AstroPhi 2.0: новый код высокого порядка точности для гидродинамического моделирования астрофизических течений на гибридных суперЭВМ, оснащенных ускорителями Intel Xeon Phi

Автор: Куликов Игорь Михайлович, Черных Игорь Геннадьевич

Журнал: Проблемы информатики @problem-info

Рубрика: Параллельные вычислительные технологии

Статья в выпуске: 3 (28), 2015 года.

Бесплатный доступ

В статье представлен новый гидродинамический программный код AstroPhi 2.0 для численного моделирования астрофизических процессов на гибридных суперЭВМ, оснащенных ускорителями Intel Xeon Phi. Описаны детали параллельной реализации кода и элементы со-дизайна численного алгоритма, которые позволили сделать эффективную программную реализацию. В рамках одного ускорителя было получено 134-кратное ускорение, 92-процентная эффективность была получена при использовании 64 ускорителей. С помощью данного кода была смоделирована задача столкновения галактик.

Математическое моделирование, суперкомпьютерные вычисления, параллельные вычислительные методы, вычислительная астрофизика, столкновение галактик, ускорители intel xeon phi

Короткий адрес: https://readera.ru/14320285

IDR: 14320285

Список литературы AstroPhi 2.0: новый код высокого порядка точности для гидродинамического моделирования астрофизических течений на гибридных суперЭВМ, оснащенных ускорителями Intel Xeon Phi

