MPI-parallel HDF5 serializer; all ranks collectively read/write a single .h5 file. More...

#include <SerializerH5.hpp>

Inheritance diagram for DNDS::Serializer::SerializerH5:

Collaboration diagram for DNDS::Serializer::SerializerH5:

Public Member Functions
	SerializerH5 (const MPIInfo &_mpi)

void	SetChunkAndDeflate (int64_t n_chunksize, int n_deflateLevel)

void	SetCollectiveRW (bool metadata, bool data)

void	OpenFile (const std::string &fName, bool read) override
	Open a backing file (H5 file or JSON file depending on subclass).

void	CloseFile () override
	Close the backing file, flushing buffers.

void	CloseFileNonVirtual ()

void	CreatePath (const std::string &p) override
	Create a sub-path (H5 group / JSON object) at the current location.

void	GoToPath (const std::string &p) override
	Navigate to an existing path. Supports `/` -separated segments.

bool	IsPerRank () override
	Whether this serializer is per-rank (JSON-file-per-rank) or collective (shared H5 file). Controls which API entry points are used.

std::string	GetCurrentPath () override
	String form of the current path.

std::set< std::string >	ListCurrentPath () override
	Names of direct children of the current path.

int	GetMPIRank () override
	Rank index cached by the serializer (relevant for collective I/O).

int	GetMPISize () override
	Rank count cached by the serializer.

const MPIInfo &	getMPI () override
	MPI context the serializer was opened with.

void	WriteInt (const std::string &name, int v) override
	Write a scalar int under `name` at the current path.

void	WriteIndex (const std::string &name, index v) override
	Write a scalar index under `name`.

void	WriteReal (const std::string &name, real v) override
	Write a scalar real under `name`.

void	WriteString (const std::string &name, const std::string &v) override
	Write a UTF-8 string under `name`.

void	WriteIndexVector (const std::string &name, const std::vector< index > &v, ArrayGlobalOffset offset) override
	Write an index vector (collective for H5). `offset` carries the distribution mode (ArrayGlobalOffset_Parts, explicit offset, etc.).

void	WriteRowsizeVector (const std::string &name, const std::vector< rowsize > &v, ArrayGlobalOffset offset) override
	Write a rowsize vector (collective for H5).

void	WriteRealVector (const std::string &name, const std::vector< real > &v, ArrayGlobalOffset offset) override
	Write a real vector (collective for H5).

void	WriteSharedIndexVector (const std::string &name, const ssp< host_device_vector< index > > &v, ArrayGlobalOffset offset) override
	Write a shared index vector; deduplicated across multiple writes that share the same `shared_ptr`.

void	WriteSharedRowsizeVector (const std::string &name, const ssp< host_device_vector< rowsize > > &v, ArrayGlobalOffset offset) override
	Write a shared rowsize vector; deduplicated across multiple writes.

void	WriteUint8Array (const std::string &name, const uint8_t *data, index size, ArrayGlobalOffset offset) override
	Write a raw byte buffer under `name`. `offset.isDist()` = true means the caller provides the exact per-rank slab; otherwise the buffer is treated according to the offset's sentinel.

void	WriteIndexVectorPerRank (const std::string &name, const std::vector< index > &v) override
	Write a per-rank index vector (replicated name, independent values).

void	ReadInt (const std::string &name, int &v) override
	Read a scalar int into `v`.

void	ReadIndex (const std::string &name, index &v) override
	Read a scalar index into `v`.

void	ReadReal (const std::string &name, real &v) override
	Read a scalar real into `v`.

void	ReadString (const std::string &name, std::string &v) override
	Read a UTF-8 string into `v`.

void	ReadIndexVector (const std::string &name, std::vector< index > &v, ArrayGlobalOffset &offset) override

void	ReadRowsizeVector (const std::string &name, std::vector< rowsize > &v, ArrayGlobalOffset &offset) override

void	ReadRealVector (const std::string &name, std::vector< real > &v, ArrayGlobalOffset &offset) override

void	ReadSharedIndexVector (const std::string &name, ssp< host_device_vector< index > > &v, ArrayGlobalOffset &offset) override

void	ReadSharedRowsizeVector (const std::string &name, ssp< host_device_vector< rowsize > > &v, ArrayGlobalOffset &offset) override

void	ReadUint8Array (const std::string &name, uint8_t *data, index &size, ArrayGlobalOffset &offset) override
	Two-pass byte array read.

	~SerializerH5 () override

Public Member Functions inherited from DNDS::Serializer::SerializerBase
virtual	~SerializerBase ()

Additional Inherited Members
Protected Member Functions inherited from DNDS::Serializer::SerializerBase
template<class T >
bool	dedupLookup (const ssp< T > &v, std::string &outPath)
	Check if a shared pointer was already written; if so return its path.

template<class T >
void	dedupRegister (const ssp< T > &v, const std::string &path)
	Register a shared pointer after writing its data.

void	dedupClear ()
	Clear all dedup state (call on CloseFile).

