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Named SoA Support #4163

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merged 10 commits into from
Oct 9, 2024
Merged

Named SoA Support #4163

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9986eef
Named SoA Support
ax3l Sep 23, 2024
91785b8
more work on named SOA components
atmyers Sep 24, 2024
8a7fd21
create test
atmyers Sep 24, 2024
d6d40cd
clean up test
atmyers Sep 25, 2024
588e0c6
remove unused type alias
atmyers Sep 25, 2024
8abc2a4
clang-tidy
atmyers Sep 25, 2024
78d7db0
fix 1D and 2D
atmyers Sep 25, 2024
7676c4d
use int instead of bool in AddRealComp
atmyers Oct 2, 2024
e7a88e1
refactor default names
atmyers Oct 2, 2024
dbd9262
fix indexing bug
atmyers Oct 2, 2024
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39 changes: 32 additions & 7 deletions Src/Particle/AMReX_ParticleContainer.H
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@
#include <memory>
#include <numeric>
#include <random>
#include <string>
#include <tuple>
#include <type_traits>
#include <utility>
Expand Down Expand Up @@ -1144,7 +1145,8 @@ public:
*/
ParticleTileType& DefineAndReturnParticleTile (int lev, int grid, int tile)
{
m_particles[lev][std::make_pair(grid, tile)].define(NumRuntimeRealComps(), NumRuntimeIntComps());
m_particles[lev][std::make_pair(grid, tile)].define(NumRuntimeRealComps(), NumRuntimeIntComps(), &m_soa_rdata_names, &m_soa_idata_names);

return ParticlesAt(lev, grid, tile);
}

Expand Down Expand Up @@ -1247,10 +1249,10 @@ public:

Long superParticleSize() const { return superparticle_size; }

template <typename T,
std::enable_if_t<std::is_same_v<T,bool>,int> = 0>
void AddRealComp (T communicate=true)
void AddRealComp (std::string const & name, int communicate=1)
{
m_soa_rdata_names.push_back(name);

m_runtime_comps_defined = true;
m_num_runtime_real++;
h_redistribute_real_comp.push_back(communicate);
Expand All @@ -1270,10 +1272,15 @@ public:
}
}

template <typename T,
std::enable_if_t<std::is_same_v<T,bool>,int> = 0>
void AddIntComp (T communicate=true)
void AddRealComp (int communicate=1)
{
AddRealComp(getDefaultCompNameReal<ParticleType>(NArrayReal+m_num_runtime_real), communicate);
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zero indexed and used before m_num_runtime_real++, looks correct.

}

void AddIntComp (std::string const & name, int communicate=1)
{
m_soa_idata_names.push_back(name);

m_runtime_comps_defined = true;
m_num_runtime_int++;
h_redistribute_int_comp.push_back(communicate);
Expand All @@ -1293,6 +1300,11 @@ public:
}
}

void AddIntComp (int communicate=1)
{
AddIntComp(getDefaultCompNameInt<ParticleType>(NArrayInt+m_num_runtime_int), communicate);
}

int NumRuntimeRealComps () const { return m_num_runtime_real; }
int NumRuntimeIntComps () const { return m_num_runtime_int; }

Expand Down Expand Up @@ -1403,6 +1415,15 @@ public:
#include "AMReX_ParticlesHDF5.H"
#endif

/** Overwrite the default names for the compile-time SoA components */
void SetSoACompileTimeNames (std::vector<std::string> const & rdata_name, std::vector<std::string> const & idata_name);

/** Get the names for the real SoA components **/
std::vector<std::string> GetRealSoANames () const {return m_soa_rdata_names;}

/** Get the names for the int SoA components **/
std::vector<std::string> GetIntSoANames () const {return m_soa_idata_names;}

protected:

template <class RTYPE>
Expand Down Expand Up @@ -1435,6 +1456,10 @@ private:
size_t particle_size, superparticle_size;
int num_real_comm_comps, num_int_comm_comps;
Vector<ParticleLevel> m_particles;

// names of both compile-time and runtime Real and Int SoA data
std::vector<std::string> m_soa_rdata_names;
std::vector<std::string> m_soa_idata_names;
};

template <int T_NStructReal, int T_NStructInt, int T_NArrayReal, int T_NArrayInt, template<class> class Allocator, class CellAssignor>
Expand Down
40 changes: 37 additions & 3 deletions Src/Particle/AMReX_ParticleContainerI.H
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
#include <type_traits>
#include <AMReX_MakeParticle.H>

#include <string>
#include <type_traits>
#include <vector>


template <typename ParticleType, int NArrayReal, int NArrayInt,
template<class> class Allocator, class CellAssignor>
void
Expand Down Expand Up @@ -60,10 +64,40 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
pp.query("do_unlink", doUnlink);
pp.queryAdd("do_mem_efficient_sort", memEfficientSort);

