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[WIP] openPMD: variableBased IterationEncoding #1909

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[WIP] openPMD: variableBased IterationEncoding #1909

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8126ff4
Added support to write to one file
Apr 23, 2021
0ae19c1
updated with the latest openPMD version
Apr 24, 2021
10c652e
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into 1f
Apr 24, 2021
78253db
[draft] openPMD-api: dev
ax3l Apr 24, 2021
99cfcd6
backward compatible comparison
Apr 24, 2021
56a5d36
Merge branch '1f' of https://github.com/guj/WarpX into 1f
Apr 24, 2021
e14ac05
updated openpmd_tspf to openpmd_encoding
May 18, 2021
a2f58b4
replaced binary option openpmd_tspf by openpmd_encoding, taking v/g/…
May 18, 2021
9599db0
Revolved conflict with openPMD.cmake
May 18, 2021
49ab520
fixed eol
May 18, 2021
a8d91ff
updated doc
May 19, 2021
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35 changes: 27 additions & 8 deletions Source/Diagnostics/WarpXOpenPMD.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -267,9 +267,10 @@ void WarpXOpenPMDPlot::CloseStep (bool isBTD, bool isLastBTDFlush)
// close BTD file only when isLastBTDFlush is true
if (isBTD and !isLastBTDFlush) callClose = false;
if (callClose) {
if (m_Series)
m_Series->iterations[m_CurrentStep].close();

if (m_Series) {
auto iterations = m_Series->writeIterations();
iterations[m_CurrentStep].close();
}
// create a little helper file for ParaView 5.9+
if (amrex::ParallelDescriptor::IOProcessor())
{
Expand All @@ -295,23 +296,37 @@ WarpXOpenPMDPlot::Init (openPMD::Access access, bool isBTD)
std::string filepath = m_dirPrefix;
GetFileName(filepath);

std::string useSteps = R"(
{
"adios2": {
"engine": {
"type": "bp4",
"usesteps": true
}
}
}
)";
// close a previously open series before creating a new one
// see ADIOS1 limitation: https://github.com/openPMD/openPMD-api/pull/686
m_Series = nullptr;
if (m_OneFilePerTS)
m_Series = nullptr;
else if (m_Series != nullptr)
return;

if (amrex::ParallelDescriptor::NProcs() > 1) {
#if defined(AMREX_USE_MPI)
m_Series = std::make_unique<openPMD::Series>(
filepath, access,
amrex::ParallelDescriptor::Communicator()
amrex::ParallelDescriptor::Communicator(),
useSteps
);
m_MPISize = amrex::ParallelDescriptor::NProcs();
m_MPIRank = amrex::ParallelDescriptor::MyProc();
#else
amrex::Abort("openPMD-api not built with MPI support!");
#endif
} else {
m_Series = std::make_unique<openPMD::Series>(filepath, access);
m_Series = std::make_unique<openPMD::Series>(filepath, access, useSteps);
m_MPISize = 1;
m_MPIRank = 1;
}
Expand Down Expand Up @@ -430,7 +445,9 @@ WarpXOpenPMDPlot::DumpToFile (ParticleContainer* pc,

WarpXParticleCounter counter(pc);

openPMD::Iteration currIteration = m_Series->iterations[iteration];
openPMD::WriteIterations iterations = m_Series->writeIterations();
auto currIteration = iterations[iteration];

openPMD::ParticleSpecies currSpecies = currIteration.particles[name];
// meta data for ED-PIC extension
currSpecies.setAttribute( "particleShape", double( WarpX::noz ) );
Expand Down Expand Up @@ -811,7 +828,9 @@ WarpXOpenPMDPlot::WriteOpenPMDFields ( //const std::string& filename,
auto const dataset = openPMD::Dataset(datatype, global_size);

// meta data
auto series_iteration = m_Series->iterations[iteration];
openPMD::WriteIterations iterations = m_Series->writeIterations();
auto series_iteration = iterations[iteration];

auto meshes = series_iteration.meshes;
if( first_write_to_iteration ) {
series_iteration.setTime( time );
Expand Down