1. Getting Started

For this, we will go through an example.

1.0. Setting up the Gray-Scott Test

Gray-Scott is a 7-point 3D stencil code for modeling the chemical diffusion of two substances.

git clone https://github.com/pnorbert/adiosvm.git
cd adiosvm/Tutorial/grey-scott
spack load adios2
mkdir build
cd build
cmake ../ -DCMAKE_BUILD_TYPE=Release
make -j8

1.1. Add COEUS to ADIOS

Modify the adios2.xml to replace all tags with the following snippet.

<engine type="Plugin">
    <parameter key="PluginName" value="/tmp/myFile.bp" />
    <parameter key="PluginLibrary" value="hermes_engine" />
    <!-- any parameters needed for your plugin can be added here in the parameter tag -->
</engine>

NOTE: /tmp/myFile.bp can be wherever you would like to put the output data for this file.

The resulting file should look as follows:

<?xml version="1.0"?>
<adios-config>
    <!--============================================
           Configuration for Gray-Scott and GS Plot
        ============================================-->

    <io name="SimulationOutput">
      <engine type="Plugin">
        <parameter key="PluginName" value="/tmp/myFile.bp" />
        <parameter key="PluginLibrary" value="hermes_engine" />
        <!-- any parameters needed for your plugin can be added here in the parameter tag -->
      </engine>
    </io>

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

    <io name="PDFAnalysisOutput">
      <engine type="Plugin">
        <parameter key="PluginName" value="/tmp/myFile.bp" />
        <parameter key="PluginLibrary" value="hermes_engine" />
        <!-- any parameters needed for your plugin can be added here in the parameter tag -->
      </engine>
    </io>

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

    <io name="IsosurfaceOutput">
      <engine type="Plugin">
        <parameter key="PluginName" value="/tmp/myFile.bp" />
        <parameter key="PluginLibrary" value="hermes_engine" />
        <!-- any parameters needed for your plugin can be added here in the parameter tag -->
      </engine>
    </io>

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

    <io name="SimulationCheckpoint">
      <engine type="Plugin">
        <parameter key="PluginName" value="/tmp/myFile.bp" />
        <parameter key="PluginLibrary" value="hermes_engine" />
        <!-- any parameters needed for your plugin can be added here in the parameter tag -->
      </engine>
    </io>
</adios-config>

1.2. Run Gray-Scott

COEUS is installed as a shared library (libhermes_engine.so). If you haven't done make install or aren't using spack, COEUS will be placed under ${CMAKE_BINARY_DIR}/bin.

# NOTE: This export is not required if using spack
export LD_LIBRARY_PATH=/path/to/coeus/lib (the directory which contians libhermes_engine.so)
mpirun -n 4 build/gray-scott simulation/settings-files.json

Your output data will be placed in /tmp/myFile.bp.