Skip to content

Commit

Permalink
use_swap option
Browse files Browse the repository at this point in the history
  • Loading branch information
@Angelyr
Angelyr committed Sep 7, 2023
1 parent 5d8d984 commit 2068f76
Show file tree
Hide file tree
Showing 2 changed files with 52 additions and 46 deletions.
10 changes: 7 additions & 3 deletions particle_structs/src/cabm/cabm.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,8 @@ namespace pumipic {
kkLidView offsets;
// parent elements for each SoA
kkLidView parentElms_;
// True: use aosoa_swap when rebuiling
bool use_swap;
// particle data
AoSoA_t* aosoa_;
// extra AoSoA copy for swapping (same size as aosoa_)
Expand Down Expand Up @@ -156,6 +158,7 @@ namespace pumipic {
if(!comm_rank)
fprintf(stderr, "building CabM\n");

use_swap = false;
// build view of offsets for SoA indices within particle elements
offsets = buildOffset(particles_per_element, num_ptcls, extra_padding, padding_start);
// set num_soa_ from the last entry of offsets
Expand All @@ -164,7 +167,7 @@ namespace pumipic {
capacity_ = num_soa_*AoSoA_t::vector_length;
// initialize appropriately-sized AoSoA and copy for swapping
aosoa_ = makeAoSoA(capacity_, num_soa_);
aosoa_swap = makeAoSoA(capacity_, num_soa_);
if (use_swap) aosoa_swap = makeAoSoA(capacity_, num_soa_);
// get array of parents element indices for particles
parentElms_ = getParentElms(num_elems, num_soa_, offsets);
// set active mask
Expand Down Expand Up @@ -198,6 +201,7 @@ namespace pumipic {
if(!comm_rank)
fprintf(stderr, "building CabM for %s\n", name.c_str());

use_swap = false;
// build view of offsets for SoA indices within particle elements
offsets = buildOffset(input.ppe, num_ptcls, extra_padding, padding_start);
// set num_soa_ from the last entry of offsets
Expand All @@ -206,7 +210,7 @@ namespace pumipic {
capacity_ = num_soa_*AoSoA_t::vector_length;
// initialize appropriately-sized AoSoA and copy for swapping
aosoa_ = makeAoSoA(capacity_, num_soa_);
aosoa_swap = makeAoSoA(capacity_, num_soa_);
if (use_swap) aosoa_swap = makeAoSoA(capacity_, num_soa_);
// get array of parents element indices for particles
parentElms_ = getParentElms(num_elems, num_soa_, offsets);
// set active mask
Expand All @@ -224,7 +228,7 @@ namespace pumipic {
template <class DataTypes, typename MemSpace>
CabM<DataTypes, MemSpace>::~CabM() {
delete aosoa_;
delete aosoa_swap;
if (use_swap) delete aosoa_swap;
}

/**
Expand Down
88 changes: 45 additions & 43 deletions particle_structs/src/cabm/cabm_rebuild.hpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ namespace pumipic {
Kokkos::atomic_increment<lid_t>(&elmDegree_d(parent));
else // count particles to be deleted
Kokkos::atomic_increment<lid_t>(&num_removed_d(0));
}
}
};
Cabana::SimdPolicy<soa_len,execution_space> simd_policy(0, capacity_);
Cabana::simd_parallel_for(simd_policy, atomic, "atomic");
Expand All @@ -65,16 +65,17 @@ namespace pumipic {
AoSoA_t* newAosoa;
lid_t newCapacity;
if (newNumSoa > num_soa_) { // if need extra space, update
swap = false;
newOffset_d = buildOffset(elmDegree_d, num_ptcls-num_removed+num_new_ptcls, extra_padding, padding_start);
newNumSoa = getLastValue(newOffset_d);
newCapacity = newNumSoa*soa_len;
delete aosoa_swap;
newAosoa = makeAoSoA(newCapacity, newNumSoa);
swap = false;
newOffset_d = buildOffset(elmDegree_d, num_ptcls-num_removed+num_new_ptcls, extra_padding, padding_start);
newNumSoa = getLastValue(newOffset_d);
newCapacity = newNumSoa*soa_len;
if (use_swap) delete aosoa_swap;
newAosoa = makeAoSoA(newCapacity, newNumSoa);
} else { // if we don't need extra space
swap = true;
newCapacity = capacity_;
newAosoa = aosoa_swap;
swap = true;
newCapacity = capacity_;
if (use_swap) newAosoa = aosoa_swap;
else newAosoa = makeAoSoA(newCapacity, newNumSoa);
}

