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Add md5sum filter to the outputs of the SWIFT plugin

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This commit is contained in:
Matthieu Schaller 2021-05-30 00:20:40 +02:00
parent ba3a82aea1
commit cc1709304a
2 changed files with 45 additions and 17 deletions
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42
include/HDF_IO.hh
View file

@ -887,17 +887,30 @@ inline void HDFWriteDatasetVector( const std::string Filename, const std::string
}
template< typename T >
inline void HDFCreateEmptyDataset( const std::string Filename, const std::string ObjName, const size_t num_particles)
inline void HDFCreateEmptyDataset( const std::string Filename, const std::string ObjName, const size_t num_particles, const bool filter = false)
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
HDF_Type,
HDF_Prop;
hsize_t HDF_Dims;
HDF_Prop = H5Pcreate(H5P_DATASET_CREATE);
if (filter)
{
// 1MB chunking
hsize_t HDF_Dims[1] = {1024 * 1024 / sizeof(T)};
H5Pset_chunk(HDF_Prop, 1, HDF_Dims);
// md5 checksum
H5Pset_fletcher32(HDF_Prop);
}
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
@ -905,25 +918,39 @@ inline void HDFCreateEmptyDataset( const std::string Filename, const std::string
HDF_Dims = (hsize_t) (num_particles);
HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
HDF_DataspaceID, HDF_Prop );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Pclose( HDF_Prop );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFCreateEmptyDatasetVector( const std::string Filename, const std::string ObjName, const size_t num_particles)
inline void HDFCreateEmptyDatasetVector( const std::string Filename, const std::string ObjName, const size_t num_particles, const bool filter = false)
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
HDF_Type,
HDF_Prop;
hsize_t HDF_Dims[2];
HDF_Prop = H5Pcreate(H5P_DATASET_CREATE);
if (filter)
{
// 1MB chunking
hsize_t HDF_Dims[2] = {1024 * 1024 / sizeof(T), 3};
H5Pset_chunk(HDF_Prop, 2, HDF_Dims);
// md5 checksum
H5Pset_fletcher32(HDF_Prop);
}
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
@ -933,11 +960,12 @@ inline void HDFCreateEmptyDatasetVector( const std::string Filename, const std::
HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
HDF_DataspaceID, HDF_Prop );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Pclose( HDF_Prop );
H5Fclose( HDF_FileID );
}
template< typename T >

20
src/plugins/output_swift.cc
View file

@ -262,30 +262,30 @@ public:
if (this->has_64bit_reals())
{
HDFCreateEmptyDatasetVector<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), global_num_particles);
HDFCreateEmptyDatasetVector<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), global_num_particles);
HDFCreateEmptyDatasetVector<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), global_num_particles, true);
HDFCreateEmptyDatasetVector<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), global_num_particles, true);
}
else
{
HDFCreateEmptyDatasetVector<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), global_num_particles);
HDFCreateEmptyDatasetVector<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), global_num_particles);
HDFCreateEmptyDatasetVector<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Coordinates"), global_num_particles, true);
HDFCreateEmptyDatasetVector<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Velocities"), global_num_particles, true);
}
if (this->has_64bit_ids())
HDFCreateEmptyDataset<uint64_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles);
HDFCreateEmptyDataset<uint64_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles, true);
else
HDFCreateEmptyDataset<uint32_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles);
HDFCreateEmptyDataset<uint32_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles, true);
if (this->has_64bit_reals())
HDFCreateEmptyDataset<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles);
HDFCreateEmptyDataset<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles, true);
else
HDFCreateEmptyDataset<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles);
HDFCreateEmptyDataset<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles, true);
if( bdobaryons_ && s == cosmo_species::baryon) {
// note: despite this being a constant array we still need to handle it in a distributed way
HDFCreateEmptyDataset<write_real_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/InternalEnergy"), global_num_particles);
HDFCreateEmptyDataset<write_real_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/SmoothingLength"), global_num_particles);
HDFCreateEmptyDataset<write_real_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/InternalEnergy"), global_num_particles, true);
HDFCreateEmptyDataset<write_real_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/SmoothingLength"), global_num_particles, true);
}
music::ilog << "Created empty arrays for PartType" << std::to_string(sid) << " into file " << fname_ << "." << std::endl;