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Leading Computational Methods on Modern Parallel Systems

Leading Computational Methods on Modern Parallel Systems

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Leading Computational Methods on Modern Parallel Systems

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  1. Leading Computational Methods on Modern Parallel Systems Leonid Oliker Lawrence Berkeley National Laboratory Joint work with: Julian Borrill, Andrew Canning, Stephane Ethier, Art Mirin, David Parks, John Shalf, David Skinner, Michael Wehner, Patrick Worley

  2. Motivation • Stagnating application performance is well-know problem in scientific computing • By end of decade numerous mission critical applications expected to have 100X computational demands of current levels • Many HEC platforms are poorly balanced for demands of leading applications • Memory-CPU gap, deep memory hierarchies, poor network-processor integration, low-degree network topology • Traditional superscalar trends slowing down • Mined most benefits of ILP and pipelining,Clock frequency limited by power concerns • Achieving next order of magnitude in computing will require O(100K) - O(1M) processors: interconnect that scale nonlinearly in cost (crossbar, fattree) become impractical

  3. Application Evaluation • Microbenchmarks, algorithmic kernels, performance modeling and prediction, are important components of understanding and improving architectural efficiency • However full-scale application performance is the final arbiter of system utility and necessary as baseline to support all complementary approaches • Our evaluation work emphasizes full applications, with real input data, at the appropriate scale • Requires coordination of computer scientists and application experts from highly diverse backgrounds • Allows advanced optimizations for given architectural platforms • In-depth studies reveal limitation of compilers, operating systems, and hardware, since all of these components must work together at scale • Our recent efforts have focused on the potential of modern parallel vector systems • Effective code vectorization is an integral part of the process • First US team to conduct Earth Simulator performance study

  4. Vector Paradigm • High memory bandwidth • Allows systems to effectively feed ALUs (high byte to flop ratio) • Flexible memory addressing modes • Supports fine grained strided and irregular data access • Vector Registers • Hide memory latency via deep pipelining of memory load/stores • Vector ISA • Single instruction specifies large number of identical operations • Vector architectures allow for: • Reduced control complexity • Efficiently utilize large number of computational resources • Potential for automatic discovery of parallelism • Can some of these features can be added to modern micros? However: most effective if sufficient regularity discoverable in program structure • Suffers even if small % of code non-vectorizable (Amdahl’s Law)

  5. Architectural Comparison • Custom vectors : High Bandwidth, Flexible addressing, Many Register, vector ISA • Less control complexity, use many ALUs, auto parallelism • ES shows best balance between memory and peak performance • Data caches of superscalar systems and X1(E) potential reduce mem costs • X1E: 2 MSP’s per MCM - increases contention for memory and interconnect • A key ‘balance point’ for vector systems is the scalar:vector ratio (8:1 or even 32:1) • Opteron/IB shows best balance for superscalar, Itanium2/Quadrics lowest latency • Cost is a critical metric - however we are unable to provide such data • Proprietary, pricing varies based on customer and time frame • Poorly balanced systems cannot solve certain class of problems/resolutions regardless of processor count!

  6. Application Overview • Examining candidate ultra-scale applications with abundant data parallelism • Codes designed for superscalar architectures, required vectorization effort • ES use requires minimum vectorization and parallelization hurdles

  7. Astrophysics: CACTUS • Numerical solution of Einstein’s equations from theory of general relativity • Among most complex in physics: set coupled nonlinear hyperbolic & elliptic systems w/ thousands of terms • CACTUS evolves these equations to simulate high gravitational fluxes, such as collision of two black holes • Evolves PDE’s on regular grid using finite differences • Gravitational Wave Astronomy: exciting new field about to be born, w/ new fundamental insight into universe Visualization of grazing collision of two black holes Developed at Max Planck Institute, vectorized by John Shalf LBNL

  8. CACTUS: Performance • SX8 attains highest per-processor performance ever attained for Cactus: 58X Power3! • Vector performance related to x-dim (vector length) • Excellent scaling on ES/SX8 using fixed data size per proc (weak scaling) • Opens possibility of computations at unprecedented scale • X1 surprisingly poor (~6x slower than SX8) - low ratio scalar:vector • Unvectorized boundary, required 15% of runtime on SX8 and 30+% on X1 • < 5% for the scalar version: unvectorized code can quickly dominate cost • To date unable to successfully execute code on X1E • Poor superscalar performance despite high computational intensity • Register spilling due to large number of loop variables • Prefetch engines inhibited due to multi-layer ghost zones calculations

  9. Plasma Physics: LBMHD • LBMHD uses a Lattice Boltzmann method to model magneto-hydrodynamics (MHD) • Performs 2D/3D simulation of high temperature plasma • Evolves from initial conditions and decaying to form current sheets • Spatial grid coupled to octagonal streaming lattice • Block distributed over processor grid • Main computational components: • Collision, Stream, Interpolation • Vectorization: loop interchange, unrolling • X1 compiler loop reordered automatically Evolution of vorticity into turbulent structures Ported by Jonathan Carter, developed by George Vahala’s group College of William & Mary

