Pencil Code: multi-purpose and multi-user maintained Axel Brandenburg (Nordita, Stockholm) Wolfgang Dobler (Univ. Calgary) and now many more…. (...just.

Slides:



Advertisements
Similar presentations
Magnetic Chaos and Transport Paul Terry and Leonid Malyshkin, group leaders with active participation from MST group, Chicago group, MRX, Wisconsin astrophysics.
Advertisements

Non-Fickian diffusion and Minimal Tau Approximation from numerical turbulence A.Brandenburg 1, P. Käpylä 2,3, A. Mohammed 4 1 Nordita, Copenhagen, Denmark.
Particle acceleration in a turbulent electric field produced by 3D reconnection Marco Onofri University of Thessaloniki.
“The interaction of a giant planet with a disc with MHD turbulence II: The interaction of the planet with the disc” Papaloizou & Nelson 2003, MNRAS 339.
Large scale simulations of astrophysical turbulence Axel Brandenburg (Nordita, Copenhagen) Wolfgang Dobler (Univ. Calgary) Anders Johansen (MPIA, Heidelberg)
Motivation The physics of inertial confinement fusion (ICF) combine hydrodynamics, plasma physics and radiation. One of the important hydrodynamic processes.
Does hyperviscosity spoil the inertial range? A. Brandenburg, N. E. L. Haugen Phys. Rev. E astro-ph/
Emerging Flux Simulations Bob Stein A.Lagerfjard Å. Nordlund D. Benson D. Georgobiani 1.
Initial Analysis of the Large-Scale Stein-Nordlund Simulations Dali Georgobiani Formerly at: Center for Turbulence Research Stanford University/ NASA Presenting.
/08/2002SMARTER meeting 1 Solution of 2D Navier-Stokes equations in velocity-vorticity formulation using FD Remo Minero Scientific Computing Group.
SSL (UC Berkeley): Prospective Codes to Transfer to the CCMC Developers: W.P. Abbett, D.J. Bercik, G.H. Fisher, B.T. Welsch, and Y. Fan (HAO/NCAR)
The Pencil Code -- a high order MPI code for MHD turbulence Anders Johansen (Sterrewacht Leiden)‏ Axel Brandenburg (NORDITA, Stockholm)‏ Wolfgang Dobler.
Numerical Hydraulics Wolfgang Kinzelbach with Marc Wolf and Cornel Beffa Lecture 1: The equations.
Magneto-hydrodynamic turbulence: from the ISM to discs
Zhaorui Li and Farhad Jaberi Department of Mechanical Engineering Michigan State University East Lansing, Michigan Large-Scale Simulations of High Speed.
Massively Parallel Magnetohydrodynamics on the Cray XT3 Joshua Breslau and Jin Chen Princeton Plasma Physics Laboratory Cray XT3 Technical Workshop Nashville,
Stratified Magnetohydrodynamics Accelerated Using GPUs:SMAUG.
How long can left and right handed life forms coexist? Axel Brandenburg, Anja Andersen, Susanne Höfner, Martin Nilsson, Tuomas Multamäki (Nordita) Orig.
Processes in Protoplanetary Disks Phil Armitage Colorado.
Magnetic field generation on long time scales Axel Brandenburg (Nordita/Stockholm) Kemel+12 Ilonidis+11Brandenburg+11Warnecke+11 Käpylä+12.
Magnetic dynamo over different astrophysical scales Axel Brandenburg & Fabio Del Sordo (Nordita) with contributions from many others seed field primordial.
Critical issues to get right about stellar dynamos Axel Brandenburg (Nordita, Copenhagen) Shukurov et al. (2006, A&A 448, L33) Schekochihin et al. (2005,
Recent advances in Astrophysical MHD Jim Stone Department of Astrophysical Sciences & PACM Princeton University, USA Recent collaborators: Tom Gardiner.
Effect of Magnetic Helicity on Non-Helical Turbulent Dynamos N. KLEEORIN and I. ROGACHEVSKII Ben-Gurion University of the Negev, Beer Sheva, ISRAEL.
Magneto-rotational instability Axel Brandenburg (Nordita, Copenhagen)
High-performance multi-user code development with Google Code  Current status  (...just google for Pencil Code)
R. Oran csem.engin.umich.edu SHINE 09 May 2005 Campaign Event: Introducing Turbulence Rona Oran Igor V. Sokolov Richard Frazin Ward Manchester Tamas I.
Modelling Tsunami Waves using Smoothed Particle Hydrodynamics (SPH) R.A. DALRYMPLE and B.D. ROGERS Department of Civil Engineering, Johns Hopkins University.
Accretion disc dynamos B. von Rekowski, A. Brandenburg, 2004, A&A 420, B. von Rekowski, A. Brandenburg, W. Dobler, A. Shukurov, 2003 A&A 398,
Bern, MHD, and shear Axel Brandenburg (Nordita, Copenhagen) Collaborators: Nils Erland Haugen (Univ. Trondheim) Wolfgang Dobler (Freiburg  Calgary) Tarek.
Decay of a simulated bipolar field in the solar surface layers Alexander Vögler Robert H. Cameron Christoph U. Keller Manfred Schüssler Max-Planck-Institute.
Magnetic activity in protoplanetary discs Mark Wardle Macquarie University Sydney, Australia Catherine Braiding (Macquarie) Arieh Königl (Chicago) BP Pandey.
