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Pure SoA Particle: Separate Array for IdCPU #3585

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merged 10 commits into from
Dec 11, 2023
Merged

Pure SoA Particle: Separate Array for IdCPU #3585

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741952d
[Draft] Pure SoA Particle: Separate Array for IdCPU
ax3l Oct 6, 2023
3aadc66
implement soa-style idcpu array
atmyers Dec 4, 2023
16a6792
Update Src/Particle/AMReX_StructOfArrays.H
atmyers Dec 4, 2023
e81be50
update redistribute cpu and test
atmyers Dec 7, 2023
7a7894a
Merge branch 'topic-pureSoA-separate-64bit-idcpu' of github.com:ax3l/…
atmyers Dec 7, 2023
cc5e31c
fix checkpoint/restart and initrandom
atmyers Dec 7, 2023
cfd769d
fix transformation functions to include 64 bit values if present
atmyers Dec 7, 2023
105c422
Inline Comment, Branch Order
ax3l Dec 8, 2023
cca5e92
turn off soa idcpu when not using pure soa particles
atmyers Dec 8, 2023
03e720d
Merge branch 'topic-pureSoA-separate-64bit-idcpu' of github.com:ax3l/…
atmyers Dec 8, 2023
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77 changes: 58 additions & 19 deletions Src/Particle/AMReX_ParticleContainerI.H
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
if (h_redistribute_int_comp[i]) {++num_int_comm_comps;}
}

if constexpr(!ParticleType::is_soa_particle) {
particle_size = sizeof(ParticleType);
if constexpr (ParticleType::is_soa_particle) {
particle_size = sizeof(uint64_t); // idcpu
} else {
particle_size = 0;
particle_size = sizeof(ParticleType);
}
superparticle_size = particle_size +
num_real_comm_comps*sizeof(ParticleReal) + num_int_comm_comps*sizeof(int);
Expand Down Expand Up @@ -1095,7 +1095,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
const size_t np_total = np + ptile.numNeighborParticles();

if (memEfficientSort) {
if constexpr(!ParticleType::is_soa_particle) {
if constexpr (!ParticleType::is_soa_particle) {
static_assert(sizeof(ParticleType)%4 == 0 && sizeof(uint32_t) == 4);
using tmp_t = std::conditional_t<sizeof(ParticleType)%8 == 0,
uint64_t, uint32_t>;
Expand Down Expand Up @@ -1530,7 +1530,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
unsigned npart = ptile_ptrs[pmap_it]->numParticles();
ParticleLocData pld;

if constexpr(!ParticleType::is_soa_particle){
if constexpr (!ParticleType::is_soa_particle){

if (npart != 0) {
Long last = npart - 1;
Expand Down Expand Up @@ -1647,7 +1647,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
}
}

} else{ // soa particle
} else { // soa particle

auto particle_tile = ptile_ptrs[pmap_it];
if (npart != 0) {
Expand All @@ -1663,6 +1663,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
}

if (p.id() < 0){
soa.GetIdCPUData()[pindex] = soa.GetIdCPUData()[last];
for (int comp = 0; comp < NumRealComps(); comp++) {
soa.GetRealData(comp)[pindex] = soa.GetRealData(comp)[last];
}
Expand All @@ -1679,6 +1680,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
particlePostLocate(p, pld, lev);

if (p.id() < 0) {
soa.GetIdCPUData()[pindex] = soa.GetIdCPUData()[last];
for (int comp = 0; comp < NumRealComps(); comp++) {
soa.GetRealData(comp)[pindex] = soa.GetRealData(comp)[last];
}
Expand All @@ -1696,6 +1698,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
// We own it but must shift it to another place.
auto index = std::make_pair(pld.m_grid, pld.m_tile);
AMREX_ASSERT(soa_local[pld.m_lev][index].size() == num_threads);
{
auto& arr = soa_local[pld.m_lev][index][thread_num].GetIdCPUData();
arr.push_back(soa.GetIdCPUData()[pindex]);
}
for (int comp = 0; comp < NumRealComps(); ++comp) {
RealVector& arr = soa_local[pld.m_lev][index][thread_num].GetRealData(comp);
arr.push_back(soa.GetRealData(comp)[pindex]);
Expand All @@ -1715,6 +1721,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
particles_to_send.resize(new_size);