  10. LBMHD-3D: Performance • Not unusual to see vector achieve > 40% peak while superscalar architectures achieve ~ 10% • There exists plenty of computation, however large working set causes register spilling scalars • Examining cache-oblivious algorithms for cache-based systems • Unlike superscalar approach, large vector register sets hide latency • Opteron shows impressive superscalar performance, 2X speed vs. Itanium2 • Opteron has >2x STREAM BW, and Itanium2 cannot store FP in L1 cache • ES sustains 68% of peak up to 4800 processors: 26TFlops - SC05 Gorden Bell FinalistThe highest performance ever attained for this code by far • SX8 shows highest raw performance, but ES shows highest efficiency • SX8: Commodity DDR2-SDRAM vs. ES: high performance custom FPLRAM • X1E achieved same performance as X1 using original code version • By turning off caching resulted in about 10% improvement over X1

  11. Analysis of Bank Conflicts • Comparison of bank conflicts shows that ES custom memory has clear advantages

  12. Magnetic Fusion: GTC • Gyrokinetic Toroidal Code: transport of thermal energy (plasma microturbulence) • Goal magnetic fusion is burning plasma power plant producing cleaner energy • GTC solves 3D gyroaveraged kinetic system w/ particle-in-cell approach (PIC) • PIC scales N instead of N2 – particles interact w/ electromagnetic field on grid • Allows solving equation of particle motion with ODEs (instead of nonlinear PDEs) • Vectorization inhibited: multiple particles may attempt to concurrently update same point in charge deposition Whole volume and cross section of electrostatic potential field, showing elongated turbulence eddies Developed at PPPL, vectorized/optimized by Stephane Ethier and ORNL/Cray/NEC

  13. GTC Particle Decomposition Vectorization: • Particle charge deposited amongst nearest grid points • Several particles can contribute to same grid point preventing vectorization • Solution: VLEN copies of charge deposition array with reduction after main loop • Greatly increases memory footprint (8x) • GTC originally optimized for superscalar SMPs using MPI/OpenMP • However: OpenMP severely increase memory for vector implementation • Vectorization and thread-level parallelism compete w/ each other • Previous vector experiments limited to only 64-way MPI parallelism • 64 is optimal domains for 1D toroidal (independent of # particles) • Updated GTC algorithm • Introduces a third level of parallelism: • Algorithm splits particles between several processors (within 1D domain) • Allows increase concurrency and number of studied particles • Larger particle simulations allow increase resolution studies • Particles not subject to Courant condition (same timestep) • Allows multiple species calculations

  14. GTC: Performance • New decomposition algorithm efficiently utilizes high P (as opposed to 64 on ES) • Breakthrough of Tflop barrier on ES for important SciDAC code • 7.2 Tflop/s on 4096 ES processors • SX8 highest raw performance (of any architecture) • Opens possibility of new set of high-phase space-resolution simulations • Scalar architectures suffer from low CI, irregular data access, and register spilling • Opteron/IB is 50% faster than Itanium2/Quadrics and only 1/2 speed of X1 • Opteron: on-chip memory controller and caching of FP L1 data • X1 suffers from overhead of scalar code portions • Original (unmodified) X1 version performed 12% *slower* on X1E • Additional optimizations increased performance by 50%! • Recent ORNL work increases performance additional 75% • SciDAC code, HPCS benchmark

  15. Material Science: PARATEC • First-principles quantum mechanical total energy calc using pseudopotentials & plane wave basis set • Density Functional Theory to calc structure & electronic properties of new materials • DFT calc are one of the largest consumers of supercomputer cycles in the world • 33% 3D FFT, 33% BLAS3, 33% Hand coded F90 • Part of calculation in real space other in Fourier space • Uses specialized 3D FFT to transform wavefunction Conduction band minimum electron state forCadmium Selenide (CdSe) quantum dot • Global transpose Fourier to real space Multiple • FFTs: reduce communication latency • Vectorize across (not within) FFTs • Custom FFT: only nonzeros sent Developed by Andrew Canning with Louie and Cohen’s groups (LBNL, UCB)

  16. PARATEC: Performance • All architectures generally perform well due to computational intensity of code (BLAS3, FFT) • ES achieves highest overall performance to date: 5.5Tflop/s on 2048 procs • Main ES/SX8 advantage for this code is fast interconnect • Allows never before possible, high resolution simulations • CdSE Q-dot: Largest cell-size atomistic experiment ever run using PARATEC • Important uses: can be attached to organic molecules as electronic dye tags • SX8 achieves highest per-processor performance (>2x X1E) • X1/X1E shows lowest % of peak • Non-vectorizable code much more expensive on X1/X1E (32:1) • Lower bisection bandwidth to computational ratio (4D-hypercube) • X1 performance is comparable to Itanium2 • Itanium2 outperforms Opteron (unlike LBMHD/GTC) because • PARATEC less sensitive to memory access issues (high computational intensity) • Opteron lacks FMA unit • Quadrics shows better scaling of all-to-all at large concurrencies

