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INCDTIM Seminar presented on 16 June 2011

INCDTIM Seminar presented on 16 June 2011



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    HPC_June2011 HPC_June2011 Presentation Transcript

    • National Institute for R&D of Isotopic and Molecular Technologies 65-103 Donath Str., P.O.Box 700 RO-400293 Cluj-Napoca 5, ROMANIA High Performance Computing - Physico-chemicalapplications to molecular and biomolecular systems Calin Gabriel Floare Max von Laue Paul Langevin Joseph Fourier 1879-1960 1879-1946 1768-1830
    • Outline• What is parallel and high performance computing ?• Why Use Parallel computing ?• IBM BG/P system @ UVT• GPU & FPGA High Performance Heterogeneous Computing• INCDTIM Data Center containing a Grid site & a cluster• The story of a serendipitous discovery• Molecular Dynamics simulations on a very big system• HPC-Europa 2 Program INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 1/30
    • What is parallel computing ?• Traditionally, software is written for serial computation:  To be run on a single computer having a single CPU  A problem is broken into a discrete series of instructions  Instructions are executed one after the other  Only one instruction may execute at any moment in time• Parallel computing is the simultaneous use of multiple computeresources to solve a computational problem:  To be run using multiple CPUs  A problem is broken into discrete parts that can be solved concurrently  Each part is further broken down to a series of instructions  Instructions from each part execute simultaneously on different CPUs• The compute resources can include:  A single computer with multiple processors  An arbitrary number of computers connected by a network  A combination of both INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 2/30
    • The Universe is parallel• Parallel computing is an evolution of serial computing that attempts to emulate what has always been the state of affairs in the natural world: many complex, interrelated events happening at the same time, yet within a sequence. The Real World is massively parallel INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 3/30
    • Why Use parallel computing ?• Historically, parallel computing has been considered to be the ―high end of computing‖, and has been used to modeldifficult scientific and engineering problems found in the real world.• Today, commercial applications provide an equal or greater driving force in the development of faster computers.These applications require the processing of large amounts of data in sophisticated ways.• Why use it ?  Save time and/or money  Solve larger problems  Provide concurrency  Use of non-local resources (SETI@home, Folding@home)  Limits of serial computing (Transmissions speeds, Limits to miniaturization, Economic limitations) https://computing.llnl.gov/tutorials/parallel_comp/ INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 4/30
    • Blue Brain and Human Brain Project http://bluebrain.epfl.chis an attempt to create a synthetic brain by reverse-engineering the mammalian and human brain down to themolecular level.Founded in May 2005 by the Brain and Mind Institute of the École Polytechnique in Lausanne, Switzerland, is tostudy the brains architectural and functional principles. The project is headed by the Institutes director, HenryMarkram. NEURON is a simulation environment for modeling individual neurons andUsing a Blue Gene supercomputer running Michael Hiness NEURON software, networks of neurons.the simulation does not consist simply of an artificial neural network, but involvesa biologically realistic model of neurons. It is hoped that it will eventually shedlight on the nature of consciousness. • IBM Blue Gene/P Massively Parallel Computer • 4 racks, one row, wired as a 16x16x16 3D torus • 4096 quad-core nodes, PowerPC 450, 850 MHz • Energy efficient, water cooled • 56 Tflops peak, 46 Tflops LINPACK • 16 TB of memory (4 GB per compute node) • 1 PB of disk space, GPFS parallel file system • OS Linux SuSE SLES 10If selected from amongst six other candidates by the Future and Emerging Technologies(FET) Flagship Program launched by the European Commission, the Blue Brain Project willupgrade to become the Human Brain Project and will receive funding up to 100 million http://www.neuron.yale.edu/neuron/euros a year for 10 years. INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 5/30