  • Kim J., Park C., Richard Gott III J., Dubinski J. The Horizon Run N-Body Simulation: Baryon Acoustic Oscillations and Topology of Large-scale Structure of the Universe//The Astrophysical Journal. 2009. V. 701, I. 2. P. 1547-1559.
  • Springel V., et al. Simulations of the formation, evolution and clustering of galaxies and quasars//Nature. 2005. V. 435. P. 629-636.
  • Teyssier R., et al. Full-sky weak-lensing simulation with 70 billion particles//Astronomy Astrophysics. 2009. V. 497, I. 2. P. 335-341.
  • Klypin A., Trujillo-Gomez S., Primack J. Dark Matter Halos in the Standard Cosmological Model: Results from the Bolshoi Simulation//The Astrophysical Journal. 2011. V. 740, I. 2, 102. P. 1-17.
  • Genel S., et al. Introducing the Illustris project: the evolution of galaxy populations across cosmic time//Monthly Notices of the Royal Astronomical Society. 2014. V. 445, I. 1. P. 175-200.
  • Vogelsberger M., et al. Introducing the Illustris Project: simulating the coevolution of dark and visible matter in the Universe//Monthly Notices of the Royal Astronomical Society. 2014. V. 444, I. 2. P. 1518-1547.
  • Vogelsberger M., et al. Properties of galaxies reproduced by a hydrodynamic simulation//Nature. 2014. V. 509. P. 177-182.
  • Crain R., et al. The EAGLE simulations of galaxy formation: calibration of subgrid physics and model variations//Monthly Notices of the Royal Astronomical Society. 2015. V. 450, I. 2. P. 1937-1961.
  • Schaye J., et al. The EAGLE project: simulating the evolution and assembly of galaxies and their environments//Monthly Notices of the Royal Astronomical Society. 2015. V. 446, I. 1. P. 521-554.
  • Milgrom M. A modification of the Newtonian dynamics as a possible alternative to the hidden mass hypothesis//The Astrophysical Journal. 1983. V. 270. P. 365-370.
  • Chilingarian I., Di Matteo P., Combes F., Melchior A., Semelin B. The GalMer database: galaxy mergers in the virtual observatory//Astronomy Astrophysics. 2010. V. 518, A61. P. 1-14.
  • Tutukov A., Lazareva G., Kulikov I. Gas Dynamics of a Central Collision of Two Galaxies: Merger, Disruption, Passage, and the Formation of a New Galaxy//Astronomy Reports. 2011. V. 55, I. 9. P. 770-783.
  • Schweizer F. Merger-Induced Starbursts//Astrophysics and Space Science Library. 2005. V. 329. P. 143-152.
  • Sol Alonso M., Lambas D., Tissera P., Coldwell G. Active galactic nuclei and galaxy interactions//Monthly Notices of the Royal Astronomical Society. 2007. V. 375, I. 3. P. 1017-1024.
  • Blecha L., Loeb A., Narayan R. Double-peaked narrow-line signatures of dual supermassive black holes in galaxy merger simulations//Monthly Notices of the Royal Astronomical Society. 2013. V. 429, I. 3. P. 2594-2616.
  • Rodriguez C., Taylor G., Zavala R., Pihlstrom Y., Peck A. Hi observations of the supermassive binary black hole system in 0402+379//The Astrophysical Journal. 2009. V. 697, I. 1. P. 37-44.
  • Combes F., Melchior A. Chemodynamical evolution of interacting galaxies//Astrophysics and Space Science. 2002. V. 281, I. 1-2. P. 383-387.
  • Glover S., Mac Low M. Simulating the Formation of Molecular Clouds. I. Slow Formation by Gravitational Collapse from Static Initial Conditions//The Astrophysical Journal Supplement Series. 2007. V. 169, I. 2. P. 239-268.
  • Glover S., Mac Low M. Simulating the Formation of Molecular Clouds. II. Rapid Formation from Turbulent Initial Conditions//The Astrophysical Journal. 2007. V. 659, I. 2. P. 1317-1337.
  • Ploeckinger S., Hensler G., Recchi S., Mitchell N., Kroupa P. Chemodynamical evolution of tidal dwarf galaxies. I. Method and IMF dependence//Monthly Notices of the Royal Astronomical Society. 2014. V. 437, I. 4. P. 3980-3993.
  • Ploeckinger S., Recchi S., Hensler G., Kroupa P. Chemodynamical evolution of tidal dwarf galaxies. II. The long-term evolution and influence of a tidal field//Monthly Notices of the Royal Astronomical Society. 2015. V. 447, I. 3. P. 2512-2525.
  • Recchi S. Chemodynamical Simulations of Dwarf Galaxy Evolution//Advances in Astronomy. 2014. V. 2014, 750754. P. 1-30.