char* dst = &particles_to_send[old_size];
{
std::memcpy(dst, &soa.GetIdCPUData()[pindex], sizeof(uint64_t));
dst += sizeof(uint64_t);
}
int array_comp_start = AMREX_SPACEDIM + NStructReal;
for (int comp = 0; comp < NumRealComps(); comp++) {
if (h_redistribute_real_comp[array_comp_start + comp]) {
Expand All @@ -1733,6 +1743,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
}

if (p.id() < 0){
soa.GetIdCPUData()[pindex] = soa.GetIdCPUData()[last];
for (int comp = 0; comp < NumRealComps(); comp++) {
soa.GetRealData(comp)[pindex] = soa.GetRealData(comp)[last];
}
Expand All @@ -1747,6 +1758,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
++pindex;
}

{
auto& iddata = soa.GetIdCPUData();
iddata.erase(iddata.begin() + last + 1, iddata.begin() + npart);
}
for (int comp = 0; comp < NumRealComps(); comp++) {
RealVector& rdata = soa.GetRealData(comp);
rdata.erase(rdata.begin() + last + 1, rdata.begin() + npart);
Expand Down Expand Up @@ -1828,6 +1843,12 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
auto& soa = ptile.GetStructOfArrays();
auto& soa_tmp = soa_local[lev][index];
for (int i = 0; i < num_threads; ++i) {
{
auto& arr = soa.GetIdCPUData();
auto& tmp = soa_tmp[i].GetIdCPUData();
arr.insert(arr.end(), tmp.begin(), tmp.end());
tmp.erase(tmp.begin(), tmp.end());
}
for (int comp = 0; comp < NumRealComps(); ++comp) {
RealVector& arr = soa.GetRealData(comp);
RealVector& tmp = soa_tmp[i].GetRealData(comp);
Expand Down Expand Up @@ -2045,20 +2066,16 @@ RedistributeMPI (std::map<int, Vector<char> >& not_ours,

Particle<NStructReal, NStructInt> p;

if constexpr (!ParticleType::is_soa_particle) {
std::memcpy(&p, pbuf, sizeof(ParticleType));
} else {
if constexpr (ParticleType::is_soa_particle) {
std::memcpy(&p.m_idcpu, pbuf, sizeof(uint64_t));

ParticleReal pos[AMREX_SPACEDIM];
std::memcpy(&pos[0], pbuf, AMREX_SPACEDIM*sizeof(ParticleReal));
std::memcpy(&pos[0], pbuf + sizeof(uint64_t), AMREX_SPACEDIM*sizeof(ParticleReal));
AMREX_D_TERM(p.pos(0) = pos[0];,
p.pos(1) = pos[1];,
p.pos(2) = pos[2]);

int idcpu[2];
std::memcpy(&idcpu[0], pbuf + NumRealComps()*sizeof(ParticleReal), 2*sizeof(int));

p.id() = idcpu[0];
p.cpu() = idcpu[1];
} else {
std::memcpy(&p, pbuf, sizeof(ParticleType));
}

bool success = Where(p, pld, lev_min, lev_max, 0);
Expand Down Expand Up @@ -2097,7 +2114,12 @@ RedistributeMPI (std::map<int, Vector<char> >& not_ours,
rcv_tile[ipart])];
char* pbuf = ((char*) &recvdata[offset]) + j*superparticle_size;

if constexpr(! ParticleType::is_soa_particle) {
if constexpr (ParticleType::is_soa_particle) {
uint64_t idcpudata;
std::memcpy(&idcpudata, pbuf, sizeof(uint64_t));
pbuf += sizeof(uint64_t);
ptile.GetStructOfArrays().GetIdCPUData().push_back(idcpudata);
} else {
ParticleType p;
std::memcpy(&p, pbuf, sizeof(ParticleType));
pbuf += sizeof(ParticleType);
Expand Down Expand Up @@ -2146,6 +2168,10 @@ RedistributeMPI (std::map<int, Vector<char> >& not_ours,
host_int_attribs.reserve(15);
host_int_attribs.resize(finestLevel()+1);