Protected Attributes inherited from DNDS::Serializer::SerializerBase
std::map< void *, std::pair< std::shared_ptr< void >, std::string > >	ptr_2_pth

std::map< std::string, void * >	pth_2_ssp
	Reverse map for read-side dedup: path -> raw pointer to the ssp local variable.

Detailed Description

MPI-parallel HDF5 serializer; all ranks collectively read/write a single .h5 file.

Definition at line 52 of file SerializerH5.hpp.

Constructor & Destructor Documentation

◆ SerializerH5()

DNDS::Serializer::SerializerH5::SerializerH5 ( const MPIInfo & _mpi )

inline

Definition at line 70 of file SerializerH5.hpp.

◆ ~SerializerH5()

DNDS::Serializer::SerializerH5::~SerializerH5 ( )

inlineoverride

Definition at line 132 of file SerializerH5.hpp.

Here is the call graph for this function:

Member Function Documentation

◆ CloseFile()

void DNDS::Serializer::SerializerH5::CloseFile ( )

overridevirtual

Close the backing file, flushing buffers.

Implements DNDS::Serializer::SerializerBase.

Definition at line 125 of file SerializerH5.cpp.

Here is the call graph for this function:

Here is the caller graph for this function:

◆ CloseFileNonVirtual()

void DNDS::Serializer::SerializerH5::CloseFileNonVirtual ( )

Definition at line 129 of file SerializerH5.cpp.

Here is the call graph for this function:

Here is the caller graph for this function:

◆ CreatePath()

void DNDS::Serializer::SerializerH5::CreatePath ( const std::string & p )

overridevirtual

Create a sub-path (H5 group / JSON object) at the current location.

Implements DNDS::Serializer::SerializerBase.

Definition at line 138 of file SerializerH5.cpp.

Here is the call graph for this function:

Here is the caller graph for this function:

◆ GetCurrentPath()

std::string DNDS::Serializer::SerializerH5::GetCurrentPath ( )

overridevirtual

String form of the current path.

Implements DNDS::Serializer::SerializerBase.

Definition at line 165 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ getMPI()

const MPIInfo & DNDS::Serializer::SerializerH5::getMPI ( )

inlineoverridevirtual

MPI context the serializer was opened with.

Implements DNDS::Serializer::SerializerBase.

Definition at line 99 of file SerializerH5.hpp.

◆ GetMPIRank()

int DNDS::Serializer::SerializerH5::GetMPIRank ( )

inlineoverridevirtual

Rank index cached by the serializer (relevant for collective I/O).

Implements DNDS::Serializer::SerializerBase.

Definition at line 97 of file SerializerH5.hpp.

◆ GetMPISize()

int DNDS::Serializer::SerializerH5::GetMPISize ( )

inlineoverridevirtual

Rank count cached by the serializer.

Implements DNDS::Serializer::SerializerBase.

Definition at line 98 of file SerializerH5.hpp.

◆ GoToPath()

void DNDS::Serializer::SerializerH5::GoToPath ( const std::string & p )

overridevirtual

Navigate to an existing path. Supports / -separated segments.

Implements DNDS::Serializer::SerializerBase.

Definition at line 153 of file SerializerH5.cpp.

Here is the call graph for this function:

Here is the caller graph for this function:

◆ IsPerRank()

bool DNDS::Serializer::SerializerH5::IsPerRank ( )

inlineoverridevirtual

Whether this serializer is per-rank (JSON-file-per-rank) or collective (shared H5 file). Controls which API entry points are used.

Implements DNDS::Serializer::SerializerBase.

Definition at line 94 of file SerializerH5.hpp.

◆ ListCurrentPath()

std::set< std::string > DNDS::Serializer::SerializerH5::ListCurrentPath ( )

overridevirtual

Names of direct children of the current path.

Implements DNDS::Serializer::SerializerBase.

Definition at line 261 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ OpenFile()

void DNDS::Serializer::SerializerH5::OpenFile	(	const std::string &	fName,
		bool	read
	)

overridevirtual

Open a backing file (H5 file or JSON file depending on subclass).

Parameters

read	`true` for reading, `false` for writing.

Implements DNDS::Serializer::SerializerBase.

Definition at line 109 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadIndex()

void DNDS::Serializer::SerializerH5::ReadIndex	(	const std::string &	name,
		index &	v
	)

overridevirtual

Read a scalar index into v.

Implements DNDS::Serializer::SerializerBase.

