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Draft: update gray-scott example to use paraview catalyst with fides #54

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Draft: update gray-scott example to use paraview catalyst with fides #54

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65 changes: 65 additions & 0 deletions Tutorial/gray-scott/README.md
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Expand Up @@ -146,3 +146,68 @@ $ mpirun -n 4 build/gray-scott simulation/settings-staging.json : \
-n 1 python3 plot/gsplot.py -i gs.bp
```


## In situ batch visualization with ParaView Catalyst

This requires ADIOS 2.8.0 or later, due to the use of `ParaViewFidesEngine` plugin for ADIOS.
Internally, this plugin uses the ADIOS inline engine to pass data pointers to ParaView's
[Fides](https://fides.readthedocs.io/en/latest/) reader
and uses ParaView [Catalyst](https://catalyst-in-situ.readthedocs.io/en/latest/index.html)
to process a user python script that contains a ParaView pipeline.
Fides is a library that provides a schema for reading ADIOS data into visualization services
such as ParaView. By integrating it with ParaView Catalyst, it is now possible to perform
in situ visualization with ADIOS2-enabled codes without writing adaptors. All that is needed
from the user is a simple JSON file describing the data.


`simulation/settings-inline.json` uses the `adios2-inline-plugin.xml` configuration file.
It sets the engine type to `plugin` and provides the `PluginName` and `PluginLibrary`
parameters required when using engine plugins. In addition, you will need to set the
environment variable `ADIOS2_PLUGIN_PATH` to contain the path to the `libADIOSInSituPlugin.so`
shared library built by ParaView.

In the `catalyst` dir, there is a `gs-fides.json`, which is the data model Fides uses to read the data.
The `gs-pipeline.py` contains the pipeline Catalyst will execute on each step.
These files are passed as parameters to the engine plugin (see parameters `DataModel` and `Script` in
the `adios2-inline-plugin.xml` file).


### Build and Run

This example is built as normal (making sure you are using ADIOS v2.8.0 or later)
and does not have build dependencies on ParaView.

The changes for this example are not yet in ParaView, but you can use the following instructions
for grabbing the branches necessary to run:

```
$ git clone --recursive https://gitlab.kitware.com/caitlin.ross/paraview.git
$ mkdir paraview-build
$ cd paraview
$ git checkout catalyst-fides
$ cd paraview/VTK
$ git remote add caitlin.ross https://gitlab.kitware.com/caitlin.ross/vtk.git
$ git fetch caitlin.ross fides-inline-engine
$ git checkout fides-inline-engine
$ cd ../../paraview-build
```

Now we're ready to build:

