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Merge pull request #309 from C0nsultant/topic/zero-extent_write
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Handle zero-extent dataset creation and dataset write
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@C0nsultant
C0nsultant authored Aug 27, 2018
2 parents 1e9c220 + cdd16de commit 2ae60d7
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Showing 4 changed files with 140 additions and 1 deletion.
6 changes: 6 additions & 0 deletions src/RecordComponent.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
#include "openPMD/RecordComponent.hpp"
#include "openPMD/Dataset.hpp"

#include <algorithm>
#include <iostream>


Expand All @@ -47,6 +48,11 @@ RecordComponent::resetDataset(Dataset d)
{
if( written )
throw std::runtime_error("A Records Dataset can not (yet) be changed after it has been written.");
if( d.extent.empty() )
throw std::runtime_error("Dataset extent must be at least 1D.");
if( std::any_of(d.extent.begin(), d.extent.end(),
[](Extent::value_type const& i) { return i == 0u; }) )
throw std::runtime_error("Dataset extent must not be zero in any dimension.");

*m_dataset = d;
dirty = true;
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7 changes: 7 additions & 0 deletions src/backend/PatchRecordComponent.cpp
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Expand Up @@ -21,6 +21,8 @@
#include "openPMD/auxiliary/Memory.hpp"
#include "openPMD/backend/PatchRecordComponent.hpp"

#include <algorithm>


namespace openPMD
{
Expand All @@ -36,6 +38,11 @@ PatchRecordComponent::resetDataset(Dataset d)
{
if( written )
throw std::runtime_error("A Records Dataset can not (yet) be changed after it has been written.");
if( d.extent.empty() )
throw std::runtime_error("Dataset extent must be at least 1D.");
if( std::any_of(d.extent.begin(), d.extent.end(),
[](Extent::value_type const& i) { return i == 0u; }) )
throw std::runtime_error("Dataset extent must not be zero in any dimension.");

*m_dataset = d;
dirty = true;
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20 changes: 19 additions & 1 deletion test/CoreTest.cpp
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Expand Up @@ -618,4 +618,22 @@ TEST_CASE( "empty_record_test", "[core]" )
Catch::Equals("A Record can not be written without any contained RecordComponents: E"));
o.iterations[1].meshes["E"][RecordComponent::SCALAR].resetDataset(Dataset(Datatype::DOUBLE, {1}));
o.flush();
}
}

TEST_CASE( "zero_extent_component", "[core]" )
{
Series o = Series("./new_openpmd_output", AccessType::CREATE);

auto E_x = o.iterations[1].meshes["E"]["x"];
E_x.setComment("Datasets with zero extent in any dimension are not allowed.");
REQUIRE_THROWS_WITH(E_x.resetDataset(Dataset(Datatype::INT64, {0})),
Catch::Equals("Dataset extent must not be zero in any dimension."));
REQUIRE_THROWS_WITH(E_x.resetDataset(Dataset(Datatype::INT64, {1, 0})),
Catch::Equals("Dataset extent must not be zero in any dimension."));
REQUIRE_THROWS_WITH(E_x.resetDataset(Dataset(Datatype::INT64, {0, 1})),
Catch::Equals("Dataset extent must not be zero in any dimension."));
E_x.setComment("Datasets must contain dimensions.");
REQUIRE_THROWS_WITH(E_x.resetDataset(Dataset(Datatype::INT64, {})),
Catch::Equals("Dataset extent must be at least 1D."));
E_x.resetDataset(Dataset(Datatype::DOUBLE, {1}));
}
108 changes: 108 additions & 0 deletions test/ParallelIOTest.cpp
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Expand Up @@ -140,6 +140,60 @@ TEST_CASE( "hdf5_write_test", "[parallel][hdf5]" )

o.flush();
}

TEST_CASE( "hdf5_write_test_zero_extent", "[parallel][hdf5]" )
{
int mpi_s{-1};
int mpi_r{-1};
MPI_Comm_size(MPI_COMM_WORLD, &mpi_s);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_r);
uint64_t size = static_cast<uint64_t>(mpi_s);
uint64_t rank = static_cast<uint64_t>(mpi_r);
Series o = Series("../samples/parallel_write_zero_extent.h5", AccessType::CREATE, MPI_COMM_WORLD);

ParticleSpecies& e = o.iterations[1].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]);
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]);

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];
}
e["position"]["x"].storeChunk({offset}, {rank}, position_local);
e["positionOffset"]["x"].storeChunk({offset}, {rank}, positionOffset_local);

//TODO read back, verify
}
#else
TEST_CASE( "no_parallel_hdf5", "[parallel][hdf5]" )
{
Expand Down Expand Up @@ -182,6 +236,60 @@ TEST_CASE( "adios_write_test", "[parallel][adios]" )
o.flush();
}

TEST_CASE( "adios_write_test_zero_extent", "[parallel][adios]" )
{
int mpi_s{-1};
int mpi_r{-1};
MPI_Comm_size(MPI_COMM_WORLD, &mpi_s);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_r);
uint64_t size = static_cast<uint64_t>(mpi_s);
uint64_t rank = static_cast<uint64_t>(mpi_r);
Series o = Series("../samples/parallel_write_zero_extent.bp", AccessType::CREATE, MPI_COMM_WORLD);

ParticleSpecies& e = o.iterations[1].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]);
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]);

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];
}
e["position"]["x"].storeChunk({offset}, {rank}, position_local);
e["positionOffset"]["x"].storeChunk({offset}, {rank}, positionOffset_local);

//TODO read back, verify
}

TEST_CASE( "hzdr_adios_sample_content_test", "[parallel][adios1]" )
{
int mpi_rank{-1};
Expand Down

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