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Bulgarian Supercomputing Centre

Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS. Bulgarian Supercomputing Centre. David Vassilev Information and Communication Systems Directorate, EA ECNIS. Bulgarian Supercomputing Centre.

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Bulgarian Supercomputing Centre

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  1. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS Bulgarian Supercomputing Centre David Vassilev Information and Communication Systems Directorate, EAECNIS Bulgarian Supercomputing Centre

  2. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS OUTLINES Inauguration Location Supercomputer - Short information IBM Blue Gene/P - Configuration IBM Blue Gene/P - Hierarchy Organization Connectivity and Access Software Application Software Users Results of supercomputer use in 2010 Questions Bulgarian Supercomputing Centre

  3. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS • INAUGURATION • 9 September 2008 – The first in the South-East Europe. • LOCATION • Bulgarian Supercomputing Centre (BSC)is located in the Building of Executive Agency Electronic Communication Network and Information Systems. • SHORT INFORMATION FOR BSC (http://scc.acad.bg) • Bulgarian Supercomputing Centre operates and provides access to the IBM Blue Gene/P Supercomputer; • Connection from Compute Nodes to the other part of the system is through 16 channels 10 GB/s; • Productivity: 27.85 Tflops; • Energy efficiency: 371.67 Mflops/W. The ranking of BGSC's system in http://top500.org list is as follows: • November 2008 – 126th place; • June 2009 – 245th place; • November 2009 – 377th place; Bulgarian Supercomputing Centre

  4. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS IBM BLUE GENE/P – HIERARCHY ORGANIZATION Rack 32 Node Cards 1024 Chips 8х8х16 13.6 TF/s, 2 TB Supercomputer 2 Racks 16х8х16 27,85 TF/s, 4 TB Compute Card 1 Chip,13.6 GF/s 2 GB DDR RAM Node Card 32 Chips 4х4х2 32 Computing + 1In/OutNode 435 GF/s, 64 GB Chip 4 Processors 13.6 GF/s Bulgarian Supercomputing Centre

  5. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS • IBM BLUE GENE/P CONFIGURATION • Hardware: • - IBM Blue Gene/P Supercomputer - 2 rackswith totalsubsystemproductivity 27.85 Tflops (27.85 trillion operations/second); • Blade Cluster – 64thSpecialized Processor Cluster. Processors - Cell/B.E.; • Hard Disk Subsystem - Memory 12.6 ТB; • Force 10 Ethernet Switch - 24 duplex I/O modules with information transmitted speed 10 Gbits/sec in both directions. • CONNECTIVITY AND ACCESS • 1 Gb/s Ethernet fiber optical link to Point-of-Presence at the Institute of Information and Communication Technologies at the Bulgarian Academy of Sciences - (IICT), Sofia. • Front End Node: • Hardware: IBM system-p 64-bit servers (not Blue Gene); • Address: bg-fen.scc.acad.bg. Bulgarian Supercomputing Centre

  6. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS • SYSTEM SOFTWARE • Front End Node operating system: SUSE Linux Enterprise Server 10 (SLES 10), Service Pack 1; • Compilers: • IBM XL C/C++ Advanced Edition for Blue Gene/P V9.0; • IBM XL Fortran Advanced Edition for Blue Gene/P V11.1; • GNU Toolchain (gcc, glibc, binutlils, gdb, python). • Libraries: • Engineering and Scientific Subroutine Library (ESSL) for Linux on Power V4.3.1; • MPI (MPICH2). • IBM Tivoli Workload Scheduler LoadLeveler Version 3 Release 4.2 PTF 1. Bulgarian Supercomputing Centre