  • Few C., Courty S., Gibson B., Michel-Dansac L., Calura F. Chemodynamics of a simulated disc galaxy: initial mass functions and Type Ia supernova progenitors//Monthly Notices of the Royal Astronomical Society. 2014. V. 444, I. 4. P. 3845-3862.
  • Minchev I., Chiappini C., Martig M. Chemodynamical evolution of the Milky Way disk. I. The solar vicinity//Astronomy Astrophysics. 2013. V. 558, A9. P. 1-25.
  • Minchev I., Chiappini C., Martig M. Chemodynamical evolution of the Milky Way disk. II. Variations with Galactic radius and height above the disk plane//Astronomy Astrophysics. 2014. V. 572, A92. P. 1-19.
  • Pilkington K., et al. Metallicity gradients in disks. Do galaxies form inside-out?//Astronomy Astrophysics. 2012. V. 540, A56. P. 1-12.
  • Recchi S., Spitoni E., Matteucci F., Lanfranchi G. The effect of differential galactic winds on the chemical evolution of galaxies//Astronomy Astrophysics. 2008. V. 489, I. 2. P. 555-565.
  • Brusadin G., Matteucci F., Romano D. Modeling the chemical evolution of the Galaxy halo//Astronomy Astrophysics. 2013. V. 554, A135. P. 1-10.
  • Harvey-Smith L., Cohen R. Discovery of large-scale methanol and hydroxyl maser filaments in W3(OH)//Monthly Notices of the Royal Astronomical Society. 2006. V. 371, I. 4. P. 1550-1558.
  • Glinskiy B., Kulikov I., Snytnikov A., Romanenko A., Chernykh I., Vshivkov V. Co-design of Parallel Numerical Methods for Plasma Physics and Astrophysics//Supercomputing frontiers and innovations. 2014. V. 1, I. 3. P. 88-98.
  • Mitchell N., Vorobyov E., Hensler G. Collisionless Stellar Hydrodynamics as an Efficient Alternative to N-body Methods//Monthly Notices of the Royal Astronomical Society. 2013. V. 428. P. 2674-2687.
  • Gingold R.A., Monaghan J.J. Smoothed particle hydrodynamics -Theory and application to non-spherical stars//Monthly Notices of the Royal Astronomical Society. 1977. V. 181. P. 375-389.
  • Lucy L.B. A numerical approach to the testing of the fission hypothesis//The Astrophysical Journal. 1977. V. 82. P. 1013-1024.
  • O'Shea B., Bryan G., Bordner J., Norman M., Abel T., Harkness R., Kritsuk A. Adaptive Mesh Refinement -Theory and Applications//Lectures Notes of Computer Science Engineering. 2005. V. 41. P. 341-350.
  • Hockney R.W., Eastwood J.W. Computer Simulation Using Particles. N.Y.: McGraw-Hill, 1981.
  • Couchman H.M.P. Mesh-refined PM: A fast adaptive N-body algorithm//The Astrophysical Journal. 1991. V. 368. P. L23-L26.
  • Barnes J., Hut P. A hierarchical O() force-calculation algorithm//Nature. 1986. V. 324. P. 446-449.
  • Dubinski J., Kim J., Park C., Humble R. GOTPM: a parallel hybrid particle-mesh treecode//New Astronomy. 2004. V. 9. P. 111-126.
  • Fedorenko R. A relaxation method for solving elliptic difference equations//USSR Computational Mathematics Mathematical Physics. 1961. V. 1. P. 1092-1096.
  • Godunov S.K. A Difference Scheme for Numerical Solution of Discontinuous Solution of Hydrodynamic Equations//Mathematichesky Sbornik. 1959. V. 47. P. 271-306.
  • Kulikovskii A.G., Pogorelov N.V., Semenov A.Yu. Mathematical Aspects of Numerical Solution of Hyperbolic Systems. M.: Fizmatlit, 2001.
  • Toro E.F. Riemann Solvers and Numerical Methods for Fluid Dynamics. Heidelberg: Springer-Verlag, 1999
  • Courant R., Isaacson E., Rees M. On the solution of nonlinear hyperbolic differential equations by finite differences//Communications on Pure and Applied Mathematics. 1952. V. 5. P. 243-256.
  • Roe P. Approximate Riemann solvers, parameter vectors, and difference solvers//Journal of Computational Physics. 1997. V. 135. P. 250-258.
  • Engquist B., Osher S.J. One-sided difference approximations for nonlinear conservation laws//Mathematics of Computational. 1981. V. 36. P. 321-351.
  • Harten A., Lax P.D., Van Leer B. On upstream differencing and Godunov-type schemes for hyperbolic conservation laws//Society for Industrial and Applied Mathematics. 1983. V. 25. P. 35-61.
  • Einfeld B. On Godunov-type methods for gas dynamics//SIAM Journal of Numerical Analysis. 1988. V. 25. P. 294-318.
