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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="author" content="Axel Huebl et al." />
<meta name="description" content="openPMD provides naming and attribute conventions that allow to exchange particle and mesh based data from scientific simulations and experiments." />
<title>openPMD</title>
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<p>For the best experience please use the latest <b>Chrome</b>, <b>Safari</b> or
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</div>
<div class="footer">
<ul>
<li id="descriptions"> </li>
</ul>
<ul class="menu">
<li><a href="#start">Start</a></li>
<li><a href="http://dx.doi.org/10.5281/zenodo.33624" target="_blank">CC-BY 4.0</a></li>
<li><a href="https://github.com/openPMD/openPMD-standard" target="_blank" id="writtenstandard">Written Standard</a></li>
</ul>
<a rel="me" href="https://github.com/openPMD" style="display: none">GitHub</a>
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<a href="https://github.com/openPMD" style="z-index: 998;pointer-events: auto;">
<img style="position: absolute; top: 0; right: 0; border: 0;"
src="./img/fork_me_on_github.png" alt="Fork me on GitHub">
</a>
<div id="impress">
<div id="start" class="step" data-x="0" data-y="0">
<span><img style="max-width: 100%;" src="img/logo_clean_hd.png" alt="openPMD" /></span>
<span class="description">A meta-data standard</span>
</div>
<div class="step" data-x="0" data-y="0">
<span><img style="max-width: 100%;" src="img/logo_mesh_hd.png" alt="openPMD" /></span>
<span class="description">for mesh based data ...</span>
</div>
<div class="step" data-x="0" data-y="0">
<span><img style="max-width: 100%;" src="img/logo_hd.png" alt="openPMD" /></span>
<span class="description">and particle data sets.</span>
</div>
<div class="step" data-x="1000" data-y="0">
<a href="#concepts" class="selectJump" onClick="this.className += ' visited';">Basic Concepts</a>
<a href="#performance" class="selectJump" onClick="this.className += ' visited';">Optimizations & Performance</a>
<a href="#timeseries" class="selectJump" onClick="this.className += ' visited';">Time Series and further Options (upcoming slide)</a><!-- Root-Group Config -->
<a href="#tools" class="selectJump" onClick="this.className += ' visited';">Developer Tools & Processing</a><!-- example files; checker script; serial high-lvl API and parallel processing (with pyDive) -->
<a href="#edpic" class="selectJump" onClick="this.className += ' visited';">Domain-Specific Extensions</a><!-- Software that currently implements the standard -->
<a href="https://doi.org/10.5281/zenodo.822396" class="selectJump" target="_blank">Overview Poster</a><!-- PASC17 Overview Poster -->
<!--<a href="#futureplans" class="selectJump" onClick="this.className += ' visited';">Future Plans</a> patches & AMR, irregular cartesian grid, ... more mesh types if required -->
<span class="description">What are you interested in?</span>
</div>
<div id="concepts" class="step" data-x="2000" data-y="0">
<img src="img/exampleHDFview2.png" alt="Example Standard" style="width:317px;border:0;margin-bottom:35%;margin-left:35%"><!-- org: w=317px -->
<span class="description">Clean Common Structure</span>
</div>
<div class="step" data-x="2000" data-y="0">
<img src="img/exampleHDFview1.png" alt="ED-PIC Extension" style="width:317px;border:0;margin-bottom:35%;margin-left:35%">
<span class="description">... and Domain Specific Extensions</span>
</div>
<div class="step" data-x="3000" data-y="0">
<div style="margin-top:-20%"> </div><br />
<a href="https://www.olcf.ornl.gov/center-projects/adios/" style="pointer-events: auto" target="_blank">
<img src="./img/ADIOS.png" alt="ADIOS" style="max-width:45%;border:0;margin-bottom:5%" /><!-- org: w=454px -->
</a>
<a href="http://hdfgroup.org/" style="pointer-events: auto" target="_blank">
<img src="./img/hdf5.png" alt="HDF5" style="max-width:45%;border:0;margin-bottom:5%;margin-left:5%" /><!-- org: w=454px -->
</a>
<p><sup>*</sup>currently implemented, but <i>not</i> limited to</p>
<span class="description">For hierarchical, self-describing data formats.</span>
</div>
<div class="step" data-x="4000" data-y="0">
<p>How to avoid confusion between actual low-level <b><span class="dataSet">data sets</span> &
<span class="attr">attributes</span></b> (HDF5 speak), <b><span class="dataSet">variables</span> &
<span class="attr">attributes</span></b> (ADIOS speak), <b>files & <span class="group">groups/folders</span></b>
and the actual physical quantities?</p>
<span class="description">openPMD naming convention</span>
</div>
<div class="step" data-x="4000" data-y="0">
Physical quanities are <b>records</b>:
<ul>
<li>discretized vector field \(\vec F(\vec r)\) on a mesh</li>
<li>discretized scalar field \(T(\vec r)\) on a mesh</li>
<li>particle property position \(\vec r_i\)</li>
<li>...</li>
</ul>
<span class="description"><b>Record</b>: each particle property or mesh</span>
</div>
<div class="step" data-x="4000" data-y="0">
Their actual <b>components</b> are stored in (multi-dimensional) <span class="dataSet">arrays</span>
(= data sets / variables) <i>inside</i> those <b>records</b>!