// add default names for SoA Real and Int compile-time arguments
for (int i=0; i<NArrayReal; ++i)
{
m_soa_rdata_names.push_back(getDefaultCompNameReal<ParticleType>(i));
}
for (int i=0; i<NArrayInt; ++i)
{
m_soa_idata_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

initialized = true;
}
}

template <typename ParticleType, int NArrayReal, int NArrayInt,
template<class> class Allocator, class CellAssignor>
void
ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssignor> :: SetSoACompileTimeNames (
std::vector<std::string> const & rdata_name, std::vector<std::string> const & idata_name
)
{
AMREX_ALWAYS_ASSERT_WITH_MESSAGE(rdata_name.size() == NArrayReal, "rdata_name must be equal to NArrayReal");
AMREX_ALWAYS_ASSERT_WITH_MESSAGE(idata_name.size() == NArrayInt, "idata_name must be equal to NArrayInt");

for (int i=0; i<NArrayReal; ++i)
{
m_soa_rdata_names.at(i) = rdata_name.at(i);
}
for (int i=0; i<NArrayInt; ++i)
{
m_soa_idata_names.at(i) = idata_name.at(i);
}
}

template <typename ParticleType, int NArrayReal, int NArrayInt,
template<class> class Allocator, class CellAssignor>
template <typename P, typename Assignor>
Expand Down Expand Up @@ -1161,7 +1195,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
}
} else {
ParticleTileType ptile_tmp;
ptile_tmp.define(m_num_runtime_real, m_num_runtime_int);
ptile_tmp.define(m_num_runtime_real, m_num_runtime_int, &m_soa_rdata_names, &m_soa_idata_names);
ptile_tmp.resize(np_total);
// copy re-ordered particles
gatherParticles(ptile_tmp, ptile, np, permutations);
Expand Down Expand Up @@ -1498,7 +1532,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
tmp_local[lev][index].resize(num_threads);
soa_local[lev][index].resize(num_threads);
for (int t = 0; t < num_threads; ++t) {
soa_local[lev][index][t].define(m_num_runtime_real, m_num_runtime_int);
soa_local[lev][index][t].define(m_num_runtime_real, m_num_runtime_int, &m_soa_rdata_names, &m_soa_idata_names);
}
}
}
Expand Down
70 changes: 23 additions & 47 deletions Src/Particle/AMReX_ParticleIO.H
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Original file line number Diff line number Diff line change
Expand Up @@ -51,20 +51,18 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
{
Vector<int> write_real_comp;
Vector<std::string> tmp_real_comp_names;
int nrc = ParticleType::is_soa_particle ? NStructReal + NumRealComps() - AMREX_SPACEDIM : NStructReal + NumRealComps();

for (int i = 0; i < nrc; ++i )
int first_rcomp = ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0;
for (int i = first_rcomp; i < NStructReal + NumRealComps(); ++i )
{
write_real_comp.push_back(1);
if (real_comp_names.empty())
{
std::stringstream ss;
ss << "real_comp" << i;
tmp_real_comp_names.push_back(ss.str());
tmp_real_comp_names.push_back(getDefaultCompNameReal<ParticleType>(i));
}
else
{
tmp_real_comp_names.push_back(real_comp_names[i]);
tmp_real_comp_names.push_back(real_comp_names[i-first_rcomp]);
}
}

Expand All @@ -75,9 +73,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
write_int_comp.push_back(1);
if (int_comp_names.empty())
{
std::stringstream ss;
ss << "int_comp" << i;
tmp_int_comp_names.push_back(ss.str());
tmp_int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}
else
{
Expand All @@ -98,24 +94,20 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
{
Vector<int> write_real_comp;
Vector<std::string> real_comp_names;
int nrc = ParticleType::is_soa_particle ? NStructReal + NumRealComps() - AMREX_SPACEDIM : NStructReal + NumRealComps();

for (int i = 0; i < nrc; ++i )
int first_rcomp = ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0;
for (int i = first_rcomp; i < NStructReal + NumRealComps(); ++i )
{
write_real_comp.push_back(1);
std::stringstream ss;
ss << "real_comp" << i;
real_comp_names.push_back(ss.str());
real_comp_names.push_back(getDefaultCompNameReal<ParticleType>(i));
}

Vector<int> write_int_comp;
Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
{
write_int_comp.push_back(1);
std::stringstream ss;
ss << "int_comp" << i;
int_comp_names.push_back(ss.str());
int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

WriteBinaryParticleData(dir, name, write_real_comp, write_int_comp,
Expand Down Expand Up @@ -182,9 +174,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
{
std::stringstream ss;
ss << "int_comp" << i;
int_comp_names.push_back(ss.str());
int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

WriteBinaryParticleData(dir, name,
Expand All @@ -211,20 +201,16 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
AMREX_ASSERT(write_int_comp.size() == NStructInt + NArrayInt );

