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SENSEI: SoA Particle Support #3349

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merged 16 commits into from
Jul 28, 2023
Merged

SENSEI: SoA Particle Support #3349

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8fb8efc
SENSEI: SoA Particle Support
ax3l Jun 6, 2023
eca2fec
more pure SoA updates for SENSEI
atmyers Jul 12, 2023
b953d6a
add a test for sensei particles with pure SOA
atmyers Jul 12, 2023
2666988
Merge branch 'development' into topic-soa-sensei
atmyers Jul 12, 2023
be07012
fix test
atmyers Jul 12, 2023
d4cc6ff
fix test
atmyers Jul 12, 2023
9ed7e5e
only run SENSEI test if AMReX_SENSEI
atmyers Jul 12, 2023
c8e7e03
missing ;
atmyers Jul 13, 2023
6c62411
ParticleContainer -> ParticleContainer_impl
atmyers Jul 13, 2023
6d81f0d
ParIter -> ParIter_impl
atmyers Jul 13, 2023
ca4dfd0
update test
atmyers Jul 13, 2023
229017e
actually update the sensei interface to the position from the SoA if …
atmyers Jul 20, 2023
9b7662a
more fixes
atmyers Jul 20, 2023
abab8c1
more fixes
atmyers Jul 20, 2023
29aebfb
update analysis adapter execute API
atmyers Jul 20, 2023
e61689c
Merge branch 'development' into topic-soa-sensei
atmyers Jul 20, 2023
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8 changes: 4 additions & 4 deletions Src/Extern/SENSEI/AMReX_AmrMeshParticleDataAdaptor.H
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@

namespace amrex
{
template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
template<typename ParticleType, int NArrayReal, int NArrayInt>
class AmrMeshParticleDataAdaptor : public sensei::DataAdaptor
{
public:
Expand All @@ -27,7 +27,7 @@ public:
AmrMesh *mesh,
const std::vector<amrex::Vector<amrex::MultiFab>*> &mesh_states,
const std::vector<std::vector<std::string>> &mesh_names,
amrex::ParticleContainer<NStructReal, NStructInt, NArrayReal, NArrayInt> * particles,
amrex::ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt> * particles,
const std::map<std::string, std::vector<int>> & rStructs = {},
const std::map<std::string, int> & iStructs = {},
const std::map<std::string, std::vector<int>> & rArrays = {},
Expand Down Expand Up @@ -55,7 +55,7 @@ protected:
AmrMeshParticleDataAdaptor()
{
m_meshAdaptor = AmrMeshDataAdaptor::New();
m_particleAdaptor = ParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::New();
m_particleAdaptor = ParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::New();
}

~AmrMeshParticleDataAdaptor()
Expand All @@ -65,7 +65,7 @@ protected:
}

private:
ParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>* m_particleAdaptor;
ParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>* m_particleAdaptor;
AmrMeshDataAdaptor* m_meshAdaptor;

const std::string m_meshName = "mesh";
Expand Down
62 changes: 31 additions & 31 deletions Src/Extern/SENSEI/AMReX_AmrMeshParticleDataAdaptorI.H
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Original file line number Diff line number Diff line change
Expand Up @@ -3,22 +3,22 @@
namespace amrex
{
//-----------------------------------------------------------------------------
template <int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>*
AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::New()
template <typename ParticleType, int NArrayReal, int NArrayInt>
AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>*
AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::New()
{
auto result = new AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>;
auto result = new AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>;
result->InitializeObjectBase();
return result;
}

//-----------------------------------------------------------------------------
template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::SetDataSource(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::SetDataSource(
AmrMesh *mesh,
const std::vector<amrex::Vector<amrex::MultiFab>*> &mesh_states,
const std::vector<std::vector<std::string>> &mesh_names,
amrex::ParticleContainer<NStructReal, NStructInt, NArrayReal, NArrayInt> * particles,
amrex::ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt> * particles,
const std::map<std::string, std::vector<int>> & rStructs,
const std::map<std::string, int> & iStructs,
const std::map<std::string, std::vector<int>> & rArrays,
Expand All @@ -31,8 +31,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::

// SENSEI API
#if SENSEI_VERSION_MAJOR >= 3
template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetMeshMetadata(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetMeshMetadata(
unsigned int id,
sensei::MeshMetadataPtr &metadata)
{
Expand All @@ -49,8 +49,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
}

#else
template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetMeshName(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetMeshName(
unsigned int id,
std::string &meshName)
{
Expand All @@ -66,8 +66,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetMeshHasGhostNodes(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetMeshHasGhostNodes(
const std::string &meshName, int &nLayers)
{
if(id == 0)
Expand All @@ -82,8 +82,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetMeshHasGhostCells(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetMeshHasGhostCells(
const std::string &meshName, int &nLayers)
{
if(id == 0)
Expand All @@ -98,8 +98,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetNumberOfArrays(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetNumberOfArrays(
const std::string &meshName,
int association,
unsigned int &numberOfArrays)
Expand All @@ -116,8 +116,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetArrayName(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetArrayName(
const std::string &meshName,
int association,
unsigned int index,
Expand All @@ -136,16 +136,16 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
}
#endif