Definition at line 598 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadIndexVector()

void DNDS::Serializer::SerializerH5::ReadIndexVector	(	const std::string &	name,
		std::vector< index > &	v,
		ArrayGlobalOffset &	offset
	)

overridevirtual

Read methods resize the output container and populate it. Internally these use a two-pass HDF5 pattern (size query, then data read). Both passes are collective. When the local size is 0, a dummy non-null pointer is passed to the second pass so the rank participates in H5Dread.

Implements DNDS::Serializer::SerializerBase.

Definition at line 828 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadInt()

void DNDS::Serializer::SerializerH5::ReadInt	(	const std::string &	name,
		int &	v
	)

overridevirtual

Read a scalar int into v.

Implements DNDS::Serializer::SerializerBase.

Definition at line 594 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadReal()

void DNDS::Serializer::SerializerH5::ReadReal	(	const std::string &	name,
		real &	v
	)

overridevirtual

Read a scalar real into v.

Implements DNDS::Serializer::SerializerBase.

Definition at line 602 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadRealVector()

void DNDS::Serializer::SerializerH5::ReadRealVector	(	const std::string &	name,
		std::vector< real > &	v,
		ArrayGlobalOffset &	offset
	)

overridevirtual

Implements DNDS::Serializer::SerializerBase.

Definition at line 846 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadRowsizeVector()

void DNDS::Serializer::SerializerH5::ReadRowsizeVector	(	const std::string &	name,
		std::vector< rowsize > &	v,
		ArrayGlobalOffset &	offset
	)

overridevirtual

Implements DNDS::Serializer::SerializerBase.

Definition at line 837 of file SerializerH5.cpp.

◆ ReadSharedIndexVector()

void DNDS::Serializer::SerializerH5::ReadSharedIndexVector	(	const std::string &	name,
		ssp< host_device_vector< index > > &	v,
		ArrayGlobalOffset &	offset
	)

overridevirtual

Implements DNDS::Serializer::SerializerBase.

Definition at line 859 of file SerializerH5.cpp.

Here is the call graph for this function:

◆ ReadSharedRowsizeVector()

void DNDS::Serializer::SerializerH5::ReadSharedRowsizeVector	(	const std::string &	name,
		ssp< host_device_vector< rowsize > > &	v,
		ArrayGlobalOffset &	offset
	)

overridevirtual

Implements DNDS::Serializer::SerializerBase.

Definition at line 893 of file SerializerH5.cpp.

Here is the call graph for this function:

◆ ReadString()

void DNDS::Serializer::SerializerH5::ReadString	(	const std::string &	name,
		std::string &	v
	)

overridevirtual

Read a UTF-8 string into v.

Implements DNDS::Serializer::SerializerBase.

Definition at line 855 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ ReadUint8Array()

void DNDS::Serializer::SerializerH5::ReadUint8Array	(	const std::string &	name,
		uint8_t *	data,
		index &	size,
		ArrayGlobalOffset &	offset
	)

overridevirtual

Two-pass byte array read.

Pass 1 (data == nullptr): queries the local element count into size and resolves offset. Pass 2 (data != nullptr): reads size bytes into data.

Warning: When size is 0 after pass 1, the caller must still pass a non-null data pointer on pass 2 so the rank participates in the collective HDF5 read. Use a stack dummy (uint8_t dummy; ... &dummy).

Implements DNDS::Serializer::SerializerBase.

Definition at line 931 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ SetChunkAndDeflate()

void DNDS::Serializer::SerializerH5::SetChunkAndDeflate	(	int64_t	n_chunksize,
		int	n_deflateLevel
	)

inline

Definition at line 75 of file SerializerH5.hpp.

◆ SetCollectiveRW()

void DNDS::Serializer::SerializerH5::SetCollectiveRW	(	bool	metadata,
		bool	data
	)

inline

Definition at line 83 of file SerializerH5.hpp.

◆ WriteIndex()

void DNDS::Serializer::SerializerH5::WriteIndex	(	const std::string &	name,
		index	v
	)

overridevirtual

Write a scalar index under name.

Implements DNDS::Serializer::SerializerBase.

Definition at line 345 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ WriteIndexVector()

void DNDS::Serializer::SerializerH5::WriteIndexVector	(	const std::string &	name,
		const std::vector< index > &	v,
		ArrayGlobalOffset	offset
	)

overridevirtual

Write an index vector (collective for H5). offset carries the distribution mode (ArrayGlobalOffset_Parts, explicit offset, etc.).

Implements DNDS::Serializer::SerializerBase.

Definition at line 466 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ WriteIndexVectorPerRank()

void DNDS::Serializer::SerializerH5::WriteIndexVectorPerRank	(	const std::string &	name,
		const std::vector< index > &	v
	)

inlineoverridevirtual

Write a per-rank index vector (replicated name, independent values).