<span class="description"><b>Position.x</b>: <u>not</u> a record, it's a <i>component</i></span>
</div>
<div class="step" data-x="5000" data-y="0">
Required <span class="attr">attributes</span> for each <b>record</b>:
<ul>
<li><b><span class="attr">unitSI</span>:</b> conversion factor to common unit system</li>
<li><b><span class="attr">unitDimension</span>:</b> parsable dimensionality</li>
<li><b><span class="attr">time</span> / <span class="attr">timeUnitSI</span>:</b> iteration != time</li>
</ul>
<span class="description">Attributes for all <b>records</b></span>
</div>
<div class="step" data-x="5000" data-y="0">
<b><span class="attr">unitDimension</span>:</b>
<ul>
<li>automate description of units</li>
<li>powers of the 7 (SI) base measures</li>
<li>e.g., `V/m` is length<sup>1.0</sup> mass<sup>1.0</sup> time<sup>-3.0</sup> electrical current<sup>-1.0</sup> thermodynamic temperature<sup>0.0</sup> ammount of substance<sup>0.0</sup> luminous intensity<sup>0.0</sup>: `[1.0, 1.0, -3.0, -1.0, 0.0, 0.0, 0.0]`</li>
<li><small>(if your record can be scaled in a general normalized way, choose a reference and write a note in the `comment` attribute)</small></li>
</ul>
<span class="description">Attributes for all <b>records</b></span>
</div>
<div class="step" data-x="6000" data-y="0">
Required <span class="attr">attributes</span> for each <b>mesh record</b>:
<ul>
<li>geometry (+ parameters)</li>
<li>grid: spacing, global offset, axis labels</li>
<li>data order (C/Fortran)</li>
</ul>
Required <span class="attr">attributes</span> for each <b>mesh record component</b>:
<ul>
<li>position (on grid)</li>
</ul>
<span class="description">Attributes for <b>mesh records</b></span>
</div>
<div class="step" data-x="7000" data-y="0">
Required records for each <b>particle species</b>:
<ul>
<li>position</li>
<li>position offset (can be constant)</li>
</ul>
<br />Optional:
<ul>
<li>id</li>
</ul>
<span class="description">Attributes for <b>particle records</b></span>
</div>
<div class="step" data-x="8000" data-y="0">
<b>Examples for <i>records</i></b>
<span class="description"> </span>
</div>
<div class="step" data-x="8000" data-y="1000">
electric field \(\vec E(\vec r)\):
<ul>
<li>/ <span class="group">...</span> / <span class="group">meshes</span> / <span class="group">E</span> /
<ul>
<li><span class="dataSet">x</span></li>
<li><span class="dataSet">y</span></li>
<li><span class="dataSet">z</span></li>
</ul>
</ul>
temperature \(T(\vec r)\):
<ul>
<li>/ <span class="group">...</span> / <span class="group">meshes</span> /
<ul>
<li><span class="dataSet">\(T\)</span></li>
</ul>
</ul>
<span class="description"><b>Legend:</b>
<span class="group">Group</span> /
<span class="dataSet">(multi-dim) Array</span>
</span>
</div>
<div class="step lastInSection" data-x="8000" data-y="2000">
electron position \(\vec r\):
<ul>
<li>/ <span class="group">...</span> / <span class="group">particles</span> / <span class="group">electrons</span> / <span class="group">position</span> /
<ul>
<li><span class="dataSet">x</span></li>
<li><span class="dataSet">y</span></li>
<li><span class="dataSet">z</span></li>
</ul>
</ul>
electron charge \(Q\):
<ul>
<li>/ <span class="group">...</span> / <span class="group">particles</span> / <span class="group">electrons</span>
<ul>
<li><span class="dataSet">charge</span></li>
</ul>
</ul>
<span class="description"><b>Legend:</b>
<span class="group">Group</span> /
<span class="dataSet">(1D) Array</span>
</span>
</div>
<div id="performance" class="step" data-x="9000" data-y="0">
Ok ok, I got it! But what about <b>constant components</b> in a record?
