Scientific visualization of HPC simulation data introduction and overview on MPG projects

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1 Scientific visualization of HPC simulation data introduction and overview on MPG projects Elena Erastova, Markus Rampp, Klaus Reuter Max Planck Computing and Data Facility (MPCDF) Interdisciplinary Cluster Workshop on Visualization, Excellence Cluster Universe 2015/11/04, Garching

2 Outline Introduction Some basics on grid-based visualization techniques Visualization workhorses: ParaView and VisIt Data handling Gallery of visualization projects Summary

3 Introduction MPCDF provides visualization infrastructure and project support for the Max-Planck Society support for adaptation and instrumentation of simulation codes guidance for selection, adoption and usage of analysis & visualization software dedicated support for individual (particularly demanding) visualization projects Main challenges broad range of scientific fields: plasma physics, astrophysics, materials science, life sciences,... variety of simulation codes: in-house developments, third-party, commercial, open source, closed source integration of legacy analysis pipelines complexity of datasets generated by HPC simulations data structures and file formats: often non-standardized and heterogeneous dimensionality: multidimensional (3D + time), multi-variate data memory requirements: massive amount of raw data topology: gridded data, mesh-free data, complex coordinates,...

4 some basics on scientific visualization [wikipedia.org] Terminology: Visualization vs Rendering visualization: visual representation of data e.g. chemical structures: create a ball-and-stick model from atom positions (and compute an image or do a 3D print) rendering: generation of a 2D image from a 1, 2, 3D model e.g. create a 2D projection of a 3D balls and sticks model [visitusers.org] Popular techniques for 3D scalar fields volume rendering ray casting: follow straight lines starting from a camera model (view point), intersecting an image plane (2D grid), and hitting objects (3D model) splatting: throw voxels at 2D image plane from back to front (like snowballs ) transfer function and color table map from data space to color space, e.g. we may intuitively mimick opacity and emissivity of a gas provides qualitative and quantitative information pseudocolor plots color table maps from data space to color space 2D is straightforward, 3D requires clipping provides mostly quantitative information iso surfaces (surfaces of constant scalar value)

5 ray casting Image Camera View Ray [adapted from wikipedia.org]

6 ray tracing Image Light Source Camera View Ray Shadow Ray [blender.org] [K. Reuter] Scene Object [adapted from wikipedia.org]

7 some basics on scientific visualization (cont'd) Popular techniques for 3D vector fields colored arrow plots streamlines, streaklines, pathlines contraction to 3D scalar field vector magnitude projection [visitusers.org] [visitusers.org] colored arrow plot streamlines streamwise vorticity velocity magnitude [by courtesy of V. Avsarkisov (TU Darmstadt)]

8 some basics on scientific visualization (cont'd) Gridded vs ungridded data depending on the simulation approach, data values may be available at the vertices of a grid or at (independent) points in space gridded data (vertices connected by edges) connectivity information greatly simplifies interpolation and parallelization many of the aforementioned algorithms require gridded data topologies: unstructured, structured, rectilinear, tetrahedral, parallelization is often easiest/work best on rectilinear grids ungridded data only suitable for certain visualization algorithms ( talk by K Dolag) triangulation (eg. Delaunay) may be used to calculate a grid (expensive!)

9 Visualization tools Overview on popular software tools for scientific visualization 1D, 2D (time dependent) data: Python/SciPy/matplotlib, R, Matlab, gnuplot, IDL,... mostly conventional plotting (2D vector graphics, publication-quality) suitable to implement data processing pipelines and (automated) quantitative analysis [gnuplot.info] 3D (time dependent) data: ParaView and VisIt implement extensive toolboxes of visualization algorithms enable interactive data exploration and quantitative analysis publication-quality plots, renderings, movies main workhorses when it comes to HPC visualization

10 comprehensive open-source toolbox for scientific visualization scalable parallel architecture, implementation based on VTK, MPI and TCP/IP mature code base, but still actively developed *2000 LANL & Kitware, since 2005 Sandia & Kitware extensible via plugins (eg. data readers, data filters, in-situ connectors) controllable via Python scripting widely used well documented ParaView's architecture enabling HPC scale parallelism ParaView's graphical user interface [ [

11 comprehensive open-source toolbox for scientific visualization scalable parallel architecture, implementation based on VTK, MPI and TCP/IP mature code base, but still actively developed *2000 LLNL extensible via plugins (eg. data readers, data filters, in-situ connectors) controllable via Python scripting widely used well documented visit.llnl.gov

