorgiaModeling of biochemical processes for

realization of thin and purposeful synthesis Biochemistry 1

HungarySequence analysis genomics application

Genomics 2Comparative genomics application

Montenegro DNA sequence analysis Bioinformatics 1

TOTAL 7 7

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Long-term vision…

Being on the technological par with the rest of Europe

Enabling local scientists to use their potential Role-model for regional developments Leading the way in wider contexts

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