LES of Turbulent Flows: Lecture 2 (ME EN )
Dynamo theory and magneto-rotational instability Axel Brandenburg (Nordita) seed field primordial (decay) diagnostic interest (CMB) AGN outflows MRI driven.
Large Scale Dynamo Action in MRI Disks Role of stratification Dynamo cycles Mean-field interpretation Incoherent alpha-shear dynamo Axel Brandenburg (Nordita,
Direct simulation of planetary and stellar dynamos II. Future challenges (maintenance of differential rotation) Gary A Glatzmaier University of California,
Catastrophic  -quenching alleviated by helicity flux and shear Axel Brandenburg (Nordita, Copenhagen) Christer Sandin (Uppsala) Collaborators: Eric G.
Astrophysical Magnetism Axel Brandenburg (Nordita, Stockholm)
Measurements in Fluid Mechanics 058:180:001 (ME:5180:0001) Time & Location: 2:30P - 3:20P MWF 218 MLH Office Hours: 4:00P – 5:00P MWF 223B-5 HL Instructor:
Magnetohydrodynamic simulations of stellar differential rotation and meridional circulation (submitted to A&A, arXiv: ) Bidya Binay Karak (Nordita.
MHD Dynamo Simulation by GeoFEM Hiroaki Matsui Research Organization for Informatuion Science & Technology(RIST), JAPAN 3rd ACES Workshop May, 5, 2002.
1 Direct Numerical Simulation of Compressible Turbulent Flows with Weighted Non-Linear Compact Schemes Alfred Gessow Rotorcraft Center Aerospace Engineering.
Numerical simulations of astrophysical dynamos Axel Brandenburg (Nordita, Stockholm) Dynamos: numerical issues Alpha dynamos do exist: linear and nonlinear.
Large scale simulations of astrophysical turbulence Axel Brandenburg (Nordita, Copenhagen) Wolfgang Dobler (Univ. Calgary) Anders Johansen (MPIA, Heidelberg)
Numerical simulations of the SN driven ISM Axel Brandenburg (NORDITA, Copenhagen, Denmark) Boris Gudiksen (Stockholm Observatory, Sweden) Graeme Sarson.
MHD in weakly-ionised media Mark Wardle Macquarie University Sydney, Australia.
High-order codes for astrophysical turbulence
Astrobiology, homochirality, and origin of life
Self-assembly of shallow magnetic spots through strongly stratified turbulence Axel Brandenburg (Nordita/Stockholm) Kemel+12 Brandenburg+13 Warnecke+11.
Simple Radiative Transfer in Decomposed Domains Tobi Heinemann Åke Nordlund Axel Brandenburg Wolfgang Dobler.
Self-organized magnetic structures in computational astrophysics Axel Brandenburg (Nordita/Stockholm) Kemel+12 Ilonidis+11Brandenburg+13Warnecke+11 Käpylä+12.
Dynamo action in shear flow turbulence Axel Brandenburg (Nordita, Copenhagen) Collaborators: Nils Erland Haugen (Univ. Trondheim) Wolfgang Dobler (Freiburg.
Turbulent transport coefficients from numerical experiments Axel Brandenburg & Matthias Rheinhardt (Nordita, Stockholm) Extracting concepts from grand.
ANGULAR MOMENTUM TRANSPORT BY MAGNETOHYDRODYNAMIC TURBULENCE Gordon Ogilvie University of Cambridge TACHOCLINE DYNAMICS
Turbulence research at Nordita 1.Bottleneck effect 2.Magnetic fields (active vector) 3.Passive scalar diffusion Haugen & Brandenburg (2006, Phys. Fl. 18,
Prandtl number dependence of magnetic-to-kinetic dissipation 1.What gets in, will get out 2.Even for vanishing viscosity 3.What if magnetic fields 4. contribute?
Application of Compact- Reconstruction WENO Schemes to the Navier-Stokes Equations Alfred Gessow Rotorcraft Center Aerospace Engineering Department University.
GOAL: To understand the physics of active region decay, and the Quiet Sun network APPROACH: Use physics-based numerical models to simulate the dynamic.
Turbulence & dynamos Axel Brandenburg (Nordita/Stockholm) Kemel+12 Ilonidis+11Brandenburg+11Warnecke+11 Käpylä+12.
THE DYNAMIC EVOLUTION OF TWISTED MAGNETIC FLUX TUBES IN A THREE-DIMENSIONALCONVECTING FLOW. II. TURBULENT PUMPING AND THE COHESION OF Ω-LOOPS.
TC303 Antenna & Propagation
Physical conditions in astrophysics Axel Brandenburg (Nordita/Stockholm) Kemel+12 Ilonidis+11Brandenburg+11Warnecke+11 Käpylä+12.
Overview of dynamos in stars and galaxies
Simulations and radiative diagnostics of turbulence and wave phenomena in the magnetised solar photosphere S. Shelyag Astrophysics Research Centre Queen’s.
Numerical Simulations of Solar Magneto-Convection
Convergence in Computational Science
Large scale simulations of astrophysical turbulence
Non linear evolution of 3D magnetic reconnection in slab geometry
Energy spectra of small scale dynamos with large Reynolds numbers
Catastrophic a-quenching alleviated by helicity flux and shear
Presentation transcript:

