Scienti c Visualization - Einstein Toolkit c Visualization ... C++ code heart with autogenerated interface code ... much freedom in expressions

Scientific Visualization

Scientific Visualization

Dr. Tanja BodeCenter for Relativistic Astrophysics, Georgia Tech

Tanja Bode Scientific Visualization 5. April 2012

Scientific Visualization ET Output Overview

Now that your simulation runs, how do you get somethingmeaningful out of it?

Data Output Pipelines

Cactus & Carpet Output Utils for GFs and GAs

Info: Runtime reductions of GFs included in the stdout.Scalar/0D: Reductions of GFs1D/2D/3D: Subsets of GFs

Direct Thorn Output

Any other type of output, e.g. AHFinderDirect BH data.

Visualization Tools

ASCII Output: gnuplot, ygraph, xgraph, matplotlib, ...

HDF5 Output: VisIt


Scientific Visualization ET Output Overview

Now that your simulation runs, how do you get somethingmeaningful out of it?

Data Output Pipelines

Cactus & Carpet Output Utils for GFs and GAs

Info: Runtime reductions of GFs included in the stdout.Scalar/0D: Reductions of GFs1D/2D/3D: Subsets of GFs

Direct Thorn Output

Any other type of output, e.g. AHFinderDirect BH data.

Visualization Tools

ASCII Output: gnuplot, ygraph, xgraph, matplotlib, ...

HDF5 Output: VisIt


Scientific Visualization Data: Thorn-Specific Output

Thorn-Specific Output

Players: AHFinderDirect, Multipole, ...

Pros:1 More compact or convenient datafile formats2 Reduce postprocessing: Runtime calculations and data organization

Cons:1 Writing own I/O interface2 Be careful of scheduling!


Scientific Visualization Data: Cactus & Carpet

Overview of Cactus & Carpet Output

Thorns IO* & CarpetIO* include the capabilities for:

Standard OutputCheckpointingFilereader

Check what, if any, output to write at the end of each timestep

Gridfunctions, Gridfunctions, Gridfunctions, ... and Grid Arrays



Reductions (Scalars)

Available for both screen (”Info”) and scalar output

Type specified by CarpetIOScalar::outScalar reductions orIOBasic::outScalar reductions

Options include count, minimum, maximum, sum, average, norm2

Output Files of form <thorn>::<variable/group>.<reduction>.asc



Reductions (Scalars)

Gnuplot tips: http://t16web.lanl.gov/Kawano/gnuplot/index-e.html


http://t16web.lanl.gov/Kawano/gnuplot/index-e.html


1D Data – Lines

Output line parameters *IOASCII::out1d *

Buffer zones, ghost zones, and boundary points→ Know what you’re looking at!

Output Files of form <thorn>::<variable/group>.[xyzd].asc

Information overload! (Unless you’re debugging)

# 1:it 2:tl 3:rl 4:c 5:ml 6:ix 7:iy 8:iz 9:time 10:x 11:y 12:z

13:data



1D Data – Lines

Brief offline foray into 1D animations with ygraph

Useful for debugging, but requires postprocessing scripts



2D Data – Planes or 2d Grid Arrays

Up to 3 simultaneous 2d planes (xy / xz / yz)

Output Files of form <thorn>::<variable/group>.(xy,xz,yz).asc

Grid arrays can use this pipeline

2D ASCII output for GFs is discouraged ...

Files get very big!Files get very big!Gnuplot can handle nice surface plots (via e.g. pm3d) ...

We can do better ....



Hierarchical Data Format 5 (HDF5)

File format containings groups and datasets with attributes.

tbode6@CRA:$ h5ls rho.xy.h5HYDROBASE::rho it=0 tl=0 rl=0 c=22 Dataset 27, 25HYDROBASE::rho it=0 tl=0 rl=0 c=23 Dataset 27, 28HYDROBASE::rho it=0 tl=0 rl=0 c=24 Dataset 27, 25...HYDROBASE::rho it=1 tl=0 rl=8 c=88 Dataset 19, 21HYDROBASE::rho it=1 tl=0 rl=8 c=89 Dataset 19, 20HYDROBASE::rho it=1 tl=0 rl=8 c=9 Dataset 19, 20Parameters and Global Attributes Group

Careful!

HDF5 files are by nature easy to corrupt. If metadata I/O errors, entiredata file can become useless.



Hierarchical Data Format 5 (HDF5)

During builds, simfactory also builds any utilities intoCactus/exe/<config>

Some key tools to working with HDF5 data

h5ls: Lists contents of HDF5 datah5dump: Like cat, dumps entire file contents to stdouthdf5 extract: Extract a dataset fromhdf5 slicer: Take a 2d slice from 3d output filehdf5 merge: Combine files (e.g. to combine variables or data fromchained runs)

Checkpointing is done in HDF5!


Scientific Visualization Visualization – 2D & 3D

VisIt

Developed since 2000 by DOE’s Advanced Simulation and ComputingInitiative for terascale simulation data

Features:

It’s open source and free under the BSD license

Supports a large variety of formats (reader for Carpet is available separately)

Parallel compute engine support (distributed support as well)

Plot Scalar, Vector, or Tensor quantities

Allows remote access to files (don’t have to bring them locally!)

Python interface allows incorporating into scripts (e.g. for generatinganimations)

Also have C++ and Java support

Available and supported on clusters such as TACC’s Spur VisualizationCluster

Extendable via plug-ins if you’re adventurous to add ... C++ code heart

with autogenerated interface code


Scientific Visualization Visualization – 2D & 3D

VisIt

Basic Usage Concepts:

1 Open a database (file), whether it’s local or not

2 Create a plot object for variable or expression (e.g., Pseudocolor, Volume)

3 Add Operators to the plot

Box – Restrict to subregionElevate – Create surface plot from pseudocolor plotReflect – Fill in for missing imaginationThreshold – Consider a range of data, ignoring the rest completely

4 Queries are possible (e.g. min/max for automating colorscales/heights)

5 Iterating through ”states” (time)

6 Save Plots

Allows multiple plots, comparing data in different files, much freedom inexpressions ....


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Scienti c Visualization - Einstein Toolkit c Visualization ... C++ code heart with autogenerated interface code ... much freedom in expressions