<span class="description"> </span>
</div>
<div class="step" data-x="9000" data-y="1000">
electron charge \(Q\) might be constant for all particles stored in species <b>electrons</b>:
<ul>
<li>/ <span class="group">...</span> / <span class="group">particles</span> / <span class="group">electrons</span>
<ul>
<li><span class="dataSet">charge</span> <small>← might be <i>very</i> large</small>
<ul>
<li><span class="attr">unitSI</span></li>
</ul></li>
</ul></li>
</ul>
<span class="description"><b>Legend:</b>
<span class="group">Group</span> /
<span class="dataSet">Array</span> /
<span class="attr">Attribute</span>
</span>
</div>
<div class="step" data-x="9000" data-y="1100" data-z="-200" data-rotate-x="-85">
<ul>
<li>/ <span class="group">...</span> / <span class="group">particles</span> / <span class="group">electrons</span>
<ul>
<li><span class="group">charge</span>
<ul>
<li><span class="attr">value</span> <small>← few bytes</small></li>
<li><span class="attr">shape</span></li>
<li><span class="attr">unitSI</span></li>
</ul></li>
</ul></li>
</ul>
<span class="description"><b>Legend:</b>
<span class="group">Group</span> /
<span class="dataSet">Array</span> /
<span class="attr">Attribute</span>
</span>
</div>
<div class="step" data-x="9000" data-y="1100" data-z="-1000" data-rotate-x="-85">
possible for <i>any</i> <b>record component</b>, e.g.:
<ul>
<li>/ <span class="group">...</span> / <span class="group">particles</span> / <span class="group">electrons</span>
<ul>
<li><span class="group">position</span>
<ul>
<li><span class="dataSet">x</span> + <span class="attr">unitSI</span></li>
<li><span class="dataSet">y</span> + <span class="attr">unitSI</span></li>
<li><span class="group">z</span>
<ul>
<li><span class="attr">value, shape</span>
<li><span class="attr">unitSI</span></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
<span class="description"><b>Legend:</b>
<span class="group">Group</span> /
<span class="dataSet">Array</span> /
<span class="attr">Attribute</span>
</span>
</div>
<div class="step" data-x="10000" data-y="0">
All right. But how to handle <b>Petabytes</b> of data written from thousands (-millions) of compute nodes?
<span class="description"> </span>
</div>
<div class="step" data-x="10000" data-y="1000">
<ul>
<li>parallel, community file formats: writing/reading based on MPI & MPI-I/O</li>
<li>examples:
<ul>
<li>PHDF5 <b>.h5</b> (parallel/strided, uncompressed)</li>
<li>ADIOS <b>.bp</b> (aggregated, compressed)</li>
</ul>
</li>
</ul>
<span class="description">Parallel file formats</span>
</div>
<div class="step" data-x="10000" data-y="2000">
<img src="./img/particlePatches_0.svg" alt="(Spatial) Domain Decomposition" style="width:100%;border:0;margin-bottom:1%" />
<span class="description">Particle Patches: Honor Decomposition</span>
</div>
<div class="step" data-x="10000" data-y="2000">
<img src="./img/particlePatches_1.svg" alt="(Spatial) Domain Decomposition" style="width:100%;border:0;margin-bottom:1%" />
<span class="description">Particle Patches: Disjoint Particle Sets</span>
</div>
<div class="step" data-x="10000" data-y="2000">
<img src="./img/particlePatches_2.svg" alt="(Spatial) Domain Decomposition" style="width:100%;border:0;margin-bottom:1%" />
<span class="description">Particle Patches: [Offset:Offset+Count]</span>
</div>
<div class="step" data-x="10000" data-y="2000">
<img src="./img/particlePatches_3.svg" alt="(Spatial) Domain Decomposition" style="width:100%;border:0;margin-bottom:1%" />
<span class="description">Particle Patches: (Spatial) Hyperrectangles</span>
</div>
<div class="step" data-x="11000" data-y="0">
<p>In principle and <i>everywhere<sup>*</sup></i>: a human-readable <b>comment</b> (text) attribute is encouraged for everything not covered by the standard.</p>
<br />
<p><sup>*</sup> reserved for each group and data set</p>
<span class="description"><b>Comment</b> Attribute</span>
</div>
<div class="step" data-x="11000" data-y="1000">
<p>openPMD defines a <b>minimal set</b> of attributes.</p>
<p><b>You can always add more attributes and records!</b></p>
<span class="description">openPMD is a <b>not exclusive</b></span>
</div>
<div class="step" data-x="11000" data-y="2000">
<p>openPMD defines a <b>minimal set</b> of <span class="attr">attributes</span>, e.g.</p><br />
<ul>
<li><span class="attr">openPMD</span>: identifier</li>
<li><span class="attr">basePath</span>: prefix, currently fixed to `/data/`</li>
<li><span class="attr">meshesPath</span>: relative sub-group, e.g., `meshes/`</li>
<li><span class="attr">particlesPath</span>: relative sub-group, e.g., `particles/`</li>
</ul>
<span class="description"><b>Required</b> Base Attributes for `/`</span>
</div>
<div class="step lastInSection" data-x="11000" data-y="3000">
<ul>
<li><span class="attr">author</span>: <i>My Name <[email protected]></i></li>
<li><span class="attr">software</span>: e.g., <i>PIConGPU</i></li>
<li><span class="attr">softwareVersion</span>: e.g., <i>0.1.0</i></li>
<li><span class="attr">date</span>: <i>2015-12-02 17:48:42 +0100</i></li>
</ul>
<span class="description"><b>Recommended</b> Base Attributes for `/`</span>
</div>
<div id="tools" class="step" data-x="12000" data-y="0">
Example files and creator scripts:
<pre><code class="bash">tools/ $ ./createExamples_h5.py</code></pre>
<span class="description">Developer Tools: Examples</span>
</div>
<div class="step" data-x="12000" data-y="1000">
<pre><code class="bash">$ ./checkOpenPMD_h5.py -i example.h5 --EDPIC
Warning: Attribute softwareVersion (recommended) does NOT exist in `/`!