  7. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS • APPLICATION SOFTWARE • GotoBLAS – currently the fastest implementation of the Basic Linear Algebra Subroutines (BLAS); • GAMMES-US – a general ab initio quantum chemistry package; • NAMD – a parallel molecular dynamics code for large bio-molecular systems; • CPMD – a parallelized plane wave/pseudo potential implementation of Density Functional Theory, particularly designed for ab initio molecular dynamics; • LAMMPS: a classical molecular dynamics simulation code designed to run efficiently on parallel computers; • Ongoing work (porting, compiling, testing and tuning): • - GROMACS –classical molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles; • - mpiBLAST-PIO – parallel implementation of NCBI BLAST (Basic Local Alignment Search Tool, an algorithm used in bioinformatics); • - OpenAtom – a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level, which implements the Car-Parrinello ab initio Molecular Dynamics (CPAIMD) method. Bulgarian Supercomputing Centre

  8. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS USERS: Total users:60active users Institutions: Sofia University, Technical University, the Institute of Information andCommunication Technologies at the Bulgarian Academy of Sciences - (IICT), Medical University and other users. • Chemistry – 12 users: • Bio-system modeling (connected with ribosomes); • New medicine (drugs) development. • Medicine – 4 users: • New materials and drugs development and simulation; • Cancer investigation and impact on humans. • Mathematics – 2 users: • Huge mathematical models analysis. • Natural disasters (fire monitoring) – 8 users: • Multi-spectral data processing of the Earth remote sensing. • Physics – 16 users: • Development and optimization of a high-frequency plasma source; • Software for optimal sensors positioning; • Theoretical investigation and modeling of the structure and electronic properties of ceramic nano-particles; • Investigation of environment pollution; • Software for image processing of human faces; • Investigation on processes and atoms, molecules and condensed media. • Education – 8 users: • Introduction into parallel programming. • Applied investigations: communications – 5 users: • Multi-processor communication networks for PetaFlops supercomputers. • Others – 13 users. Bulgarian Supercomputing Centre

  9. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS • RESULTS OF SUPERCOMPUTER USE IN 2010 • Development of software for acquisition and hierarchical processing of sensor information – 60 000 lv. • Model of predicting distribution of pollutants in the atmosphere – 40 000 lv. • Computer modeling of fluid dynamics and heat transfer for enhancement of competitiveness and safety of energy resources – 70 000 lv. • Software medium for solving classes of computational problems with very great size applying the finite-elements method – 40 000 lv. • Modeling and analysis of bio-molecules interaction with application in biochemistry, molecular biology, drugs synthesis and molecular medicine – 75 000 lv. • Virtual screening and modeling of the interaction of drug substances with bio-molecules – 30 000 lv. • Processing of multi-spectral data from Earth remote sensing – 40 000 lv. • Mass screening for early detection of prostate gland cancer using 3D ultra-sonic diagnostics and real-time computer processing of 3D ultra-sonic images of the gland – 75 000 lv. • Computer modeling of theinfluence of all known genetic deviations inBRCA1 andBRCA2 (Breast Cancer 1&2)genes on the structure of coded proteins and assessment of the change in interactions with other proteins – 25 000 lv. • Creation and testing of a dynamic model of resilience during seismic impact on open mines and the adjoining settlements, energy and infrastructural sites - 30 000lv. Bulgarian Supercomputing Centre

  10. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS Attached File system (e.g. GPFS) Job Dispatching (mpirun or MMCS) Job scheduler Data Staging Gateway BLUE GENE FRONT-END NODE Job dispatching synchronized withdata transfer 2 Web services: Apache Tomcat + AXIS Soap engine 300 MB (44 files in CSV format) 6 1 9 7 3 300 MB 8 MB 8 8 MB (7 files in CSV format) MPI_Gather MPI_Bcast SQL query • Client Risk applicationas web service • Command-line tool • Web browser • JSDL-based job descriptor 4 10 SQL update 5 File Transfer 11 300 MB (SQL result) Data Servers Data is automaticallystaged to HPC file system DB2 Representative values have been used for the data sizes Blue Gene 4 GB database Remote Files Bulgarian Supercomputing Centre

  11. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS Thank you for your attention! Bulgarian Supercomputing Centre

  12. Ministry of Transport, Information Technology and Communications EXECUTIVE AGENCY ELECTRONIC COMMUNICATION NETWORKS AND INFORMATION SYSTEMS Questions? Bulgarian Supercomputing Centre

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