HP-SEE High-Performance Computing Infrastructure for South East Europe’s Research Communities 2 nd HellasHPC Workshop, Athens, October 2010 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

HP-SEE  Contract n°: RI  Project type: CP & CSA  Call: INFRA : VRCs  Start date: 01/09/2010  Duration: 24 months  Total budget: €  Funding from the EC: €  Total funded effort, PMs:  Web site: HellasHPC 2 nd Workshop, Athens, 22 Oct 20102

HP-SEE Partnership Contractors (14) Third Party / JRU mechanism used associate universities / research centres HellasHPC 2 nd Workshop, Athens, 22 Oct 20103

Context: the Timeline HellasHPC 2 nd Workshop, Athens, 22 Oct 20104

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 2 nd 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 HellasHPC 2 nd Workshop, Athens, 22 Oct 20105

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 HellasHPC 2 nd Workshop, Athens, 22 Oct 20106

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 7 HellasHPC 2 nd Workshop, Athens, 22 Oct 20107

Work Organization - PERT HellasHPC 2 nd Workshop, Athens, 22 Oct 20108

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= Tflops;  Energy efficiency: MFlops/W: Green top 10  Application software:  GotoBLAS  GAMMES  NAMD  CPMD  LAMMPS  GROMACS  OpenAtom HellasHPC 2 nd Workshop, Athens, 22 Oct 20109

Existing infrastructure – BG HPC Cluster at IICT-BAS  HP Cluster Platform Express 7000 enclosures with 36 blades BL 280c with dual Intel Xeon 2.8Ghz (total 576 cores), 24 GB RAM per blade  8 controlling nodes HP DL 380 G6 with dual Intel 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 HellasHPC 2 nd Workshop, Athens, 22 Oct

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. HellasHPC 2 nd Workshop, Athens, 22 Oct

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 Gbps 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. HellasHPC 2 nd Workshop, Athens, 22 Oct

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. HellasHPC 2 nd Workshop, Athens, 22 Oct

Introduction to VRCs  Comp. Physics 6 countries, 8 apps.  Comp. Chemistry 6 countries, 7 apps.  Life Sciences 5 countries, 7 apps. HellasHPC 2 nd Workshop, Athens, 22 Oct

Description of Computational Physics applications CountryApplication NameDomains # of candidate appls. AlbaniaComputational 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 Transport Cond. Matter, nanoelectronics MoldovaAdaptive Mesh Refinement General purpose1 FYR 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, Meteorology2 Serbia Numerical study of ultra-cold quantum gases Cond. Matter, Atomic Phys. 1 TOTAL810 HellasHPC 2 nd Workshop, Athens, 22 Oct

Description of Computational Chemistry applications CountryApplication NameDomains # of candidate appls. Bosnia- Herzegovina Design of a chemical reactors, burners, boilers or furnaces CFD1 Bulgaria Principal Component Analysis of the Conformational Interconversions in large- ring Cyclodextrins Quantum Chem 2 Molecular design of platinum group metal complexes as potential non-classical cisplatin analogues Quantum Chem. Greece Design 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 RomaniaSimulation and modelling of biomolecules. Biophys., Biochem.1 Serbia Molecular-orbital simulations of chemical reactions Quantum Chem.1 TOTAL77 HellasHPC 2 nd Workshop, Athens, 22 Oct

Description of Life Sciences applications CountryApplication NameDomains # of candidate appls. Armenia Simulations for Biological Model Membranes and Surfactant Systems Biophys., Biochem.1 Greece Network models of short and long term memory. 2 Searching for novel miRNA genes and their targets Genomics Georgia Modeling of biochemical processes for realization of thin and purposeful synthesis Biochemistry1 Hungary Sequence analysis genomics application Genomics2 Comparative genomics application MontenegroDNA sequence analysis Bioinformatics1 TOTAL77 HellasHPC 2 nd Workshop, Athens, 22 Oct

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 HellasHPC 2 nd Workshop, Athens, 22 Oct