12 Workflow (VitIt example)

13 Data management How to get data from an HPC code into your favourite visualization tool? Criteria for selecting an IO library (and data format): performance: a parallel code requires parallel IO portability: code maturity, availability at HPC centers usability: code changes, debug options For small data sets (time series of aggregate variables) it may work to write text or binary files in a proprietary format during a code run apply a data conversion pipeline as a second step (e.g. using Python) However, for larger data sets (~ few hundred MB) this procedure is inefficient and will finally become the bottleneck. VTK ( provides among others an extensive framework to handle gridded and ungridded data of various kinds, including file formats that are compatible with ParaView and VisIt. Pro: Python bindings are helpful to implement postprocessing including format conversion. Caveat: VTK's (complex!) C++ code may be hard to integrate with existing HPC code.

14 Data management (cont'd) Software solutions for HPC MPI-IO (low-level), HDF5 (library, tools), NetCDF (library, tools) popular strategy: HDF5 for data to be visualized, raw MPI-IO or HDF5 for checkpoints future: in-situ visualization HDF5 in a nutshell Hierarchical Data Format Hierarchical Data Format (groups, dataset) correspond to POSIX (directory, file) efficient parallel IO (MPI-IO, GPFS) supported by tools such as ParaView and VisIt use XDMF to add XML grid information [

15 Data management: workflows Wrap-up: How to get data from an HPC code into your favourite visualization tool? Explicit data conversion allows some basic post-processing and/or data reduction of simulation output quick (& dirty) programming: copy/paste from I/O statements in simulation code duplication of data which format? Silo (VisIt's "proprietary" data format), HDF5, VTK,... Development of a reader plugin for VisIt or Paraview no data duplication, no additional pre-processing step plugin is dynamically loaded (code may reside in $HOME) development requires C programming and compilation against a ParaView/VisIt installation Adaptation of I/O in simulation code no data duplication, no additional preprocessing step may promote interoperability with other tools (depending on chosen format, e.g. hdfview) implications for software management (code policies, access to source code, ) which format? HDF5 (may require XDMF for metadata), VTK,...

16 Outline Introduction Some basics on grid-based visualization techniques Visualization workhorses: ParaView and VisIt Data handling Gallery of visualization projects Summary

17 MPCDF visualization projects Project selection scientific domains: plasma physics, astrophysics, CFD, molecular dynamics,... data structures/grids: regular: cartesian, polar (2D, 3D), block-structured ( Yin-Yan ) irregular: (mapped) point clouds data sizes, dimensions: up to (cartesian), (polar), (cylindrical) up to 106 particles in 3D, 107 nodes in 3D unstructured mesh multi-variable (scalar, vector), time-dependent tools: parallel HDF5 (+XDMF), VisIt, ParaView, Splotch Aims Sketch results & experiences from real-world visualization projects Answer user questions: What can be done? Can certain tools support my research?

18 Core-collapse supernova Simulations by N. Hammer, Th. Janka & E. Müller (MPA) supernova explosion of 15 Msol star first 3D simulations of long-term evolution (Hammer et al., ApJ 714, 1371, 2010) instabilities & mixing of heavy elements simulation code: PROMETHEUS/HOTB (3D hydrodynamics, finite-volume, PPM) Visualisation approach (M. Rampp, MPCDF) movie data: ( ) zones on a non-uniform, polar grid approx. 700 output files (time steps) proprietary output format was converted to VisIt's Silo format first using a simple FORTRAN code multi-channel volume-rendering (non-standard use-case for VisIt) elements Ni56, O16, C12 shine in blue, green, red gained experience with stereo rendering

19 Core-collapse supernova (cont'd) Visualization techniques using VisIt 3D Volume rendering operators: box, spherical to cartesian coordinate transform rendering algorithms: splatting (for interactive exploration), ray casting (for producing the final HQ result) movie was coded up using a Python script and then rendered non-interactively created individual image files for each of the 3 scalar variables finally applied RGB image composition using ImageMagick Quantitative analysis plots: pseudocolor operators: box, spherical to cartesian coordinate transform, isosurface, slice (2D projection)

20 Core-collapse supernova (cont'd) Quantitative analysis using VisIt plots are taken directly from Hammer et al., ApJ 714, 1371, 2010 multiple isosurfaces shed light on the morphology of the instability analyze different scalar fields in slice planes, in particular the chemical composition