  • Batten P., Clarke N., Lambert C., Causon D.M. On the Choice of Wavespeeds for the HLLC Riemann Solver//SIAM Journal of Computing. 1997. V. 18. P. 1553-1570.
  • Van Leer B. Towards the Ultimate Conservative Difference Scheme, V. A Second Order Sequel to Godunov's Method//Journal of Computational Physics. 1979. V. 32. P. 101-136.
  • Jin S., Xin Z. The Relaxation Schemes for Systems of Conservation Laws in Arbitrary Space Dimensions//Communications on Pure and Applied Mathematics. 1995. V. 48. P. 235-276.
  • Collela P., Woodward P.R. The Piecewise Parabolic Method (PPM) Gas-Dynamical simulations//Journal of Computational Physics. 1984. V. 54. P. 174-201.
  • Liu X., Osher S., Chan T. Weighted essentially non-oscillatory schemes//Journal of Computational Physics. 1994. V. 115. P. 200-212.
  • Godunov S.K., Manuzina Yu.D., Nazareva M.A. Experimental analysis of convergence of the numerical solution to a generalized solution in fluid dynamics//Computational Mathematics and Computational Physics. 2011. V. 51. P. 88-95.
  • Popov M., Ustyugov S. Piecewise parabolic method on local stencil for gasdynamic simulations//Computational Mathematics and Mathematical Physics. 2007. V. 47, I. 12. P. 1970-1989.
  • Popov M., Ustyugov S. Piecewise parabolic method on a local stencil for ideal magnetohydrodynamics//Computational Mathematics and Mathematical Physics. 2008. V. 48, I. 3. P. 477-499.
  • Pearcea F.R., Couchman H.M.P. Hydra: a parallel adaptive grid code//New Astronomy. 1997. V. 2. P. 411-427.
  • Wadsley J.W., Stadel J., Quinn T. Gasoline: a flexible, parallel implementation of TreeSPH//New Astronomy. 2004. V. 9. P. 137-158.
  • Matthias S. GRAPESPH: cosmological smoothed particle hydrodynamics simulations with the special-purpose hardware GRAPE//Monthly Notices of the Royal Astronomical Society. 1996. V. 278. P. 1005-1017.
  • Springel V. The cosmological simulation code GADGET-2//Monthly Notices of the Royal Astronomical Society. 2005. V. 364. P. 1105-1134.
  • Ziegler U. Self-gravitational adaptive mesh magnetohydrodynamics with the NIRVANA code//Astronomy Astrophysics. 2005. V. 435. P. 385-395.
  • Mignone A., Plewa T., Bodo G. The Piecewise Parabolic Method for Multidimensional Relativistic Fluid Dynamics//The Astrophysical Journal. 2005. V. 160. P. 199-219.
  • Hayes J., Norman M., Fiedler R. et al. Simulating Radiating and Magnetized Flows in Multiple Dimensions with ZEUS-MP//The Astrophysical Journal Supplement Series. 2006. V. 165. P. 188-228.
  • Teyssier R. Cosmological hydrodynamics with adaptive mesh refinement. A new high resolution code called RAMSES//Astronomy Astrophysics. 2002. V. 385. P. 337-364.
  • Kravtsov A., Klypin A., Hoffman Y. Constrained Simulations of the Real Universe. II. Observational Signatures of Intergalactic Gas in the Local Supercluster Region//The Astrophysical Journal. 2002. V. 571. P. 563-575.
  • Stone J. et al. Athena: A New Code for Astrophysical MHD//The Astrophysical Journal Supplement Series. 2008. V. 178. P. 137-177.
  • Brandenburg A., Dobler W. Hydromagnetic turbulence in computer simulations//Computer Physics Communications. 2002. V. 147. P. 471-475.
  • Gonzalez M., Audit E., Huynh P. HERACLES: a three-dimensional radiation hydrodynamics code//Astronomy Astrophysics. 2007. V. 464. P. 429-435.
  • Krumholz M.R., Klein R.I., McKee C.F., Bolstad, J. Equations and Algorithms for Mixed-frame Flux-limited Diffusion Radiation Hydrodynamics//The Astrophysical Journal. 2007. V. 667. P. 626-643.
  • Mignone A. et al. PLUTO: a Numerical Code for Computational Astrophysics//The Astrophysical Journal Supplement Series. 2007. V. 170. P. 228-242.
  • Almgren A. et al. CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-gravity//The Astrophysical Journal. 2010. V. 715. P. 1221-1238.
  • Schive H., Tsai Y., Chiueh T. GAMER: a GPU-accelerated Adaptive-Mesh-Refinement Code for Astrophysics//The Astrophysical Journal. 2010. V. 186. P. 457-484.