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetNumberOfMeshes(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetNumberOfMeshes(
unsigned int &numMeshes)
{
numMeshes = 2;
return 0;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::GetMesh(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::GetMesh(
const std::string &meshName,
bool structureOnly,
svtkDataObject *&mesh)
Expand All @@ -162,8 +162,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::AddGhostNodesArray(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::AddGhostNodesArray(
svtkDataObject* mesh,
const std::string &meshName)
{
Expand All @@ -179,8 +179,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::AddGhostCellsArray(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::AddGhostCellsArray(
svtkDataObject* mesh,
const std::string &meshName)
{
Expand All @@ -196,8 +196,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::AddArray(
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::AddArray(
svtkDataObject* mesh,
const std::string &meshName,
int association,
Expand All @@ -215,8 +215,8 @@ int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::
return -1;
}

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::ReleaseData()
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::ReleaseData()
{
this->m_particleAdaptor->ReleaseData();
this->m_meshAdaptor->ReleaseData();
Expand Down
12 changes: 6 additions & 6 deletions Src/Extern/SENSEI/AMReX_AmrMeshParticleInSituBridge.H
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Original file line number Diff line number Diff line change
Expand Up @@ -33,26 +33,26 @@ public:

// invoke the in situ analysis with data from an AmrMesh and ParticleContainer
// instance.
template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
template<typename ParticleType, int NArrayReal, int NArrayInt>
int update(
long step, double time,
amrex::AmrMesh *mesh,
const std::vector<amrex::Vector<amrex::MultiFab>*> &mesh_states,
const std::vector<std::vector<std::string>> &mesh_names,
amrex::ParticleContainer<NStructReal, NStructInt, NArrayReal, NArrayInt> * particles,
amrex::ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt> * particles,
const std::map<std::string, std::vector<int>> & particles_rStructs = {},
const std::map<std::string, int> & particles_iStructs = {},
const std::map<std::string, std::vector<int>> & particles_rArrays = {},
const std::map<std::string, int> & particles_iArrays = {});
};

template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
template<typename ParticleType, int NArrayReal, int NArrayInt>
int AmrMeshParticleInSituBridge::update(
long step, double time,
amrex::AmrMesh *mesh,
const std::vector<amrex::Vector<amrex::MultiFab>*> &mesh_states,
const std::vector<std::vector<std::string>> &mesh_names,
amrex::ParticleContainer<NStructReal, NStructInt, NArrayReal, NArrayInt> * particles,
amrex::ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt> * particles,
const std::map<std::string, std::vector<int>> & particles_rStructs,
const std::map<std::string, int> & particles_iStructs,
const std::map<std::string, std::vector<int>> & particles_rArrays,
Expand All @@ -73,8 +73,8 @@ int AmrMeshParticleInSituBridge::update(
return -1;
}

amrex::AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt> *data_adaptor
= amrex::AmrMeshParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::New();
amrex::AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt> *data_adaptor
= amrex::AmrMeshParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::New();

if (comm != MPI_COMM_NULL)
data_adaptor->SetCommunicator(comm);
Expand Down
8 changes: 4 additions & 4 deletions Src/Extern/SENSEI/AMReX_AmrParticleDataAdaptor.H
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@

namespace amrex
{
template<int NStructReal, int NStructInt, int NArrayReal, int NArrayInt>
template<typename ParticleType, int NArrayReal, int NArrayInt>
class AmrParticleDataAdaptor : public sensei::DataAdaptor
{
public:
Expand All @@ -25,7 +25,7 @@ public:

int SetDataSource(
Amr *amr,
amrex::ParticleContainer<NStructReal, NStructInt, NArrayReal, NArrayInt> * particles,
amrex::ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt> * particles,
const std::map<std::string, std::vector<int>> & rStructs = {},
const std::map<std::string, int> & iStructs = {},
const std::map<std::string, std::vector<int>> & rArrays = {},
Expand Down Expand Up @@ -53,7 +53,7 @@ protected:
AmrParticleDataAdaptor()
{
m_meshAdaptor = AmrDataAdaptor::New();
m_particleAdaptor = ParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>::New();
m_particleAdaptor = ParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>::New();
}

~AmrParticleDataAdaptor()
Expand All @@ -63,7 +63,7 @@ protected:
}

private:
ParticleDataAdaptor<NStructReal, NStructInt, NArrayReal, NArrayInt>* m_particleAdaptor;
ParticleDataAdaptor<ParticleType, NArrayReal, NArrayInt>* m_particleAdaptor;
AmrDataAdaptor* m_meshAdaptor;

const std::string m_meshName = "mesh";
Expand Down
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