  17. Atmospheric Modeling: FVCAM • CAM3.1: Atmospheric component of CCSM3.0 • Our focus is the Finite Volume (FV) approach • AGCM: consists of physics (PS) and dynamical core (DC) • DC approximates dynamics of atmosphere • PS: calculates source terms to equations of motion: • Turbulence, radiative transfer, clouds, boundary, etc • DC default: Eulerian spectral transform - maps onto sphere • Allows only 1D decomposition in latitude • FVCAM grid is rectangular (longitude, latitude, level) • Allows 2D decomp (latitude, level) in dynamics phase • Singularity at pole prevents longitude decomposition • Dynamical eqns bounded by Lagrangian surfaces • Requires remapping to Eulerian reference frame • Hybrid (MPI/OpenMP) programming • MPI tasks limited by # of latitude lines • Increase potential parallelism and improves S2V ratio • Is not always effective on some platforms Simulated Class IV hurricane at 0.5. This storm was produced solely through the chaos of the atmospheric model. It is one of the many events produced by FVCAM at resolution of 0.5. Experiments/vectorization Art Mirin, Dave Parks, Michael Wehner, Pat Worley

  18. FVCAM Decomposition and Vectorization • Processor communication topology and volume for 1D and 2D FVCAM • Generated by IPM profiling tool - used to understand interconnect requirements • 1D approach straightforward nearest neighbor communication • 2D communication bulk is nearest neighbor - however: • Complex pattern due to vertical decomp and transposition during remapping • Total volume in 2D remap is reduced due to improved surface/volume ratio • Vectorization - 5 routines, about 1000 lines • Move latitude calculation to inner loops to maximize parallelism • Reduce number of branches, performing logical tests in advance (indirect indexing) • Vectorize across (not within) FFT’s for Polar filters • However, higher concurrency for fixed size problem limit performance of vectorized FFTs

  19. FVCAM3.1: Performance • FVCAM 2D decomposition allows effective use of >2X as many processors • Increasing vertical discretizations (1,4,7) allows higher concurrencies • Results showing high resolution vector performance 361x576x26 (0.5 x 0.625) • X1E achieves speedup of over 4500 on P=672 - highest ever achieved • To date only results from 1D decomp available on SX-8 • Power3 limited to speedup of 600 regardless of concurrency • Factor of at least 1000x necessary for simulation to be tractable • Raw speed X1E: 1.14X X1, 1.4X ES, 3.7X Thunder, 13X Seaborg • At high concurrencies (P= 672) all platforms achieve low % peak (< 7%) • ES achieves highest sustained performance (over 10% at P=256) • Vectors suffer from short vector length of fixed problem size, esp FFTs • Superscalars generally achieve lower efficiencies/performance than vectors • Finer resolutions requires increased number of more powerful processors

  20. Cosmology: MADCAP • Anisotropy Dataset Computational Analysis Package • Optimal general algorithm for extracting key cosmological data from Cosmic Microwave Background Radiation (CMB) • Anisotropies in the CMB contains early history of the Universe • Recasts problem in dense linear algebra: ScaLAPACK • Out of core calculation: holds ~3 of the 50 matrices in memory Temperature anisotropies in CMB (Boomerang) Developed by Julian Borrill, LBNL

  21. MADCAP: Performance • Overall performance can be surprising low, for dense linear algebra code • I/O takes a heavy toll on Phoenix and Columbia: I/O optimization currently in progress • NERSC Power3 shows best system balance with respect to I/O • ES lacks high-performance parallel I/O - code rewritten to utilize local disks • Preliminary SX8 experiments unsuccessful due to poor I/O performance

  22. % of Theoretical Peak Performance Overview Speedup vs. ES • Tremendous potential of vector systems: SX8 achieves unprecedented raw performance • Demonstrated importance of vector platforms: allows solutions at unprecedented scale • ES achieves highest efficiency on almost all test applications • LBMHD-3D achieves 26 TF/s using 4800 procs, GTC achieves 7.2 TF/s on 4096 ES procs, PARATEC achieves 5.5 TF/s on 2048 procs • Porting several of our apps to SX8 in progress:Madbench (slow I/O), FVCAM 2D decomp, Hyperclaw AMR (templated C++) • Investigating how to incorporate vector-like facilities into modern micros • Many methods unexamined (more difficult to vectorize): Implicit, Multigrid, AMR, Unstructured (Adaptive), Iterative and Direct Sparse Solvers, N-body, Fast Multiple • One size does not fit all: need a range of architectural designs to best fit algorithms • Heterogeneous supercomputing designs are on the horizon • Moving on to latest generation of HEC platforms: Power5, BG/L, XT3