```
$ cmake -GNinja -DPARAVIEW_USE_PYTHON=ON -DPARAVIEW_USE_MPI=ON -DPARAVIEW_ENABLE_FIDES=ON -DADIOS2_DIR=/path/to/adios2.8.0 -DCMAKE_BUILD_TYPE=Release ../paraview
$ ninja
```

The lib directory should contain `libADIOSInSituPlugin.so`.
Set the following env variables.
```
$ export ADIOS2_PLUGIN_PATH=/path/to/paraview-build/lib
$ export CATALYST_IMPLEMENTATION_NAME=paraview
$ export CATALYST_IMPLEMENTATION_PATHS=/path/to/paraview-build/lib/catalyst
```

To run:
```
$ mpirun -n 4 build/gray-scott simulation/settings-inline.json
```
135 changes: 135 additions & 0 deletions Tutorial/gray-scott/adios2-inline-plugin.xml
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<?xml version="1.0"?>
<adios-config>

<!--============================================
Configuration for Gray-Scott and GS Plot
============================================-->

<io name="SimulationOutput">
<engine type="plugin">
<!-- general plugin engine parameters -->
<parameter key="PluginName" value="fides"/>
<parameter key="PluginLibrary" value="ADIOSInSituPlugin"/>
<!-- ParaViewFides engine parameters -->
<parameter key="DataModel" value="catalyst/gs-fides.json"/>
<parameter key="Script" value="catalyst/gs-pipeline.py"/>
</engine>
</io>

<!--===========================================
Configuration for PDF calc and PDF Plot
===========================================-->

<io name="PDFAnalysisOutput">
<engine type="FileStream">
<!-- SST engine parameters -->
<parameter key="RendezvousReaderCount" value="1"/>
<parameter key="QueueLimit" value="5"/>
<parameter key="QueueFullPolicy" value="Block"/>
<!-- BP4/SST engine parameters -->
<parameter key="OpenTimeoutSecs" value="10.0"/>
<!-- SSC engine parameters -->
<parameter key="MaxStreamsPerApp" value="2"/>
</engine>

<!-- Compress variables -->
<!--
<variable name="U">
<operation type="sz">
<parameter key="accuracy" value="0.001"/>
</operation>
</variable>
<variable name="V">
<operation type="sz">
<parameter key="accuracy" value="0.001"/>
</operation>
</variable>
-->
</io>

<!--====================================
Configuration for isosurface,
find_blobs and render_isosurface
====================================-->

<io name="IsosurfaceOutput">
<engine type="FileStream">
</engine>
</io>

<!--================================================
Configuration for Gray-Scott (checkpointing)
================================================-->

<io name="SimulationCheckpoint">
<engine type="FileStream">
</engine>
</io>


<!-- example engines

<engine type="BPFile"/>
<engine type="BP4"/>
<engine type="HDF5"/>
<engine type="SST"/>
<engine type="InSituMPI"/>

=== SST ===
SST can be set up to force blocking the producer on a consumer
or to discard unused data. Separately, it can be also set up
so that the producer is waiting for a first connection or
just starts running alone.

Producer start alone, and it does not keep data.
Consumer will get recent data when connects.
If consumer(s) goes away, producer runs alone and
discards data.
<engine type="SST">
<parameter key="RendezvousReaderCount" value="0"/>
<parameter key="QueueLimit" value="1"/>
<parameter key="QueueFullPolicy" value="Discard"/>
</engine>

Producer will wait for 1 consumer to connect before proceeding.
Producer will buffer 5 output steps so a consumer may lag behind a bit.
If consumer(s) goes away, producer will block indefinitely after
the buffer is full.
<engine type="SST">
<parameter key="RendezvousReaderCount" value="1"/>
<parameter key="QueueLimit" value="5"/>
<parameter key="QueueFullPolicy" value="Block"/>
</engine>

=== BP4 ===
BP4 is a new file format.
'SubStreams' parameter controls how many files
are created under the output folder. By default, each process
writes its own file (N-to-N pattern), which is fast but is
not scalable to tens of thousands of processes. The number of
substreams should be chosen for the capability of the underlying
filesystem (e.g. twice the number of OST servers on a Lustre file system).
'OpenTimeoutSecs' paramter specifies how long to wait on a reading Open
for the file to appear. Useful for streaming when the reader starts up
faster than the writer produce any output.
<engine type="BPFile">
<parameter key="SubStreams" value="4"/>
<parameter key="OpenTimeoutSecs" value="10.0"/>
</engine>

=== BPFile ===
BPFile is a token name for the BP3 old file format.
It will refer to BP4 in the future.
'SubStreams' parameter is the same as for BP4.
<engine type="BPFile">
<parameter key="SubStreams" value="4"/>
</engine>

=== InSituMPI ===
One must launch producer and consumer as one MPI appliction in MPMD mode.
See Readme.md
Note: This engine does not support the high-level Python API in the plot
scripts, so it can only be used to couple the simulation and PDF calculation.
-->
</adios-config>

60 changes: 60 additions & 0 deletions Tutorial/gray-scott/catalyst/gs-fides.json
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{
"VTK-Cartesian-grid": {
"data_sources": [
{
"name": "source",
"filename_mode": "input"
}
],
"step_information": {
"data_source": "source",
"variable": "step"
},
"coordinate_system" : {
"array" : {
"array_type" : "uniform_point_coordinates",
"dimensions" : {
"source" : "variable_dimensions",
"data_source": "source",
"variable" : "U"
},
"origin" : {
"source" : "array",
"values" : [0.0, 0.0, 0.0]
},
"spacing" : {
"source" : "array",
"values" : [0.1, 0.1, 0.1]
}
}
},
"cell_set": {
"cell_set_type" : "structured",
"dimensions" : {
"source" : "variable_dimensions",
"data_source": "source",
"variable" : "U"
}
},
"fields": [
{
"name": "U",
"association": "points",
"array" : {
"array_type" : "basic",
"data_source": "source",
"variable" : "U"
}
},
{
"name": "V",
"association": "points",
"array" : {
"array_type" : "basic",
"data_source": "source",
"variable" : "V"
}
}
]
}
}
64 changes: 64 additions & 0 deletions Tutorial/gray-scott/catalyst/gs-pipeline.py
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from paraview.simple import *
from paraview import print_info

# catalyst options
from paraview.catalyst import Options
options = Options()

# print start marker
print_info("begin '%s'", __name__)

# directory under which to save all extracts
# generated using Extractors defined in the pipeline
# (optional, but recommended)
options.ExtractsOutputDirectory = '/tmp'
SaveExtractsUsingCatalystOptions(options)

view = CreateRenderView()
# when using Fides, registrationName is always 'fides'
producer = TrivialProducer(registrationName='fides')
display = Show(producer)
view.ResetCamera()
ColorBy(display, ('POINTS', 'U'))
display.RescaleTransferFunctionToDataRange(True, False)
display.SetScalarBarVisibility(view, True)
transFunc = GetColorTransferFunction('U')
transFunc.RescaleOnVisibilityChange = 1

display.SetRepresentationType('Surface')

clip = Clip(registrationName="clip1", Input=producer)
clip.ClipType = 'Plane'
clip.Scalars = ['POINTS', 'U']
clip.ClipType.Origin = [1.5, 1.5, 1.5]
clip.ClipType.Normal = [0.0, 1.0, 0.0]
clipDisplay = Show(clip, view, 'UnstructuredGridRepresentation')

Hide(producer, view)
view.ResetCamera()

camera = GetActiveCamera()
camera.Azimuth(45)
camera.Elevation(45)

# the extractor will save the view on each time step
extractor = CreateExtractor('PNG', view, registrationName='PNG1')
extractor.Writer.FileName = 'output-{timestep}.png'
extractor.Writer.ImageResolution = [800, 800]


def catalyst_execute(info):
print_info("in '%s::catalyst_execute'", __name__)
global producer
producer.UpdatePipeline()
print("updating pipeline and saving image")

#print("-----------------------------------")
#print("executing (cycle={}, time={})".format(info.cycle, info.time))
#print("bounds:", producer.GetDataInformation().GetBounds())
#print("U-range:", producer.PointData['U'].GetRange(0))
#print("V-range:", producer.PointData['V'].GetRange(0))


# print end marker
print_info("end '%s'", __name__)
19 changes: 19 additions & 0 deletions Tutorial/gray-scott/simulation/settings-inline.json
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{
"L": 64,
"Du": 0.2,
"Dv": 0.1,
"F": 0.02,
"k": 0.048,
"dt": 2.0,
"plotgap": 10,
"steps": 100,
"noise": 0.0000001,
"output": "gs.bp",
"checkpoint": false,
"checkpoint_freq": 10,
"checkpoint_output": "gs_ckpt.bp",
"adios_config": "adios2-inline-plugin.xml",
"adios_span": false,
"adios_memory_selection": false,
"mesh_type": "image"
}