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Fix particle I/O prepost #5571

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Fix particle I/O prepost #5571

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29 changes: 14 additions & 15 deletions Src/Extern/HDF5/AMReX_ParticleHDF5.H
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Original file line number Diff line number Diff line change
Expand Up @@ -453,19 +453,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
Long maxnextid = ParticleType::NextID();

for (int lev = 0; lev < std::ssize(m_particles); lev++) {
const auto& pmap = m_particles[lev];
for (const auto& kv : pmap) {
const auto& aos = kv.second.GetArrayOfStructs();
for (int k = 0; k < aos.numParticles(); ++k) {
const ParticleType& p = aos[k];
if (p.id().is_valid()) {
//
// Only count (and checkpoint) valid particles.
//
nparticles++;
}
}
}
nparticles += NumberOfParticlesAtLevel(lev, true, true);
}
ParallelDescriptor::ReduceLongSum(nparticles, IOProcNumber);

Expand Down Expand Up @@ -729,18 +717,21 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
}

#ifdef AMREX_USE_MPI
// Collect the number of mf and total size of mf from each rank
// Collect the number of non-empty grids from each rank
MPI_Allgather(&my_mfi_cnt, 1, ParallelDescriptor::Mpi_typemap<int>::type(), &(all_mfi_cnt[0]), 1,
ParallelDescriptor::Mpi_typemap<int>::type(), ParallelDescriptor::Communicator());
#else
all_mfi_cnt[0] = my_mfi_cnt;
#endif

for (int i = 0; i < ParallelDescriptor::NProcs(); i++)
total_mfi += all_mfi_cnt[i];

// Create the int data
#ifdef AMREX_USE_MPI
MPI_Allgather(&my_mfi_int_total_size, 1, ParallelDescriptor::Mpi_typemap<ULong>::type(),
&(all_mfi_int_total_size[0]), 1, ParallelDescriptor::Mpi_typemap<ULong>::type(), ParallelDescriptor::Communicator());
#else
all_mfi_cnt[0] = my_mfi_cnt;
all_mfi_int_total_size[0] = my_mfi_int_total_size;
#endif

Expand Down Expand Up @@ -1295,6 +1286,14 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
amrex::Abort(msg.c_str());
}

htri_t const has_particles = H5Lexists(grp, "nparticles_grid", H5P_DEFAULT);
if (has_particles < 0) {
amrex::Abort("ParticleContainer::RestartHDF5(): unable to check for nparticles_grid dataset");
} else if (has_particles == 0) {
H5Gclose(grp);
continue;
}

dset = H5Dopen(grp, "nparticles_grid", H5P_DEFAULT);
Vector<int> count(ngrids[lev]);
ret = H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &(count[0]));
Expand Down
14 changes: 1 addition & 13 deletions Src/Particle/AMReX_ParticleIO.H
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Original file line number Diff line number Diff line change
Expand Up @@ -460,19 +460,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator, CellAssig
Long maxnextid = ParticleType::NextID();

for (int lev = 0; lev < std::ssize(m_particles); lev++) {
const auto& pmap = m_particles[lev];
for (const auto& kv : pmap) {
const auto& aos = kv.second.GetArrayOfStructs();
for (int k = 0; k < aos.numParticles(); ++k) {
const ParticleType& p = aos[k];
if (p.id().is_valid()) {
//
// Only count (and checkpoint) valid particles.
//
nparticles++;
}
}
}
nparticles += NumberOfParticlesAtLevel(lev, true, true);
}
ParallelDescriptor::ReduceLongSum(nparticles, IOProcNumber);

Expand Down
5 changes: 5 additions & 0 deletions Tests/Particles/CheckpointRestartDualGridHDF5SOA/main.cpp
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Expand Up @@ -166,12 +166,17 @@ void test_fewer_levels ()
auto mesh2 = build_mesh(ncells, 2, max_grid_size);
MyPC pc_write(mesh2.geom, mesh2.dmap, mesh2.ba, mesh2.ref_ratio);
pc_write.SetVerbose(false);
pc_write.SetUsePrePost(true);
pc_write.InitRandom(nppc * AMREX_D_TERM(ncells, *ncells, *ncells),
iseed, pdata, /*serialize=*/false);
#ifdef AMREX_USE_HDF5
pc_write.CheckpointPreHDF5();
pc_write.CheckpointHDF5(chkdir, "particles", true, real_names, int_names);
pc_write.CheckpointPostHDF5();
#else
pc_write.CheckpointPre();
pc_write.Checkpoint(chkdir, "particles", real_names, int_names);
pc_write.CheckpointPost();
#endif

AsyncOut::Finish();
Expand Down
3 changes: 3 additions & 0 deletions Tests/Particles/CheckpointRestartSOA/inputs
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Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,6 @@ nparticlefile = 1
restart_check = 1

directory=.

# Exercise the pre/post checkpoint path for pure-SoA particles.
particles.use_prepost = 1
2 changes: 2 additions & 0 deletions Tests/Particles/CheckpointRestartSOA/main.cpp
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Expand Up @@ -134,7 +134,9 @@ void test ()

amrex::Print() << "Writing particle file [" << fname << "] ..." << '\n';

myPC.CheckpointPre();
myPC.Checkpoint(fname, "particle0", false, particle_realnames, particle_intnames);
myPC.CheckpointPost();

amrex::Print() << " done \n";
}
Expand Down
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