Vector<std::string> real_comp_names;
int nrc = ParticleType::is_soa_particle ? NStructReal + NumRealComps() - AMREX_SPACEDIM : NStructReal + NumRealComps();
for (int i = 0; i < nrc; ++i )
int first_rcomp = ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0;
for (int i = first_rcomp; i < NStructReal + NumRealComps(); ++i )
{
std::stringstream ss;
ss << "real_comp" << i;
real_comp_names.push_back(ss.str());
real_comp_names.push_back(getDefaultCompNameReal<ParticleType>(i));
}

Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
{
std::stringstream ss;
ss << "int_comp" << i;
int_comp_names.push_back(ss.str());
int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

WriteBinaryParticleData(dir, name, write_real_comp, write_int_comp,
Expand Down Expand Up @@ -259,24 +245,20 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
{
Vector<int> write_real_comp;
Vector<std::string> real_comp_names;
int nrc = ParticleType::is_soa_particle ? NStructReal + NumRealComps() - AMREX_SPACEDIM : NStructReal + NumRealComps();

for (int i = 0; i < nrc; ++i )
int first_rcomp = ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0;
for (int i = first_rcomp; i < NStructReal + NumRealComps(); ++i )
{
write_real_comp.push_back(1);
std::stringstream ss;
ss << "real_comp" << i;
real_comp_names.push_back(ss.str());
real_comp_names.push_back(getDefaultCompNameReal<ParticleType>(i));
}

Vector<int> write_int_comp;
Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
{
write_int_comp.push_back(1);
std::stringstream ss;
ss << "int_comp" << i;
int_comp_names.push_back(ss.str());
int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

WriteBinaryParticleData(dir, name, write_real_comp, write_int_comp,
Expand Down Expand Up @@ -345,9 +327,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
{
std::stringstream ss;
ss << "int_comp" << i;
int_comp_names.push_back(ss.str());
int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

WriteBinaryParticleData(dir, name,
Expand All @@ -374,20 +354,16 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
AMREX_ASSERT(write_int_comp.size() == NStructInt + NumIntComps() );

Vector<std::string> real_comp_names;
int nrc = ParticleType::is_soa_particle ? NStructReal + NumRealComps() - AMREX_SPACEDIM : NStructReal + NumRealComps();
for (int i = 0; i < nrc; ++i )
int first_rcomp = ParticleType::is_soa_particle ? AMREX_SPACEDIM : 0;
for (int i = first_rcomp; i < NStructReal + NumRealComps(); ++i )
{
std::stringstream ss;
ss << "real_comp" << i;
real_comp_names.push_back(ss.str());
real_comp_names.push_back(getDefaultCompNameReal<ParticleType>(i));
}

Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
{
std::stringstream ss;
ss << "int_comp" << i;
int_comp_names.push_back(ss.str());
int_comp_names.push_back(getDefaultCompNameInt<ParticleType>(i));
}

WriteBinaryParticleData(dir, name, write_real_comp, write_int_comp,
Expand Down
12 changes: 10 additions & 2 deletions Src/Particle/AMReX_ParticleTile.H
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,10 @@
#include <AMReX_RealVect.H>

#include <array>
#include <string>
#include <type_traits>
#include <vector>


namespace amrex {

Expand Down Expand Up @@ -730,10 +733,15 @@ struct ParticleTile
ParticleTile& operator= (ParticleTile &&) noexcept = default;
#endif

void define (int a_num_runtime_real, int a_num_runtime_int)
void define (
int a_num_runtime_real,
int a_num_runtime_int,
std::vector<std::string>* soa_rdata_names=nullptr,
std::vector<std::string>* soa_idata_names=nullptr
)
{
m_defined = true;
GetStructOfArrays().define(a_num_runtime_real, a_num_runtime_int);
GetStructOfArrays().define(a_num_runtime_real, a_num_runtime_int, soa_rdata_names, soa_idata_names);
m_runtime_r_ptrs.resize(a_num_runtime_real);
m_runtime_i_ptrs.resize(a_num_runtime_int);
m_runtime_r_cptrs.resize(a_num_runtime_real);
Expand Down
20 changes: 20 additions & 0 deletions Src/Particle/AMReX_ParticleUtil.H
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Original file line number Diff line number Diff line change
Expand Up @@ -883,6 +883,26 @@ void PermutationForDeposition (Gpu::DeviceVector<index_type>& perm, index_type n
});
}

template <typename P>
std::string getDefaultCompNameReal (const int i) {
int first_r_name = 0;
if constexpr (P::is_soa_particle) {
if (i < AMREX_SPACEDIM) {
constexpr int x_in_ascii = 120;
std::string const name{char(x_in_ascii+i)};
return name;
}
first_r_name = AMREX_SPACEDIM;
}
std::string const name{("real_comp" + std::to_string(i-first_r_name))};
return name;
}

template <typename P>
std::string getDefaultCompNameInt (const int i) {
std::string const name{("int_comp" + std::to_string(i))};
return name;
}

#ifdef AMREX_USE_HDF5_ASYNC
void async_vol_es_wait_particle();
Expand Down
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