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Adjust images to the new reality of dark mode and clean up
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recipe--simulator diagram.
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@thorstenhater
thorstenhater committed Dec 8, 2023
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91 changes: 53 additions & 38 deletions doc/concepts/domdec-diag-1.html
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<div class="diag-cont">
<div class="diag-cont" style="color: #202020; max-width: 100%; margin-left: 0%;">
<div id="recipe_src">Recipe
<div>Cell descriptions
<div>gid 1
<div>type <code>lif_cell_0</code>
<div>...</div>
</div>
<div>
gid 1</br>
type <code>lif_cell</code></br>
description</br>
...
</div>
<div>...</div>
<div> gid 37
<div>type <code>cable_cell_A</code>
<div>Morphology</div>
<div>Decor
<div>Mechanisms</div>
<div>Connection sites</div>
</div>
<div>Label dictionary</div>
</div>
<div>
gid 37</br>
type <code>cable_cell</code></br>
description
<ul>
<li>Morphology</li>
<li>Ion channels</li>
<li>Connection sites</li>
<li>Labels</li>
</ul>
</div>
</div>
<div>Cell kinds
<div>gid 1
<div>type <code>arbor.lif_cell</code>
</div>
</div>
<div>gid 1 <code>lif_cell</code></div>
<div>...</div>
<div>gid 37
<div>type <code>arbor.cable_cell</code></div>
</div>
</div>
<div>...
<div>gid 37 <code>cable_cell</code></div>
</div>
<div>...</div>
</div>
<div class="diag-col">

<div class="diag-col" style="width: auto;">
<div class="diag-right">
Simulator: requests cell description of <code>gid=37</code>
Simulator: kind of <code>gid=1</code>?
</div>
<div class="diag-left">
Recipe: <code>type=cable_cell_A</code>.
Recipe: <code>lif_cell</code>.
</div>
<div class="diag-right2">
...
</div>
<div class="diag-right">
Simulator: requests cell kind of <code>gid=37</code>
Simulator: kind of <code>gid=37</code>?
</div>
<div class="diag-left">
Recipe: <code>kind=arbor.cable_cell</code>.
</div>
<div class="diag-right">
Simulator: look up cell group implementation for kind <code>arbor.cable_cell</code>.
Recipe: <code>cable_cell</code>.
</div>
<div class="diag-right2">
Domain decomposition: <code>cable_cell_group_gpu</code>
Group implementations for <code>lif_cell</code>, <code>cable_cell</code></br>
Domain decomposition: <code>group-0</code>, <code>group-1</code>
</div>

<div class="diag-right">
Simulator: <code>cable_cell_group_gpu</code> construct <code>cable_cell_A</code> object.
Simulator requests cell description of <code>gid=37</code>
</div>
<div class="diag-right3">
<code>cable_cell_group_gpu</code>: Construction complete.
<div class="diag-left">
Recipe: <code>morphology, ...</code>.
</div>
<div class="diag-right2">
Simulator:</br>
<code>group-0</code> make <code>cable_cell</code></br>
<code>group-1</code> make <code>lif_cell</code>
</div>
<div class="diag-right">
Simulator: <code>cable_cell_group_gpu</code> simulate for <code>t .. t + dt</code>
Simulator:</br>
<code>group-0</code> simulate for <code>dt</code>
</br>
<code>group-1</code> simulate for <code>dt</code>
</div>
</div>
<div>Simulation
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</div>
<div id="domdec_src">Domain decomposition
<div>
cable_cell_group_gpu
<div>1 GPU</div>
<code>group-0</code></br>
kind: <code>cable</code></br>
hardware: 1 GPU</br>
gids: <code>37, ...</code>
</div>
<div>
<code>group-1</code></br>
kind: <code>lif</code></br>
hardware: 12 threads</br>
gids: <code>1, ...</code>
</div>
<div>
...
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4 changes: 2 additions & 2 deletions doc/concepts/hardware.rst
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Expand Up @@ -19,15 +19,15 @@ first, it might be instructive to see how recipes are used by Arbor:
An *allocation* enumerates the computational resources to be used for a
simulation, typically a subset of the resources available on a physical hardware
node. It also contains flags to enable thread and process `affinity
<https://en.wikipedia.org/wiki/Processor_affinity>`. When asked to set affinity,
<https://en.wikipedia.org/wiki/Processor_affinity>`_. When asked to set affinity,
Arbor will try to maximize the use of the available resources, i.e. it will
spread out processes and threads such that each gets a maximal share of compute
units and cache. Existing affinity settings will honoured, so setting it for
processes while an external mechanism (e.g. SLURM or OpenMPI) does the same is
ill advised. Threads can not be managed externally, thus requesting thread
binding is generally safe and may yield significant performance improvements for
CPU-only simulations and/or the model build phase. Affinity requires `hwloc
<https://www.open-mpi.org/projects/hwloc/>` to be found during build time.
<https://www.open-mpi.org/projects/hwloc/>`_ to be found during build time.

New users can find using contexts a little verbose. The design is very
deliberate, to allow fine-grained control over which computational resources an
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2 changes: 1 addition & 1 deletion doc/concepts/recipe-diag-1.html
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<div class="diag-cont">
<div class="diag-cont" style="color: #202020;">
<div id="recipe_src">Recipe
<div>
<input id="collapsible1" type="checkbox" checked><label for="collapsible1">Cell descriptions</label>
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11 changes: 7 additions & 4 deletions doc/ecosystem/index-sims.html
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<div class="diag-cont">
<div id="nm">Neural Mass Models
<div id="nm" style="color: #202020;">Neural Mass Models
<div>The Virtual Brain</div>
</div>
<div id="pn">Point Neurons
<div id="pn" style="color: #202020;">
Point Neurons
<div>NEST</div>
<div>BRIAN</div>
</div>
<div id="dt">Detailed Neurons
<div id="dt" style="color: #202020;">
Detailed Neurons
<div>Arbor</div>
<div>(Core)NEURON, NeuroGPU</div>
<div>GENESIS</div>
Expand All @@ -15,7 +17,8 @@
<div>jNML</div>
<div>EDEN</div>
</div>
<div id="md">Molecular Dynamics
<div id="md" style="color: #202020;">
Molecular Dynamics
<div>ALMOST</div>
<div>NAMD</div>
</div>
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12 changes: 6 additions & 6 deletions doc/static/htmldiag.css
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.diag-cont {
display: flex;
max-width: 50%;
margin: auto;
margin-left: 10%;
}
.diag-cont code {
font-family: monospace;
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background-color: rgb(195, 221, 146);
border-radius: 10px 10px 10px 0px;
float: left;
width: 75%;
width: 80%;
}
.diag-cont .diag-left2 {
border: none;
background-color: rgb(194, 146, 221);
border-radius: 10px 10px 10px 0px;
float: left;
width: 75%;
width: 80%;
}
.diag-cont .diag-right {
border: none;
background-color: rgb(221, 164, 146);
border-radius: 10px 10px 0px 10px;
float: right;
width: 75%;
width: 80%;
}
.diag-cont .diag-right2 {
border: none;
background-color: rgb(146, 151, 221);
border-radius: 10px 10px 0px 10px;
float: right;
width: 75%;
width: 80%;
}
.diag-cont .diag-right3 {
border: none;
background-color: rgb(255, 231, 196);
border-radius: 10px 10px 0px 10px;
float: right;
width: 75%;
width: 80%;
}
.diag-cont div {
border: 1px solid rgb(0, 0, 0, 0.5);
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5 changes: 3 additions & 2 deletions doc/tutorial/network_two_cells_gap_junctions_circuit.svg
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