Paraview: A (novice) user perspective

Transcription

1 PARAVIEW Copenhagen Paraview: A (novice) user perspective Rony Keppens Centre for Plasma-Astrophysics, K.U.Leuven (Belgium) & FOM-Institute for Plasma Physics Rijnhuizen & Astronomical Institute, Utrecht University Solaire postgraduate school, Copenhagen 3-7 November 2008 With special thanks to collaborators: Zakaria Meliani, Peter Delmont,...

2 PARAVIEW Copenhagen Paraview: user perspective Overview of lectures Introduction on Paraview Moreland & Greenfield SC07 Tutorial basic usage illustration hands-on session Multi-D HD and MHD case studies typical use for own applications hands-on session brief summary of slightly advanced stuff (not all tried... )

3 PARAVIEW Copenhagen Paraview open-source application for handling 2D and 3D datasets free, downloadable from I will use version 3.4.0, on MacBook Pro OS X (Tiger ), Intel precompiled binary downloaded 2 months ago was I have since started basic usage: novice user several problem issues resolved 2-3 weeks ago: version from this perspective, I will mention pros/cons has a fairly long history: The ParaView project started in 2000 as a collaborative effort between Kitware Inc. and Los Alamos National Laboratory. Today, ParaView development continues as a collaboration between Kitware, Sandia National Labs, CSimSoft, Los Alamos National Lab, Army Research Lab and others.

4 PARAVIEW Copenhagen What is it designed for? designed for analyzing/visualizing large data sets in parallel large: SC07 tutorial (follows) mentions: 250M unstructured data set, up to 6 billion structured cell p.34 shows examples from 10M unstructured, 1 billion structured shock physics MHD simulations: is 8M cells (8 unknowns), has 125M as soon as you use AMR: structured unstructured!!! motivation: visualize data from grid-adaptive AMRVAC code demonstrates great potential, has been used on variety of platforms we will pay attention to the simple Paraview client application real promise is in client-server mode, where visualization and data manipulation is performed in parallel standalone mode will be sufficient for most users here!!!

5 PARAVIEW Copenhagen Info 1 Information on Paraview: website Paraview uses Visualization Toolkit (VTK) to do rendering etc. advanced usage: will need to learn some of it (avoided here) textbooks include: The visualization toolkit, VTK s users guide, Paraview guide sample books brought along, do not expect to learn much! change last year from (may 2007), some info outdated Kitware Inc organizes (non-free) courses (cfr. Peter Delmont) Paraview wiki/faq: We are working on updating the wiki paraview mailing list (searchable, fairly quick response time) Online help in Paraview GUI

6 PARAVIEW Copenhagen Info 2 Google on paraview brought up: Paraview 3 tutorial, Moreland & Greenfield (Sandia Nat. Lab.) Supercomputing 2007 (SC07): I will use this to demonstrate basic usage Tutorial for Paraview 3.2 cs.unc.edu/ taylorr/comp715/paraview3 2 Tutorial.html (outdated) tutorial for Paraview at Pittsburgh Supercomputing centre a tutorial for high school students at Barcelona (version 2.4) truja.lsi.upc.edu/movibio/soft/paraview/workshop/ I collected some PDF documents, SC07 tutorial most useful I brought data used at these tutorials along furthermore: Useful info on VTK file formats

7 PARAVIEW Copenhagen Lecture material PDF documents: in folder extra pdf documents and SC07 tot107 Paraview hansdouts.pdf augmented with these lecture sheets HTML files of second Paraview 3.2 tutorial in Tutorial3.2

8 PARAVIEW Copenhagen data files for this two-part Paraview session in paraviewdata subdirectory tutorialdata for today rhotests, hdtests, mhdtests tomorrow: self-produced data from AMRVAC for fun: extra data some figures produced with paraview in paraviewfigures a directory with/for state files (explanation follows)

9 PARAVIEW Copenhagen on startup of paraview you should obtain the following screen:

10 PARAVIEW Copenhagen Tutorial will introduce How to load visualizable data in Paraview distinction between read from file and generated by source Thus far, getting your data into Paraview is non-trivial we use VTK data formats, better may exist: requires creation of a VTK reader to plug into VTK framework I did not explore the (dis)advantages of other file formats yet... illustrate the use of filters to plot isosurfaces, the use of color tables, volume rendering, streamlines, vector plots,... illustrate the use of source objects to label plots with text how to extract data in cutting plane, along a line,... how to create figures for later use in papers very powerful use of multiple views on same data set how to realize some simple animations

11 PARAVIEW Copenhagen Specific tasks use the data file disk out ref.ex2 as described in SC07 tutorial (pages 9-25) make an animation of a spherical object using the Animation View (pages 30-31) make a movie where the sphere first uses an increasing theta range, then shrinks in radius, then grows in radius to its original size, then decreases in theta range: sphere mania try to reproduce the movie visualizing the proces of gas injected into a liquid: follows the Pittsburgh tutorial and should yield gas mania use the dataset jets*.vtu, visualize void-fraction isosurfaces (0.5) using contour, velocity field, provide descriptive text labels (use text and animate time sources), animate and save will need to use cell data to point data filter combine calculator tool, use of treshold filter, glyph filter manipulate the opacity of the contour isosurface