    • IBM BG/P system @ UVT• IBM Blue Gene/P Massively Parallel Computer• 1x rack, 1024 compute cards (32 compute cards / node)• 1x Quad PowerPC 450 @ 850 MHz – Double FPU• 4x TB of memory (4 Gb RAM / compute card)• 4x power servers p520• 2x DS3524 and EXP3000 – totally 2×48 SAS HDD• GPFS parallel file system• One Cisco Nexus 7010 Switch with 64x10GbE and 98x1GbE• 1x Torus Network, 1x Collective network, 1x10GbE network (for I/O’s)• OS Linux SuSE SLES 10 IBM BG/P Compute Card • System-on-a-Chip (SoC) • PowerPC 450 CPU  850 MHz Frequency  Quad Core • 4 GB RAM • Network Connections Blue Gene/P system overview INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 6/30
    • GPUs (Graphical Processing Units)In the future, 2010 may be known as the year of the GPU. The Tesla C2050 / Tesla C2070 is capable of running 515 GFLOPs/sec of double precision processing performance. Tesla C2050 comes standard with 3 GB of GDDR5 memory Tesla C2050/C2070 at 144 GB/s bandwidth. Tesla C2070 comes standard with 6 GB of GDDR5 memory. Fermi Architecture The soul of a supercomputer in the body of a GPU Octoputer Microway - 8 Tesla cards NVIDIA Fermi GF100 Block Diagram CUDA (Compute Unified Device Architecture) is the computing engine in NVIDIA GPUs http://www.nvidia.com/cuda INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 7/30
    • FPGAs (Field Programmable Gate Arrays)A Field Programmable Gate Arrays (FPGA) is an integrated circuit designed to be configured by the customeror designer after manufacturing—hence "field-programmable".Reconfigurable Computing uses FPGAs as Attached Processing Elements in a Computing System, in order toDramatically Increase the Processing Speed.Annapolis Micro Systems, Inc. (Annapolis, Maryland), the leader in CommercialOff the Shelf (COTS) Field Programmable Gate Array (FPGA) Based HighPerformance Computing, announces the availability of its new WILDSTAR 6PCIe Card, with up to three Xilinx Virtex 6 FPGAs. Dini Group DNV6F6PCIe Xilinx Virtex LX550T Hightech Global Xilinx Virtex 6 PCIe Development Board Annapolis’s Wildstar 6 PCIe Dr. Wim Vanderbauwhede from Glasgow University creates 1000 core processor using FPGAs The Gannet platform aims to make it easier to design complex reconfigurable Systems-on-Chip. http://www.dcs.gla.ac.uk/~wim/ http://www.gannetcode.org/ INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 8/30
    • INCDTIM Data Center• Hewlett Packard Blade C7000 with 16 Proliant BL280c G6 (2 Intel Quad-core Xeon x5570 @ 2.93 GHz, 16 Gb RAM, 500 Gb HDD) running, TORQUE, MAUI, GANGLIA (http://hpc.itim- cj.ro), NAGIOS, configured from scratch – Scientific Linux 5.3 (Boron)• We installed different Intel compilers, mathematical and MPI libraries• We are using different Quantum chemistry codes like: AMBER, GROMACS, NAMD, LAMMPS, CPMD, CP2K, Gaussian, NWCHEM, GAMESS, ORCA, MOLPRO, DFTB+, Siesta, VASP, Accelrys Materials Studio• We are hosting also the RO-14-ITIM Grid site (http://grid.itim-cj.ro) INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 9/30
    • http://hpc.itim-cj.ro/ganglia INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 10/30
    • The story of a serendipitous discovery1 α-cyclodextrine, αCD: the association of 6 glucose units: (C6O5H10)6 4-methylpyridine, 4MP: C6NH7 …..and a bit of water1M. Plazanet, C. Floare, M. R. Johnson, R. Schweins, H. P. Tommsdorff, Freezing on heating of liquid solutions, J. Chem. Phys., 121(11),5031 (2004), ILL Annual Report 2004, 54-55 and the papers which followed. INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 11/30
    • 80Temperature °C 70 Solid phase 60 Liquid phase 50 40 100 150 200 250 300 Concentration, αCD[g]/4MP[l] 200g/l ~ 1 αCD for 50 4MP INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 12/30
    • A movie by A. Filhol, Laue-Langevin Institute Azobenzene : melts at 66oC CD-4MP : freezes at 66oC http://www.ill.eu/about/movies/experiments/in16-a-liquid-paradox/ INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 13/30
    • 300 250 Solubility αCD in 4MPConcentration mg/ml 200 150 100 50 0 40 45 50 55 60 65 70 75 80 85 90 95 100 Temperature °C INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 14/30
    • How we can rationalize these surprising observations?As temperature increases, entropy must increase, howis this compatible with the observation that crystallineorder is established and that molecular motions areslowed down? Characterize the changes of the structure and of the molecular dynamics by: • elastic and inelastic neutron scattering • neutron and X-ray diffraction, • low-field NMR and • molecular dynamics simulations INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 15/30
    • INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 17/30
    • a) Hysteresis-like fixed window (elastic) scan, IN10, ILL; b) Quasi-elastic neutron spectra, IN5, ILL INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 18/30