Pencil Code: multi-purpose and multi-user maintained Axel Brandenburg (Nordita, Stockholm) Wolfgang Dobler (Univ. Calgary) and now many more…. (...just google for Pencil Code)

Pencil Code Started in Sept with Wolfgang Dobler High order (6 th order in space, 3 rd order in time) Cache & memory efficient MPI, can run PacxMPI (across countries!) Maintained/developed by ~40 people (SVN) Automatic validation (over night or any time) Max resolution so far , 4096 procs Isotropic turbulence –MHD, passive scl, CR Stratified layers –Convection, radiation Shearing box –MRI, dust, interstellar –Self-gravity Sphere embedded in box –Fully convective stars –geodynamo Other applications –Homochirality –Spherical coordinates

3 Pencil formulation In CRAY days: worked with full chunks f(nx,ny,nz,nvar) –Now, on SGI, nearly 100% cache misses Instead work with f(nx,nvar), i.e. one nx-pencil No cache misses, negligible work space, just 2N –Can keep all components of derivative tensors Communication before sub-timestep Then evaluate all derivatives, e.g. call curl(f,iA,B) –Vector potential A=f(:,:,:,iAx:iAz), B=B(nx,3)

4 Switch modules magnetic or nomagnetic (e.g. just hydro) hydro or nohydro (e.g. kinematic dynamo) density or nodensity (burgulence) entropy or noentropy (e.g. isothermal) radiation or noradiation (solar convection, discs) dustvelocity or nodustvelocity (planetesimals) Coagulation, reaction equations Chemistry (reaction-diffusion-advection equations) Other physics modules: MHD, radiation, partial ionization, chemical reactions, selfgravity

5 High-order schemes Alternative to spectral or compact schemes –Efficiently parallelized, no transpose necessary –No restriction on boundary conditions –Curvilinear coordinates possible (except for singularities) 6th order central differences in space Non-conservative scheme –Allows use of logarithmic density and entropy –Copes well with strong stratification and temperature contrasts

6 (i) High-order spatial schemes Main advantage: low phase errors x x x x x x x x x Near boundaries: ghost zonesinterior points

7 Wavenumber characteristics

8 Higher order – less viscosity

9 Less viscosity – also in shocks

10 (ii) High-order temporal schemes Main advantage: low amplitude errors 3 rd order 2 nd order 1 st order 2N-RK3 scheme (Williamson 1980)

11 Shock tube test

12 Increase in # of auto tests

13 Evolution of code size User meetings: 2005 Copenhagen 2006 Copenhagen 2007 Stockholm 2008 Leiden 2009 Heidelberg

14 Pencil Code check-ins

15 Vector potential B=curlA, advantage: divB=0 J=curlB=curl(curlA) =curl2A Not a disadvantage: consider Alfven waves B-formulation A-formulation 2 nd der once is better than 1 st der twice!

16 Comparison of A and B methods

17 Faster and bigger machines

processor run at

19 Hyperviscous, Smagorinsky, normal Inertial range unaffected by artificial diffusion Haugen & Brandenburg (PRE, astro-ph/ ) height of bottleneck increased onset of bottleneck at same position

20 Online data reduction and visualization non-helically forced turbulence

21 Scalars on periphery of the box

22 MRI turbulence MRI = magnetorotational instability w/o hypervisc. t = 600 = 20 orbits w/o hypervisc.  t = 60 = 2 orbits

23 Vorticity and Density See poster by Tobi Heinemann on density wave excitation!