Vector<std::map<std::pair<int, int>, Gpu::HostVector<uint64_t> > > host_idcpu;
host_idcpu.reserve(15);
host_idcpu.resize(finestLevel()+1);

ipart = 0;
for (int i = 0; i < nrcvs; ++i)
{
Expand All @@ -2159,7 +2185,15 @@ RedistributeMPI (std::map<int, Vector<char> >& not_ours,

char* pbuf = ((char*) &recvdata[offset]) + j*superparticle_size;

if constexpr(! ParticleType::is_soa_particle) {
host_real_attribs[lev][ind].resize(NumRealComps());
host_int_attribs[lev][ind].resize(NumIntComps());

if constexpr (ParticleType::is_soa_particle) {
uint64_t idcpudata;
std::memcpy(&idcpudata, pbuf, sizeof(uint64_t));
pbuf += sizeof(uint64_t);
host_idcpu[lev][ind].push_back(idcpudata);
} else {
ParticleType p;
std::memcpy(&p, pbuf, sizeof(ParticleType));
pbuf += sizeof(ParticleType);
Expand Down Expand Up @@ -2210,7 +2244,12 @@ RedistributeMPI (std::map<int, Vector<char> >& not_ours,
auto new_size = old_size + src_tile.size();
dst_tile.resize(new_size);

if constexpr(! ParticleType::is_soa_particle) {
if constexpr (ParticleType::is_soa_particle) {
Gpu::copyAsync(Gpu::hostToDevice,
host_idcpu[host_lev][std::make_pair(grid,tile)].begin(),
host_idcpu[host_lev][std::make_pair(grid,tile)].end(),
dst_tile.GetStructOfArrays().GetIdCPUData().begin() + old_size);
} else {
Gpu::copyAsync(Gpu::hostToDevice,
src_tile.begin(), src_tile.end(),
dst_tile.GetArrayOfStructs().begin() + old_size);
Expand Down
14 changes: 11 additions & 3 deletions Src/Particle/AMReX_ParticleIO.H
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -964,6 +964,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
host_int_attribs.reserve(15);
host_int_attribs.resize(finest_level_in_file+1);

Vector<std::map<std::pair<int, int>, Gpu::HostVector<uint64_t> > > host_idcpu;
host_idcpu.reserve(15);
host_idcpu.resize(finestLevel()+1);

for (int i = 0; i < cnt; i++) {
// note: for pure SoA particle layouts, we do write the id, cpu and positions as a struct
// for backwards compatibility with readers
Expand Down Expand Up @@ -1031,8 +1035,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
host_real_attribs[pld.m_lev][ind][j].push_back(ptemp.pos(j));
}

host_int_attribs[pld.m_lev][ind][0].push_back(ptemp.id());
host_int_attribs[pld.m_lev][ind][1].push_back(ptemp.cpu());
host_idcpu[pld.m_lev][ind].push_back(ptemp.m_idcpu);

// read all other SoA
// add the real...
Expand All @@ -1042,7 +1045,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
}

// ... and int array data
for (int icomp = 2; icomp < NumIntComps(); icomp++) {
for (int icomp = 0; icomp < NumIntComps(); icomp++) {
host_int_attribs[lev][ind][icomp].push_back(*iptr);
++iptr;
}
Expand Down Expand Up @@ -1071,6 +1074,11 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
{
Gpu::copyAsync(Gpu::hostToDevice, src_tile.begin(), src_tile.end(),
dst_tile.GetArrayOfStructs().begin() + old_size);
} else {
Gpu::copyAsync(Gpu::hostToDevice,
host_idcpu[host_lev][std::make_pair(grid,tile)].begin(),
host_idcpu[host_lev][std::make_pair(grid,tile)].end(),
dst_tile.GetStructOfArrays().GetIdCPUData().begin() + old_size);
}

for (int i = 0; i < NumRealComps(); ++i) { // NOLINT(readability-misleading-indentation)
Expand Down
28 changes: 24 additions & 4 deletions Src/Particle/AMReX_ParticleInit.H
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1062,6 +1062,10 @@ InitRandom (Long icount,
host_int_attribs.reserve(15);
host_int_attribs.resize(finestLevel()+1);