Every rank writes its own vector under name; in the H5 case each rank's slab is placed in a separate dataset.

Parameters

name	Dataset name (identical on every rank).
v	Rank-local vector; size may differ between ranks.

Implements DNDS::Serializer::SerializerBase.

Definition at line 114 of file SerializerH5.hpp.

Here is the call graph for this function:

◆ WriteInt()

void DNDS::Serializer::SerializerH5::WriteInt	(	const std::string &	name,
		int	v
	)

overridevirtual

Write a scalar int under name at the current path.

Implements DNDS::Serializer::SerializerBase.

Definition at line 341 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ WriteReal()

void DNDS::Serializer::SerializerH5::WriteReal	(	const std::string &	name,
		real	v
	)

overridevirtual

Write a scalar real under name.

Implements DNDS::Serializer::SerializerBase.

Definition at line 349 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ WriteRealVector()

void DNDS::Serializer::SerializerH5::WriteRealVector	(	const std::string &	name,
		const std::vector< real > &	v,
		ArrayGlobalOffset	offset
	)

overridevirtual

Write a real vector (collective for H5).

Implements DNDS::Serializer::SerializerBase.

Definition at line 474 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ WriteRowsizeVector()

void DNDS::Serializer::SerializerH5::WriteRowsizeVector	(	const std::string &	name,
		const std::vector< rowsize > &	v,
		ArrayGlobalOffset	offset
	)

overridevirtual

Write a rowsize vector (collective for H5).

Implements DNDS::Serializer::SerializerBase.

Definition at line 470 of file SerializerH5.cpp.

◆ WriteSharedIndexVector()

void DNDS::Serializer::SerializerH5::WriteSharedIndexVector	(	const std::string &	name,
		const ssp< host_device_vector< index > > &	v,
		ArrayGlobalOffset	offset
	)

overridevirtual

Write a shared index vector; deduplicated across multiple writes that share the same shared_ptr.

Implements DNDS::Serializer::SerializerBase.

Definition at line 482 of file SerializerH5.cpp.

Here is the call graph for this function:

◆ WriteSharedRowsizeVector()

void DNDS::Serializer::SerializerH5::WriteSharedRowsizeVector	(	const std::string &	name,
		const ssp< host_device_vector< rowsize > > &	v,
		ArrayGlobalOffset	offset
	)

overridevirtual

Write a shared rowsize vector; deduplicated across multiple writes.

Implements DNDS::Serializer::SerializerBase.

Definition at line 495 of file SerializerH5.cpp.

Here is the call graph for this function:

◆ WriteString()

void DNDS::Serializer::SerializerH5::WriteString	(	const std::string &	name,
		const std::string &	v
	)

overridevirtual

Write a UTF-8 string under name.

Implements DNDS::Serializer::SerializerBase.

Definition at line 478 of file SerializerH5.cpp.

Here is the caller graph for this function:

◆ WriteUint8Array()

void DNDS::Serializer::SerializerH5::WriteUint8Array	(	const std::string &	name,
		const uint8_t *	data,
		index	size,
		ArrayGlobalOffset	offset
	)

overridevirtual

Write a raw byte buffer under name. offset.isDist() = true means the caller provides the exact per-rank slab; otherwise the buffer is treated according to the offset's sentinel.

Implements DNDS::Serializer::SerializerBase.

Definition at line 927 of file SerializerH5.cpp.

Here is the caller graph for this function:

The documentation for this class was generated from the following files:

/home/runner/work/DNDSR/DNDSR/src/DNDS/SerializerH5.hpp
/home/runner/work/DNDSR/DNDSR/src/DNDS/SerializerH5.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SerializerH5()

◆ ~SerializerH5()

Member Function Documentation

◆ CloseFile()

◆ CloseFileNonVirtual()

◆ CreatePath()

◆ GetCurrentPath()

◆ getMPI()

◆ GetMPIRank()

◆ GetMPISize()

◆ GoToPath()

◆ IsPerRank()

◆ ListCurrentPath()

◆ OpenFile()

◆ ReadIndex()

◆ ReadIndexVector()

◆ ReadInt()

◆ ReadReal()

◆ ReadRealVector()

◆ ReadRowsizeVector()

◆ ReadSharedIndexVector()

◆ ReadSharedRowsizeVector()

◆ ReadString()

◆ ReadUint8Array()

◆ SetChunkAndDeflate()

◆ SetCollectiveRW()

◆ WriteIndex()

◆ WriteIndexVector()

◆ WriteIndexVectorPerRank()

◆ WriteInt()

◆ WriteReal()

◆ WriteRealVector()

◆ WriteRowsizeVector()

◆ WriteSharedIndexVector()

◆ WriteSharedRowsizeVector()

◆ WriteString()

◆ WriteUint8Array()