12 PARAVIEW Copenhagen Paraview Part II: HD and MHD tests For most users here: interest in 2D and 3D HD and MHD problems will gradually introduce more filters, options for representative data demonstrate usage in combination with AMRVAC simulations AMRVAC: see e.g. B. van der Holst & R. Keppens, 2007, JCP 226, will use data from simple (fairly low resolution) grid-adaptive runs after simulation, individual snapshots can be converted to vtu format can also postprocess to tecplotplt files, opendx files, idl input,... along the way: use of state files, saving screenshots, making movies

13 PARAVIEW Copenhagen Specific tasks II use the data from 2D and 3D advection tests to make animations for 2D: combine 2D surface view with 1D cut midway through data use scatter plot for 1D cut (play around with resolution etc) note how animation alternates the two views in computation, while eventual movie shows them simultaneous (as desired and expected) VAC mania

14 PARAVIEW Copenhagen need just to load the data, and use plot over line filter experiment with the control over line plot appearance

15 PARAVIEW Copenhagen for 3D advection test: make movie showing isosurface (change opacity), slice plane, text and time sphere mania II

16 PARAVIEW Copenhagen for 2D HD tests: start with Liska test Shocks in a box then compare the end result for 2 schemes as follows also a single snapshot of a 3D variant included

17 PARAVIEW Copenhagen for 2D HD tests: Then do WC test Shock reflection

18 PARAVIEW Copenhagen for 2D HD tests: Similar setup: Richtmeyer-Meshkov run use the calculator tool to compute entropy, pressure,...

19 PARAVIEW Copenhagen D to 3D HD tests: focus on Rayleigh-Taylor test Mixing stuff for getting streamlines: use Delaunay2D filter to remap 3D snapshot: not distributed: close to limit on my laptop (1GB data)

20 PARAVIEW Copenhagen More 2D HD tests: This time on polar (cylindrical) grid

21 PARAVIEW Copenhagen or on a spherical grid... use of transform to create a doubled image

22 PARAVIEW Copenhagen D MHD test: Play around with Orszag-tang evolution deliberately saved/run on 1 grid, so that streamlines/fieldlines can be shown

23 PARAVIEW Copenhagen D MHD tests: Play around with initial condition of space weather run use tetrahedralize for getting streamlines to function

24 PARAVIEW Copenhagen for fun: check the robot, the head scan, the ironprotein, the lobster,...

25 PARAVIEW Copenhagen So far: vtu file format produced in a postprocess step on AMRVAC data is recognized ok, data gets read in HOWEVER: when more than 1 grid (even on same grid level) used for vtu problems with streamline visualization due to insufficient insight into vtu data structure, will work to improve this has to do with lacking info on connectivity between grids (similar issue at play when using tecplot, but less severe) work-around: use filters delaunay2d and tetrahedralize for regridding NOT an issue for structured grid computations (see e.g. Orszag-Tang study) we deliberately did not mix vector/salar quantities in output easy to create vectors when (cartesian) components passed did not yet experiment greatly with div/curl on vectors always best to simply compute them in your code (known discretization errors!)

26 PARAVIEW Copenhagen PROS: use of state files to save a session, restart from it later use of save screenshot, save animation, all very straightforward use of multiple views, connected (linked) camera positions seem to have continued funding, lots of effort ongoing (SC08,... ) CONS: data file formats not easy to modify (?) scripting/filter development needs advanced knowledge of VTK dependent on (not fully updated) online info books (VTK, Paraview guide): fairly useless

27 PARAVIEW Copenhagen not yet done: use on parallel machine (but conceptually identical) then need to compile the package from source (use of CMake, Qt, CVS) according to website info (september 2008): Collaborative Visualization with ParaView: Kitware has won a 100K Phase I SBIR with the Department of Energy. The proposed work aims to develop a parallel visualization system that will enable effective multiple remote collaborations for complex analysis in a large-scale data environment. We are partnering with the Stanford Linear Accelerat Center (SLAC). We expect to commercialize this work...

28 PARAVIEW Copenhagen Some questions... How to put greek symbols as labels? How to manipulate better the line plot layout? using plot over line gives default ranges can be changed using View settings (or right mouse button shortcut) can not very easy change labels, introduce subscripts, superscripts (like in IDL) sometimes still erratic behavior (movie saving/screenshot saving) for however, most of it works very well! For data formats: would like to add some extra scalar info into the vtu files such as time (now deduced from file extension), ratio of specific heats, etc GUI documentation: sometimes missing, I have worked to correct various simple problems mixed material from to (online version is similar!) NOTE: we can give (constructive) feedback to developers...!!!