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HP-SEE
High-Performance Computing Infrastructure for
South East Europe’s Research Communities
2nd HellasHPC Workshop, Athens, October 2010
www.hp-see.eu
Ioannis Liabotis
Project Technical Coordinator
GRNET
iliaboti 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
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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 used
associate universities / research centres
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Context: the Timeline
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SEE eInfrastructure activities – past 6
years
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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
Seismology,
Meteorology,
Environment
Comp physics,
Comp chem, Life sciences
HP-SEE
SEE-LIGHT & BSI & GEANT
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HP-SEE Project Objectives
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Objective 1 – Empowering multi-disciplinary virtual research
communities
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Objective 2 – Deploying integrated infrastructure for virtual
research communities
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Including a GEANT link to Southern Caucasus
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Objective 3 – Policy development and stimulating regional
inclusion in pan-European HPC trends
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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
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IBM Blue Gene/P –two racks, 2048
PowerPC 450processors (32 bits, 850
MHz), a total of 8192 cores;
Double-precision, dual pipe floatingpoint 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:
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GotoBLAS
GAMMES
NAMD
CPMD
LAMMPS
GROMACS
OpenAtom
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Existing infrastructure – BG
HPC Cluster at IICT-BAS
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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
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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:
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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
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The computing centers at IFIN-HH and UPB:
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Application software:
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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.
NAMD, CHARMM, VASP, ATLAS, GotoBLAS, FFTW, GAUSSIAN, Turbomole, Matlab,
etc.
Planned:
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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
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Serbia joined the PRACE initiative in December 2008, represented by IPB. Institute of
Physics Belgrade (IPB) as a coordinating institution for all HPC activities.
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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.
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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
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Comp. Physics
6 countries,
8 apps.
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Comp. Chemistry
6 countries,
7 apps.
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Life Sciences
5 countries,
7 apps.
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Description of Computational
Physics applications
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, microdevices mod.
Country
Simulation of Electron Transport
Moldova
FYR
Macedonia
Romania
Serbia
TOTAL
Adaptive Mesh Refinement
Study of atomic collisions of highly
charged ions in plasma
Dissemination, Developing and Deploying
of Graphics Processing Unit
Feature Extraction from Satellite Images
Using a Hybrid Computing Architecture
Numerical study of ultra-cold quantum
gases
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Cond. Matter,
nanoelectronics
General purpose
1
Plasma Phys.
1
HE&P Phys., Electromagn., Astrophys.
2
Geophysics, Meteorology
2
Cond. Matter, Atomic
Phys.
1
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Description of Computational
Chemistry applications
Country
Application Name
BosniaHerzegovina
Domains
FYR
Macedonia
Design of a chemical reactors, burners,
CFD
boilers or furnaces
Principal Component Analysis of the
Conformational Interconversions in largeQuantum Chem
ring Cyclodextrins
Molecular design of platinum group metal
complexes as potential non-classical
Quantum Chem.
cisplatin analogues
Design of fullerene and metal-diothiolene- Quantum Chem., Cond.
based materials for photonic applications
Matter Phys
Quantum Chem., Cond.
Quantum Mechanical Computer
Simulation of Condensed Phases
Matter Phys
Romania
Simulation and modelling of biomolecules.
Bulgaria
Greece
Serbia
TOTAL
Molecular-orbital simulations of chemical
reactions
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# of
candidate
appls.
1
2
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1
Biophys., Biochem.
1
Quantum Chem.
1
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Description of Life Sciences
applications
Country
Armenia
Greece
Application Name
Domains
# of
candidate
appls.
Simulations for Biological Model Membranes
and Surfactant Systems
Biophys., Biochem.
1
Network models of short and long term
memory
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Searching for novel miRNA genes and their
targets
Modeling of biochemical processes for
realization of thin and purposeful synthesis
Georgia
2
Genomics
Biochemistry
1
Genomics
2
Bioinformatics
1
Sequence analysis genomics application
Hungary
Comparative genomics application
Montenegro
TOTAL
DNA sequence analysis
7
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Long-term vision…
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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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