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Parallel Test: Declare From Some (openPMD#671)
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Declare records in MPI-parallel writes only from some ranks.
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@ax3l
ax3l authored Mar 5, 2020
1 parent 18ac98b commit 4f8c276
Showing 1 changed file with 69 additions and 49 deletions.
118 changes: 69 additions & 49 deletions test/ParallelIOTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -90,8 +90,7 @@ TEST_CASE( "parallel_multi_series_test", "[parallel]" )
allSeries.clear();
}

void write_test_zero_extent( bool fileBased, std::string file_ending, bool writeAllChunks )
{
void write_test_zero_extent( bool fileBased, std::string file_ending, bool writeAllChunks, bool declareFromAll ) {
int mpi_s{-1};
int mpi_r{-1};
MPI_Comm_size(MPI_COMM_WORLD, &mpi_s);
Expand All @@ -110,45 +109,47 @@ void write_test_zero_extent( bool fileBased, std::string file_ending, bool write
Iteration it = o.iterations[step];
it.setAttribute("yolo", "yo");

ParticleSpecies e = it.particles["e"];

/* every rank n writes n consecutive cells, increasing values
* rank 0 does a zero-extent write
* two ranks will result in {1}
* three ranks will result in {1, 2, 3}
* four ranks will result in {1, 2, 3, 4, 5, 6} */
uint64_t num_cells = ((size - 1) * (size - 1) + (size - 1)) / 2; /* (n^2 + n) / 2 */
if (num_cells == 0u) {
std::cerr << "Test can only be run with at least two ranks" << std::endl;
return;
}

std::vector<double> position_global(num_cells);
double pos{1.};
std::generate(position_global.begin(), position_global.end(), [&pos] { return pos++; });
std::shared_ptr<double> position_local(new double[rank], [](double const *p) { delete[] p; });
uint64_t offset;
if (rank != 0)
offset = ((rank - 1) * (rank - 1) + (rank - 1)) / 2;
else
offset = 0;

e["position"]["x"].resetDataset(Dataset(determineDatatype(position_local), {num_cells}));

std::vector<uint64_t> positionOffset_global(num_cells);
uint64_t posOff{1};
std::generate(positionOffset_global.begin(), positionOffset_global.end(), [&posOff] { return posOff++; });
std::shared_ptr<uint64_t> positionOffset_local(new uint64_t[rank], [](uint64_t const *p) { delete[] p; });

e["positionOffset"]["x"].resetDataset(Dataset(determineDatatype(positionOffset_local), {num_cells}));

for (uint64_t i = 0; i < rank; ++i) {
position_local.get()[i] = position_global[offset + i];
positionOffset_local.get()[i] = positionOffset_global[offset + i];
}
if (rank != 0 || writeAllChunks) {
e["position"]["x"].storeChunk(position_local, {offset}, {rank});
e["positionOffset"]["x"].storeChunk(positionOffset_local, {offset}, {rank});
if( rank != 0 || declareFromAll ) {
ParticleSpecies e = it.particles["e"];

/* every rank n writes n consecutive cells, increasing values
* rank 0 does a zero-extent write
* two ranks will result in {1}
* three ranks will result in {1, 2, 3}
* four ranks will result in {1, 2, 3, 4, 5, 6} */
uint64_t num_cells = ((size - 1) * (size - 1) + (size - 1)) / 2; /* (n^2 + n) / 2 */
if (num_cells == 0u) {
std::cerr << "Test can only be run with at least two ranks" << std::endl;
return;
}

std::vector<double> position_global(num_cells);
double pos{1.};
std::generate(position_global.begin(), position_global.end(), [&pos] { return pos++; });
std::shared_ptr<double> position_local(new double[rank], [](double const *p) { delete[] p; });
uint64_t offset;
if (rank != 0)
offset = ((rank - 1) * (rank - 1) + (rank - 1)) / 2;
else
offset = 0;

e["position"]["x"].resetDataset(Dataset(determineDatatype(position_local), {num_cells}));

std::vector<uint64_t> positionOffset_global(num_cells);
uint64_t posOff{1};
std::generate(positionOffset_global.begin(), positionOffset_global.end(), [&posOff] { return posOff++; });
std::shared_ptr<uint64_t> positionOffset_local(new uint64_t[rank], [](uint64_t const *p) { delete[] p; });

e["positionOffset"]["x"].resetDataset(Dataset(determineDatatype(positionOffset_local), {num_cells}));

for (uint64_t i = 0; i < rank; ++i) {
position_local.get()[i] = position_global[offset + i];
positionOffset_local.get()[i] = positionOffset_global[offset + i];
}
if (rank != 0 || writeAllChunks) {
e["position"]["x"].storeChunk(position_local, {offset}, {rank});
e["positionOffset"]["x"].storeChunk(positionOffset_local, {offset}, {rank});
}
}
o.flush();
}
Expand Down Expand Up @@ -247,8 +248,8 @@ TEST_CASE( "hdf5_write_test", "[parallel][hdf5]" )

TEST_CASE( "hdf5_write_test_zero_extent", "[parallel][hdf5]" )
{
write_test_zero_extent( false, "h5", true );
write_test_zero_extent( true, "h5", true );
write_test_zero_extent( false, "h5", true, true );
write_test_zero_extent( true, "h5", true, true );
}

TEST_CASE( "hdf5_write_test_skip_chunk", "[parallel][hdf5]" )
Expand All @@ -257,8 +258,21 @@ TEST_CASE( "hdf5_write_test_skip_chunk", "[parallel][hdf5]" )
auto const hdf5_collective = auxiliary::getEnvString( "OPENPMD_HDF5_INDEPENDENT", "ON" );
if( hdf5_collective == "ON" )
{
write_test_zero_extent( false, "h5", false );
write_test_zero_extent( true, "h5", false );
write_test_zero_extent( false, "h5", false, true );
write_test_zero_extent( true, "h5", false, true );
}
else
REQUIRE(true);
}

TEST_CASE( "hdf5_write_test_skip_declare", "[parallel][hdf5]" )
{
//! @todo add via JSON option instead of environment read
auto const hdf5_collective = auxiliary::getEnvString( "OPENPMD_HDF5_INDEPENDENT", "OFF" );
if( hdf5_collective == "ON" )
{
write_test_zero_extent( false, "h5", false, false );
write_test_zero_extent( true, "h5", false, false );
}
else
REQUIRE(true);
Expand Down Expand Up @@ -311,14 +325,20 @@ TEST_CASE( "adios_write_test", "[parallel][adios]" )

TEST_CASE( "adios_write_test_zero_extent", "[parallel][adios]" )
{
write_test_zero_extent( false, "bp", true );
write_test_zero_extent( true, "bp", true );
write_test_zero_extent( false, "bp", true, true );
write_test_zero_extent( true, "bp", true, true );
}

TEST_CASE( "adios_write_test_skip_chunk", "[parallel][adios]" )
{
write_test_zero_extent( false, "bp", false );
write_test_zero_extent( true, "bp", false );
write_test_zero_extent( false, "bp", false, true );
write_test_zero_extent( true, "bp", false, true );
}

TEST_CASE( "adios_write_test_skip_declare", "[parallel][adios]" )
{
write_test_zero_extent( false, "bp", false, false );
write_test_zero_extent( true, "bp", false, false );
}

TEST_CASE( "hzdr_adios_sample_content_test", "[parallel][adios1]" )
Expand Down

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