  • Murphy J., Burrows A. BETHE-Hydro: An Arbitrary Lagrangian-Eulerian Multidimensional Hydrodynamics Code for Astrophysical Simulations//The Astrophysical Journal Supplement Series. 2008. V. 179. P. 209-241.
  • Springel V. E pur si muove: Galilean-invariant cosmological hydrodynamical simulations on a moving mesh//Monthly Notices of the Royal Astronomical Society. 2010. V. 401. P. 791-851.
  • Bruenn S. et al. 2D and 3D core-collapse supernovae simulation results obtained with the CHIMERA code//Journal of Physics. 2009. V. 180. P. 1-5.
  • Hopkins P. A new class of accurate, mesh-free hydrodynamic simulation methods//Monthly Notices of the Royal Astronomical Society. 2015. V. 450, I. 1. P. 53-110.
  • Vshivkov V., Lazareva G., Snytnikov A., Kulikov I., Tutukov A. Hydrodynamical code for numerical simulation of the gas components of colliding galaxies//The Astrophysical Journal Supplement Series. 2011. V. 194, I. 47. P. 1-12.
  • Kulikov I. GPUPEGAS: A New GPU-accelerated Hydrodynamic Code for Numerical Simulations of Interacting Galaxies//The Astrophysical Journal Supplements Series. 2014. V. 214, I. 12. P. 1-12.
  • Kulikov I.M., Chernykh I.G., Snytnikov A.V., Glinskiy B.M., Tutukov A.V. AstroPhi: A code for complex simulation of dynamics of astrophysical objects using hybrid supercomputers//Computer Physics Communications. 2015. V. 186. P. 71-80.
  • Bergin E., Hartmann L., Raymond J., Ballesteros-Paredes J. Molecular Cloud Formation behind Shock Waves//The Astrophysical Journal. 2004. V. 612. P. 921-939.
  • Tielens A., Hollenbach D. Photodissociation regions. I -Basic model. II -A model for the Orion photodissociation region//The Astrophysical Journal. 1985. V. 291. P. 722-754.
  • Cazaux S., Tielens A. Formation on Grain Surfaces//The Astrophysical Journal. 2004. V. 604. P. 222-237.
  • Caselli P., Walmsley C., Terzieva R., Herbst E. The Ionization Fraction in Dense Cloud Cores//The Astrophysical Journal. 1998. V. 499. P. 234-249.
  • Bergin E., Plume R., Williams J., Myers P. The Ionization Fraction in Dense Molecular Gas. II. Massive Cores//The Astrophysical Journal. 1999. V. 512. P. 724-739.
  • Van Der Tak F., Van Dishoeck E. Limits on the cosmic-ray ionization rate toward massive young stars//Astronomy Astrophysics. 2000. V. 358. P. L79-L82.
  • Draine B., Bertoldi F. Structure of Stationary Photodissociation Fronts//The Astrophysical Journal. 1996. V. 468. P. 269-289.
  • Draine B. Photoelectric heating of interstellar gas//The Astrophysical Journal Supplement Series. 1978. V. 36. P. 595-619.
  • Katz N., Weinberg D., Hernquist L. Cosmological simulations with TreeSPH//The Astrophysical Journal Supplement Series. 1996. V. 105. P. 19-35.
  • Springel V., Hernquist L. Cosmological smoothed particle hydrodynamics simulations: a hybrid multiphase model for star formation//Monthly Notices of the Royal Astronomical Society. 2003. V. 339, I. 2. P. 289-311.
  • Sutherland R., Dopita M. Cooling functions for low-density astrophysical plasmas//The Astrophysical Journal Supplement Series. 1993. V. 88. P. 253-327.
  • Kulikov I., Vorobyov E. Using the PPML approach for constructing a low-dissipation, operator-splitting scheme for numerical simulations of hydrodynamic flows//New Astronomy. 2015. (in progress).
  • Vshivkov V., Lazareva G., Snytnikov A., Kulikov I., Tutukov A. Computational methods for ill-posed problems of gravitational gasodynamics//Journal of Inverse and Ill-posed Problems. 2011. V. 19, I. 1. P. 151-166.
  • Godunov S., Kulikov I. Computation of Discontinuous Solutions of Fluid Dynamics Equations with Entropy Nondecrease Guarantee//Computational Mathematics and Mathematical Physics. 2014. V. 54, I. 6. P. 1012-1024.
  • Frigo M., Johnson S. The Design and Implementation of FFTW3//Proceedings of the IEEE. 2005. V. 93, I. 2. P. 216-231.
  • Kalinkin A., Laevsky Y., Gololobov S. 2D Fast Poisson Solver for High-Performance Computing//Lecture Notes in Computer Science. 2009. V. 5698. P. 112-120.
  • Jeffers J., Reinders J. Intel Xeon Phi Coprocessor High Performance Programming. Elsevier, 2013
Еще
Статья научная