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Optimizations for BP5 engine of ADIOS2: Use span-based API and avoid flushing before closing an Iteration #3200

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Optimizations for BP5 engine of ADIOS2: Use span-based API and avoid flushing before closing an Iteration #3200

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456a68a
Use span-based API where applicable
franzpoeschel Jun 23, 2022
b0f93b4
Avoid flushing before Iteration::close()
franzpoeschel Jun 24, 2022
a5de601
Revert "Avoid flushing before Iteration::close()"
franzpoeschel Jun 27, 2022
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67 changes: 26 additions & 41 deletions Source/Diagnostics/WarpXOpenPMD.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -756,14 +756,10 @@ WarpXOpenPMDPlot::DumpToFile (ParticleContainer* pc,
auto const positionComponents = detail::getParticlePositionComponentLabels();
#if defined(WARPX_DIM_RZ)
{
std::shared_ptr<amrex::ParticleReal> z(
new amrex::ParticleReal[numParticleOnTile],
[](amrex::ParticleReal const *p) { delete[] p; }
);
auto z = currSpecies["position"]["z"].storeChunk<amrex::ParticleReal>({offset}, {numParticleOnTile64});
auto zBuffer = z.currentBuffer();
for (auto i = 0; i < numParticleOnTile; i++)
z.get()[i] = aos[i].pos(1); // {0: "r", 1: "z"}
std::string const positionComponent = "z";
currSpecies["position"]["z"].storeChunk(z, {offset}, {numParticleOnTile64});
zBuffer[i] = aos[i].pos(1); // {0: "r", 1: "z"}
}

// reconstruct x and y from polar coordinates r, theta
Expand All @@ -773,47 +769,39 @@ WarpXOpenPMDPlot::DumpToFile (ParticleContainer* pc,
WARPX_ALWAYS_ASSERT_WITH_MESSAGE(int(soa.GetRealData(PIdx::theta).size()) == numParticleOnTile,
"openPMD: theta and tile size do not match");
{
std::shared_ptr< amrex::ParticleReal > x(
new amrex::ParticleReal[numParticleOnTile],
[](amrex::ParticleReal const *p){ delete[] p; }
);
std::shared_ptr< amrex::ParticleReal > y(
new amrex::ParticleReal[numParticleOnTile],
[](amrex::ParticleReal const *p){ delete[] p; }
);
auto x = currSpecies["position"]["x"].storeChunk<amrex::ParticleReal>({offset}, {numParticleOnTile64});
auto y = currSpecies["position"]["y"].storeChunk<amrex::ParticleReal>({offset}, {numParticleOnTile64});
auto xBuffer = x.currentBuffer();
auto yBuffer = y.currentBuffer();
for (auto i=0; i<numParticleOnTile; i++) {
auto const r = aos[i].pos(0); // {0: "r", 1: "z"}
x.get()[i] = r * std::cos(theta[i]);
y.get()[i] = r * std::sin(theta[i]);
xBuffer[i] = r * std::cos(theta[i]);
yBuffer[i] = r * std::sin(theta[i]);
}
currSpecies["position"]["x"].storeChunk(x, {offset}, {numParticleOnTile64});
currSpecies["position"]["y"].storeChunk(y, {offset}, {numParticleOnTile64});
}
#else
for (auto currDim = 0; currDim < AMREX_SPACEDIM; currDim++) {
std::shared_ptr<amrex::ParticleReal> curr(
new amrex::ParticleReal[numParticleOnTile],
[](amrex::ParticleReal const *p) { delete[] p; }
);
for (auto i = 0; i < numParticleOnTile; i++) {
curr.get()[i] = aos[i].pos(currDim);
}
// std::shared_ptr<amrex::ParticleReal> curr(
// new amrex::ParticleReal[numParticleOnTile],
// [](amrex::ParticleReal const *p) { delete[] p; }
// );
std::string const positionComponent = positionComponents[currDim];
currSpecies["position"][positionComponent].storeChunk(curr, {offset},
auto curr = currSpecies["position"][positionComponent].storeChunk<amrex::ParticleReal>({offset},
{numParticleOnTile64});
auto currBuffer = curr.currentBuffer();
for (auto i = 0; i < numParticleOnTile; i++) {
currBuffer[i] = aos[i].pos(currDim);
}
}
#endif

// save particle ID after converting it to a globally unique ID
std::shared_ptr<uint64_t> ids(
new uint64_t[numParticleOnTile],
[](uint64_t const *p) { delete[] p; }
);
auto const scalar = openPMD::RecordComponent::SCALAR;
auto ids = currSpecies["id"][scalar].storeChunk<uint64_t>({offset}, {numParticleOnTile64});
auto idsBuffer = ids.currentBuffer();
for (auto i = 0; i < numParticleOnTile; i++) {
ids.get()[i] = ablastr::particles::localIDtoGlobal(aos[i].id(), aos[i].cpu());
idsBuffer[i] = ablastr::particles::localIDtoGlobal(aos[i].id(), aos[i].cpu());
}
auto const scalar = openPMD::RecordComponent::SCALAR;
currSpecies["id"][scalar].storeChunk(ids, {offset}, {numParticleOnTile64});

}
// save "extra" particle properties in AoS and SoA
Expand Down Expand Up @@ -932,16 +920,13 @@ WarpXOpenPMDPlot::SaveRealProperty (ParticleIter& pti,
auto currRecord = currSpecies[record_name];
auto currRecordComp = currRecord[component_name];

std::shared_ptr< amrex::ParticleReal > d(
new amrex::ParticleReal[numParticleOnTile],
[](amrex::ParticleReal const *p){ delete[] p; }
);
auto d = currRecordComp.storeChunk<amrex::ParticleReal>(
{offset}, {numParticleOnTile64});

auto dBuffer = d.currentBuffer();
for( auto kk=0; kk<numParticleOnTile; kk++ )
d.get()[kk] = aos[kk].rdata(idx);
dBuffer[kk] = aos[kk].rdata(idx);

currRecordComp.storeChunk(d,
{offset}, {numParticleOnTile64});
}
}
}
Expand Down