RecordTime(name + " move/destroy setup", setup_timer.seconds());
Expand All @@ -84,33 +85,34 @@ namespace pumipic {
AoSoA_t aosoa_copy = *aosoa_; // copy of member variable aosoa_ (necessary, Kokkos doesn't like member variables)
AoSoA_t newAosoa_copy = *newAosoa;
auto copyPtcls = KOKKOS_LAMBDA(const lid_t& soa, const lid_t& tuple) {
const lid_t destParent = new_element(soa*soa_len + tuple);
if (active.access(soa,tuple) && destParent != -1) {
// Compute the destSoa based on the destParent and an array of
// counters for each destParent tracking which particle is the next
// free position. Use atomic fetch and incriment with the
// 'elmPtclCounter_d' array.
const lid_t occupiedTuples = Kokkos::atomic_fetch_add(&elmPtclCounter_d(destParent), 1);
// use newOffset_d to figure out which soa is the first for destParent
const lid_t firstSoa = newOffset_d(destParent);
const lid_t destSoa = firstSoa + occupiedTuples/soa_len;
const lid_t destTuple = occupiedTuples%soa_len;
Cabana::Impl::tupleCopy(
newAosoa_copy.access(destSoa), destTuple, // dest
aosoa_copy.access(soa), tuple); // src
}
const lid_t destParent = new_element(soa*soa_len + tuple);
if (active.access(soa,tuple) && destParent != -1) {
// Compute the destSoa based on the destParent and an array of
// counters for each destParent tracking which particle is the next
// free position. Use atomic fetch and incriment with the
// 'elmPtclCounter_d' array.
const lid_t occupiedTuples = Kokkos::atomic_fetch_add(&elmPtclCounter_d(destParent), 1);
// use newOffset_d to figure out which soa is the first for destParent
const lid_t firstSoa = newOffset_d(destParent);
const lid_t destSoa = firstSoa + occupiedTuples/soa_len;
const lid_t destTuple = occupiedTuples%soa_len;
Cabana::Impl::tupleCopy(
newAosoa_copy.access(destSoa), destTuple, // dest
aosoa_copy.access(soa), tuple); // src
}
};
Cabana::simd_parallel_for(simd_policy, copyPtcls, "copyPtcls");

// swap the old aosoa and use the new one in the CabanaM object
if (swap) {
auto temp = aosoa_;
aosoa_ = newAosoa;
aosoa_swap = temp;
auto temp = aosoa_;
aosoa_ = newAosoa;
if (use_swap) aosoa_swap = temp;
else delete temp;
} else { // destroy old aosoas and make new ones
delete aosoa_;
aosoa_ = newAosoa;
aosoa_swap = makeAoSoA(newCapacity, newNumSoa);
delete aosoa_;
aosoa_ = newAosoa;
if (use_swap) aosoa_swap = makeAoSoA(newCapacity, newNumSoa);
}
// update member variables (note that these are set before particle addition)
num_soa_ = newNumSoa;
Expand All @@ -125,18 +127,18 @@ namespace pumipic {

// add new particles
if (num_new_ptcls > 0 && new_particles != NULL) {
kkLidView offsets_cpy = offsets; // copy of offsets (necessary, Kokkos doesn't like member variables)
// calculate SoA and ptcl in SoA indices for next CopyMTVsToAoSoA
kkLidView soa_indices(Kokkos::ViewAllocateWithoutInitializing("soa_indices"), num_new_ptcls);
kkLidView soa_ptcl_indices(Kokkos::ViewAllocateWithoutInitializing("soa_ptcl_indices"), num_new_ptcls);
Kokkos::parallel_for("soa_and_ptcl", num_new_ptcls,
KOKKOS_LAMBDA(const lid_t ptcl) {
soa_indices(ptcl) = offsets_cpy(new_particle_elements(ptcl))
+ (particle_indices(ptcl)/soa_len);
soa_ptcl_indices(ptcl) = particle_indices(ptcl)%soa_len;
});
CopyMTVsToAoSoA<CabM<DataTypes, MemSpace>, DataTypes>(*aosoa_, new_particles,
soa_indices, soa_ptcl_indices); // copy data over
kkLidView offsets_cpy = offsets; // copy of offsets (necessary, Kokkos doesn't like member variables)
// calculate SoA and ptcl in SoA indices for next CopyMTVsToAoSoA
kkLidView soa_indices(Kokkos::ViewAllocateWithoutInitializing("soa_indices"), num_new_ptcls);
kkLidView soa_ptcl_indices(Kokkos::ViewAllocateWithoutInitializing("soa_ptcl_indices"), num_new_ptcls);
Kokkos::parallel_for("soa_and_ptcl", num_new_ptcls,
KOKKOS_LAMBDA(const lid_t ptcl) {
soa_indices(ptcl) = offsets_cpy(new_particle_elements(ptcl))
+ (particle_indices(ptcl)/soa_len);
soa_ptcl_indices(ptcl) = particle_indices(ptcl)%soa_len;
});
CopyMTVsToAoSoA<CabM<DataTypes, MemSpace>, DataTypes>(*aosoa_, new_particles,
soa_indices, soa_ptcl_indices); // copy data over
}

RecordTime(name + " add particles", add_timer.seconds());
Expand Down

0 comments on commit 2068f76

Please sign in to comment.