Found 1 iteration(s)
Iteration 0 : found 2 meshes
Iteration 0 : found 1 particle species
Result: 0 Errors and 1 Warning.</code></pre>
<span class="description">Developer Tools: Checker Script</span>
</div>
<div class="step" data-x="13000" data-y="0">
Serial processing: high-level API
<ul>
<li>meta-data parsing</li>
<li>file-format independent (ADIOS & HDF5)</li>
<li>object oriented: meshes, particles & iterations</li>
</ul>
<span class="description">Developer Tools: Serial Processing</span>
</div>
<div class="step" data-x="13000" data-y="1000">
<a href="https://github.com/openPMD/openPMD-viewer" target="_blank"><b>openPMD viewer</b></a>
<ul>
<li>Python API: openPMD object aware</li>
<li>GUI: IPython Notebook (interactive, remote)</li>
<li>ideal for investigating 1-2D data (or slices)</li>
<li>modular: e.g., domain specific analysis chains</li>
</ul>
<span class="description">Developer Tools: Parallel Processing</span>
</div>
<div class="step" data-x="13000" data-y="2000">
Parallel processing I: integration in suites such as
<ul>
<li><a href="https://github.com/openPMD/openPMD-visit-plugin" target="_blank">VisIt</a>, Paraview (GUI, Python)</li>
<li><a href="https://github.com/ComputationalRadiationPhysics/libSplash" target="_blank">libSplash (C/C++)</a></li>
</ul>
<span class="description">Developer Tools: Parallel Processing</span>
</div>
<div class="step" data-x="13000" data-y="2000">
Parallel processing II: integration in parallel python processing via
<a href="https://github.com/ComputationalRadiationPhysics/pyDive" target="_blank"><b>pyDive</b></a>
<ul>
<li>numpy-like parallel access</li>
<li>read and write support</li>
<li>based on zeroMQ / Jupyter notebook</li>
</ul>
<span class="description">Developer Tools: Parallel Processing</span>
</div>
<div class="step lastInSection" data-x="13000" data-y="3000">
Common tools
<ul>
<li><a href="https://github.com/openPMD/openPMD-viewer" target="_blank"><b>openPMD-viewer</b></a> numpy-like parallel access</li>
<li>read and write support</li>
<li>GUI: Jupyter notebook widgets</li>
</ul>
<span class="description">Developer Tools: Parallel Processing</span>
</div>
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<img src="./img/extensions.png" alt="Extensions" style="max-width:95%;border:0;margin-bottom:15%" /><!-- org: w=1565px -->
<span class="description"><b>Extensions:</b> Domain-Specific Additions</span>
</div>
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Implemented by PIConGPU & Warp
<ul>
<li>electro-dynamic and electro-static PIC</li>
<li>additional attributes</li>
<li>naming conventions for records</li>
</ul>
<span class="description">The ED-PIC Extension</span>
</div>
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One could add extensions for
<ul>
<li>Experimental data: CCD images, interferograms, ...</li>
<li>Simulations: MD, FEM, ...</li>
</ul>
<span class="description">Other Domain-Specific Extensions</span>
</div>
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For future versions
<ul>
<li>record patches and AMR support</li>
<li>irregular cartesian grids</li>
<li>more mesh types: if required</li>
</ul>
<span class="description">Future Plans</span>
</div>
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