21 Core-collapse supernova (another case) Simulations by Th. Janka et al. (MPA) neutrino-driven explosions of massive stars from first principles simulation code: VERTEX (3D, time-dependent radiation hydrodynamics with detailed microphysics)-first 3D simulations of long-term evolution code writes HDF5 and XDMF a spiral mode was discovered with the help of 3D visualization Visualisation approach (E. Erastova, M. Rampp) data: ( ) zones on non-uniform, polar grid approx output files (time steps) pseudo-color plots for data exploration and quantitative analysis combined volume renderings for HQ movies alternative technique: multiple, semi-transparent iso-surfaces (Melson et al. arxiv: )

22 Core-collapse supernova (cont'd) Interactive graphics with X3DOM in a web browser supplements publication of simulation results, e.g. by APJ 3D data format and object model ( X3D(OM) file export supported by Paraview, VisIT (2.10) controls: mouse enables zoom and interaction plain HTML5, no browser plugin required.x3d file export.x3d file reference

23 DNS of turbulence Simulations by L. Shi, M. Avila, B. Hof (MPI f. Dynamics and Self Organization, FAU Erlangen, IST Austria) DNS of fluids (pipe flows, Taylor-Couette flows) Code NSCOUETTE: Solves incompressible Navier Stokes equations using a pseudospectral method (Shi, Rampp, Hof, Avila, Computers and Fluids, 2015) Basic research in turbulence: lab experiments, numerical simulations, astrophysis: accretion in cold discs (Hof et al., Science, 2010, Avila et al., Science, 2011) PRACE/DECI project HYDRAD Visualisation approach (M. Rampp, L. Shi) data: ( ) zones on non-uniform, cylindrical grid approx output files (time steps) developed an I/O and visualisation strategy changes to the simulation code NSCOUETTE parallel HDF5 output of physical variables, p(θ,z,r), (uθ,uz,ur) generation of XDMF metadata and output in separate XML files visualisation with VisIt applied swap coordinates operator to transpose coordinates: (θ,z,r) (r,θ,z)

24 DNS of turbulence (cont'd) Visualization pipeline implemented using VisIt expressions: vorticity(ur,uθ,uz)= ur / z uz / r operator swap coordinates : (θ,z,r) (r,θ,z) operator transform coordinates : (r,θ,z) (x,y,z) plots: pseudocolor, volume, (+vector,...) Python code (streamwise vorticity: ur / z uz / r)

25 SPH visualization Simulations by S. Kochfahr et al. (MPE) SPH simulations produce point clouds with a strongly varying particle density (SPH's adaptive resolution ) Background: SPH "particles" sample scalar fields, particles carry size information (smoothing kernel) very limited support by standard software, specialpurpose software does not cover full spectrum of features: interactivity, slicing, quantitative analysis visualization as particles? visualization as a smooth density field

26 SPH visualization (cont'd) Visualisation approach (C. Simion, MPE and ) mapping to unstructured grids which can be handled by VisIt and Paraview approach: 3D Delaunay triangulation to create a tetrahedral mesh preserves resolution, avoids interpolation to a regular grid initially used inefficient VTK library implementation CPU time scales as N2 huge memory requirements implemented custom code using the faster Qhull library Synergies with a materials science project (FHI) principle/code was reused to analyze materials science data visualization as a smooth density field

27 SPH visualization (cont'd) Splotch is a special ray tracer to visualize SPH simulation data (without conversion). Talk by K. Dolag (LMU) this afternoon will give you all the technical details. K. Dolag, et al., New Journal of Physics, Volume 10, Issue 12, pp (2008) Code extension to tackle time-dependent visualizations of large simulation data sets (~1010 particles) (, 2011). Implemented MPI parallelization of particle handling and frame interpolation. Parallelization enabled visualization support for users at the MPE and MPA, movie rendering utilized the complete memory of the VIZ cluster at the MPCDF.

28 Geospatial data and bird migration Data by M. Wikelski (MPI for Ornithology) observational data a bird s (gull) GPS track correlated with wind data topography data, earth's magnetic field data, time-dependent data movie presented by M. Wikelski at the general assembly of the MPG, 2012 Visualisation approach ( & K. Safi, MPI-Orn., 2012) visualization with ParaView, lots of Python scripting tedious generation and optimization of camera movement better use artist's tools such as Blender? Visualization adapted to wall-projection at the hennhouse, ie. the visitors and media center MPI-Orn at Radolfzell/Bodensee.

29 Summary and Conclusions ParaView and VisIt provide (partly parallel) implementations of many state-of-the-art visualization algorithms spohisticated and mature open-source tools end-user ready strong in visualizing gridded data at HPC scale Use HDF5 (& XDMF) to implement IO, if possible Check out our visualization gallery at

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