Vector<std::map<std::pair<int, int>, Gpu::HostVector<uint64_t> > > host_idcpu;
host_idcpu.reserve(15);
host_idcpu.resize(finestLevel()+1);

for (Long j = 0; j < icount; j++)
{
Particle<0, 0> ptest;
Expand Down Expand Up @@ -1117,8 +1121,9 @@ InitRandom (Long icount,
host_real_attribs[pld.m_lev][ind][i].push_back(pos[j*AMREX_SPACEDIM+i]);
}

host_int_attribs[pld.m_lev][ind][0].push_back(ParticleType::NextID());
host_int_attribs[pld.m_lev][ind][1].push_back(MyProc);
host_idcpu[pld.m_lev][ind].push_back(0);
ParticleIDWrapper(host_idcpu[pld.m_lev][ind].back()) = ParticleType::NextID();
ParticleCPUWrapper(host_idcpu[pld.m_lev][ind].back()) = ParallelDescriptor::MyProc();

host_particles[pld.m_lev][ind];

Expand Down Expand Up @@ -1157,6 +1162,11 @@ InitRandom (Long icount,
{
Gpu::copyAsync(Gpu::hostToDevice, src_tile.begin(), src_tile.end(),
dst_tile.GetArrayOfStructs().begin() + old_size);
} else {
Gpu::copyAsync(Gpu::hostToDevice,
host_idcpu[host_lev][std::make_pair(grid,tile)].begin(),
host_idcpu[host_lev][std::make_pair(grid,tile)].end(),
dst_tile.GetStructOfArrays().GetIdCPUData().begin() + old_size);
}

for (int i = 0; i < NArrayReal; ++i) { // NOLINT(readability-misleading-indentation)
Expand Down Expand Up @@ -1201,6 +1211,10 @@ InitRandom (Long icount,
host_int_attribs.reserve(15);
host_int_attribs.resize(finestLevel()+1);

Vector<std::map<std::pair<int, int>, Gpu::HostVector<uint64_t> > > host_idcpu;
host_idcpu.reserve(15);
host_idcpu.resize(finestLevel()+1);

for (Long icnt = 0; icnt < M; icnt++) {
Particle<0, 0> ptest;
for (int i = 0; i < AMREX_SPACEDIM; i++) {
Expand Down Expand Up @@ -1261,8 +1275,9 @@ InitRandom (Long icount,
host_real_attribs[pld.m_lev][ind][i].push_back(ptest.pos(i));
}

host_int_attribs[pld.m_lev][ind][0].push_back(ptest.id());
host_int_attribs[pld.m_lev][ind][1].push_back(ptest.cpu());
host_idcpu[pld.m_lev][ind].push_back(0);
ParticleIDWrapper(host_idcpu[pld.m_lev][ind].back()) = ParticleType::NextID();
ParticleCPUWrapper(host_idcpu[pld.m_lev][ind].back()) = ParallelDescriptor::MyProc();

host_particles[pld.m_lev][ind];

Expand Down Expand Up @@ -1300,6 +1315,11 @@ InitRandom (Long icount,
{
Gpu::copyAsync(Gpu::hostToDevice, src_tile.begin(), src_tile.end(),
dst_tile.GetArrayOfStructs().begin() + old_size);
} else {
Gpu::copyAsync(Gpu::hostToDevice,
host_idcpu[host_lev][std::make_pair(grid,tile)].begin(),
host_idcpu[host_lev][std::make_pair(grid,tile)].end(),
dst_tile.GetStructOfArrays().GetIdCPUData().begin() + old_size);
}

for (int i = 0; i < NArrayReal; ++i) { // NOLINT(readability-misleading-indentation)
Expand Down
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