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Make rank 0 create the arrays in the hdf5 file for the SWIFT i/o plugin.

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This commit is contained in:
Matthieu Schaller 2021-03-14 12:26:38 +01:00
parent 7a463aad2e
commit c1ebf38aa1
2 changed files with 94 additions and 2 deletions
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54
include/HDF_IO.hh
View file

@ -886,6 +886,60 @@ inline void HDFWriteDatasetVector( const std::string Filename, const std::string
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFCreateEmptyDataset( const std::string Filename, const std::string ObjName, const size_t num_particles)
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
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 );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFCreateEmptyDatasetVector( const std::string Filename, const std::string ObjName, const size_t num_particles)
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims[2];
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
HDF_Dims[0] = (hsize_t) (num_particles);
HDF_Dims[1] = (hsize_t) 3;
HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
inline void HDFCreateGroup( const std::string Filename, const std::string GroupName )
{
hid_t HDF_FileID, HDF_GroupID;

42
src/plugins/output_swift.cc
View file

@ -60,7 +60,7 @@ public:
// SWIFT uses a single file as IC */
num_files_ = 1;
this_rank_ = 0;
num_files_ = 1;
num_ranks_ = 1;
real_t astart = 1.0 / (1.0 + cf_.get_value<double>("setup", "zstart"));
const double rhoc = 27.7519737; // in h^2 1e10 M_sol / Mpc^3
@ -251,7 +251,45 @@ public:
else
mass_[sid] = Omega_species * munit_ / pc.get_global_num_particles();
HDFCreateGroup(fname_, std::string("PartType") + std::to_string(sid));
const size_t global_num_particles = pc.get_global_num_particles();
// start by creating the full empty datasets in the file
if (this_rank_ == 0) {
HDFCreateGroup(fname_, std::string("PartType") + std::to_string(sid));
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);
}
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);
}
if (this->has_64bit_ids())
HDFCreateEmptyDataset<uint64_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles);
else
HDFCreateEmptyDataset<uint32_t>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/ParticleIDs"), global_num_particles);
if( pc.bhas_individual_masses_ ){
if (this->has_64bit_reals())
HDFCreateEmptyDataset<double>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles);
else
HDFCreateEmptyDataset<float>(fname_, std::string("PartType") + std::to_string(sid) + std::string("/Masses"), global_num_particles);
}
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("/SmoothinLength"), global_num_particles);
}
}
// Now each node writes its own chunk in a round-robin fashion, appending at the end of the currently existing data
//... write positions and velocities.....
if (this->has_64bit_reals())