    • F. Ding and N. Dokholyan, Trends in Biotechnology 23(9) 450 (2005) INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 19/30
    • Model studied system:2004 - NPT molecular dynamics simulations using Accelrys CERIUS2 v4.6 withCOMPASS forcefield running on different SGI workstation A periodic box with the dimensions 24Å× 24Å× 24Å, containing:  one a-CD molecule  50 molecules of 4MP 826 atoms INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 20/30
    •  20 a-CD molecules  1120 molecules of 4MP  240 water molecules  NPT ensemble MD using AMBER9  60 A3 box 18920 atoms An AMBER benchmark on IBM SP5 cluster (IBM p575 speed of 0.22ns day (1 core), 0.39ns day Power 5, bassi.nersc.gov, 118 8-cpu nodes, 1.9 GHz (2 cores) and 0.69 (4 cores) Power 5+ cpu, 2 MB L2 cache, 36 MB L3 cache, 32 GB memory per node) produced 22ns/day when using 256 Infiniband is needed for a further scale up cores, on a system containing around 23500 atoms. • Initially we have to optimize the force fields using the force-matching method • 100 ns long trajectories at different temperatures must be calculated for good statistics • Hydrogen-bond dynamics and cluster formation analysis • Correlation coefficients This system will be studied at CINECA, Italy, on a project founded by HPC-Europa2 program on 256 CPUs INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 21/30
    • GPU Codes INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 22/30
    • 1 Million atoms systems simulation nowpossible on a desktop workstationAmber 11 GPU performance compared with thaton Kracken@ORNL, Dihydrofolate reductase(DHFR) solvated in water, 23558 atoms.INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 23/30
    • • Milu (Miramare Interoperable Lite User Interface), a tool to set up easily an UI on (almost) any machine (https://eforge.escience-lab.org/gf/project/milu/)• BEMuSE: Bias-Exchange Metadynamics Submission Environment (https://euindia.ictp.it/bemuse/)• EPICO – eLab Procedure for Installation and Configuration (http://epico.escience-lab.org/)• Training Tools: GRID Seed (http://gridseed.escience-lab.org) Moodle Platform (http://www.moodle.org)• Amazon Elastic Compute Cloud (EC2) - from $0.02 per hour http://aws.amazon.com/ec2/pricing/ http://aws.amazon.com/ec2/instance-types/ INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 24/30
    • To know more about it :• Freezing on heating of liquid solutions, M. Plazanet, C. Floare, M.R. Johnson, R. Schweins, H.P. Trommsdorff, J. Chem. Phys. 121 (2004) 5031• J. Chem. Phys. 125 (2005) 154504• Chem. Phys. 317 (2006) 153• Chem. Phys. 331 (2006) 35• J. Phys. Cond. Mat. 19 (2007) 205108• Phys. Chem. Chem. Phys. 12 (2010) 7026 INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 25/30
    • INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 26/30
    • INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 27/30
    • •PhysicsWeb, 24/09/2004•Science News, 16/10/2004•Physics World, 11/2004•ILL bulletin, 11/2004•Science et avenir, 12/2004•Science et vie, 01/2005•Geo magasine, german edition, 01/2005•http://www.scienceinschool.org/repository/docs/defying.pdf•… INCDTIM Seminar, June 16, 2011, Cluj-Napoca, Romania 28/30
    • Thank you for your attention
    • Annexes
    • Molecular Dynamics Method―Molecular dynamics (MD) provides the methodology for detailed microscopic modeling onthe molecular scale. The theoretical underpinnings amount on little more than Newton’s lawsof motion. After all, the nature of matter is to be found in the structure and motion of itsconstituent building blocks, and the dynamics is contained in the solution of the N-bodyproblem‖*  Classical N-body problem lacks a  the only path open is the numerical general analytical solution oneDeterministic – provides us with a trajectory of the system • From atom positions, velocities, and accelerations, calculate atom positions and velocities at the next time step. • Integrating infinitesimal steps yields the trajectory of the system for any desired time range. • There are efficient methods for integrating these elementary steps with Verlet and leapfrog algorithms being the most commonly used.  Use physics to find the potential energy between all pairs of atoms  Move atoms to the next state  Repeat* D. C. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press (2004)
    • Energy function• Target function that MD tries to optimize• Describes the interaction energies of all atoms and molecules in the system• Always an approximation - closer to real physics (accuracy increases) if more computation time, smaller time steps and more interactions AMBER bond Force FieldCovalent terms angle dihedral van der Waals electrostaticNon-covalent terms polarization implicit solvation