File I/O for FabArray<FArrayBox>. Wrapper class for reading/writing FabArray<FArrayBox> objects to disk in various "smart" ways. More...

#include <AMReX_VisMF.H>

Inheritance diagram for amrex::VisMF:

Classes
struct	FabOnDisk
	A structure containing info regarding an on-disk FAB. More...

struct	FabReadLink
	This structure is used to store the read order for each FabArray file. More...

struct	Header
	An on-disk FabArray<FArrayBox> contains this info in a header file. More...

struct	PersistentIFStream
	This structure is used to store file ifstreams that remain open. More...

Public Types
enum	How { OneFilePerCPU , NFiles }
	How we write out FabArray<FArrayBox>s. These are deprecated, we always use NFiles. For OneFilePerCPU, set NFiles to NProcs. More...

Public Types inherited from amrex::VisMFBuffer
enum	{ IO_Buffer_Size = 262144 * 8 }
	We try to do I/O with buffers of this size. More...

using	Setbuf_Char_Type = char
	The type of a char buffer required by [p]setbuf().

using	IO_Buffer = Vector< Setbuf_Char_Type >
	A simple character buffer for setbuf() usage.

Public Member Functions
	VisMF (std::string fafab_name)
	Construct by reading in the on-disk VisMF of the specified name. The FABs in the on-disk FabArray are read on demand unless the entire FabArray is requested. The name here is the name of the FabArray not the name of the on-disk files.

	~VisMF ()=default

	VisMF (const VisMF &)=delete

	VisMF (VisMF &&)=delete

VisMF &	operator= (const VisMF &)=delete

VisMF &	operator= (VisMF &&)=delete

int	nComp () const
	The number of components in the on-disk FabArray<FArrayBox>.

int	nGrow () const
	The grow factor of the on-disk FabArray<FArrayBox>.

IntVect	nGrowVect () const

int	size () const

const BoxArray &	boxArray () const
	The BoxArray of the on-disk FabArray<FArrayBox>.

Real	min (int fabIndex, int nComp) const
	The min of the FAB (in valid region) at specified index and component.

Real	min (int nComp) const
	The min of the FabArray (in valid region) at specified component.

Real	max (int fabIndex, int nComp) const
	The max of the FAB (in valid region) at specified index and component.

Real	max (int nComp) const
	The max of the FabArray (in valid region) at specified component.

const FArrayBox &	GetFab (int fabIndex, int compIndex) const
	The FAB at the specified index and component. Reads it from disk if necessary. This reads only the specified component.

void	clear (int fabIndex, int compIndex)
	Delete()s the FAB at the specified index and component.

void	clear (int fabIndex)
	Delete()s the FAB at the specified index (all components).

void	clear ()
	Delete()s all the FABs.

FArrayBox *	readFAB (int idx, const std::string &mf_name)
	Read the entire fab (all components).

FArrayBox *	readFAB (int idx, int icomp)
	Read the specified fab component.

Static Public Member Functions
static std::ifstream *	OpenStream (const std::string &fileName)
	Open the stream if it is not already open Close the stream if not persistent or forced Close all open streams.

static void	CloseStream (const std::string &fileName, bool forceClose=false)

static void	DeleteStream (const std::string &fileName)

static void	CloseAllStreams ()

static bool	NoFabHeader (const VisMF::Header &hdr)

static Long	Write (const FabArray< FArrayBox > &mf, const std::string &name, VisMF::How how=NFiles, bool set_ghost=false)
	Write a FabArray<FArrayBox> to disk in a "smart" way. Returns the total number of bytes written on this processor. If set_ghost is true, sets the ghost cells in the FabArray<FArrayBox> to one-half the average of the min and max over the valid region of each contained FAB.

static void	AsyncWrite (const FabArray< FArrayBox > &mf, const std::string &mf_name, bool valid_cells_only=false)

static void	AsyncWrite (FabArray< FArrayBox > &&mf, const std::string &mf_name, bool valid_cells_only=false)

static Long	WriteOnlyHeader (const FabArray< FArrayBox > &mf, const std::string &mf_name, VisMF::How how=NFiles)
	Write only the header-file corresponding to FabArray<FArrayBox> to disk without the corresponding FAB data. This writes BoxArray information (which might still be needed by data post-processing tools such as yt) when the FAB data is not needed. Returns the total number of bytes written on this processor.

static void	RemoveFiles (const std::string &name, bool verbose=false)
	this will remove nfiles associated with name and the header

static void	Read (FabArray< FArrayBox > &mf, const std::string &name, const char *faHeader=nullptr, int coordinatorProc=ParallelDescriptor::IOProcessorNumber(), int allow_empty_mf=0)
	Read a FabArray<FArrayBox> from disk written using VisMF::Write(). If the FabArray<FArrayBox> fafab has been fully defined, the BoxArray on the disk must match the BoxArray in fafab. If it is constructed with the default constructor, the BoxArray on the disk will be used and a new DistributionMapping will be made. A pre-read FabArray header can be passed in to avoid a read and broadcast.

static bool	Exist (const std::string &name)
	Does FabArray exist?

static void	ReadFAHeader (const std::string &fafabName, Vector< char > &header)
	Read only the header of a FabArray, header will be resized here.

static bool	Check (const std::string &name)
	Check if the multifab is ok, false is returned if not ok.

static Long	FileOffset (std::ostream &os)
	The file offset of the passed ostream.

static int	GetNOutFiles ()

static void	SetNOutFiles (int noutfiles, MPI_Comm comm=ParallelDescriptor::Communicator())

static int	GetMFFileInStreams ()

static void	SetMFFileInStreams (int nstreams, MPI_Comm comm=ParallelDescriptor::Communicator())

static int	GetVerbose ()

static void	SetVerbose (int v)

static VisMF::Header::Version	GetHeaderVersion ()

static void	SetHeaderVersion (VisMF::Header::Version version)

static bool	GetGroupSets ()

static void	SetGroupSets (bool groupsets)

static bool	GetSetBuf ()

static void	SetSetBuf (bool setbuf)

static bool	GetUseSingleRead ()

static void	SetUseSingleRead (bool usesingleread)

static bool	GetUseSingleWrite ()

static void	SetUseSingleWrite (bool usesinglewrite)

static bool	GetCheckFilePositions ()

static void	SetCheckFilePositions (bool cfp)

static bool	GetUsePersistentIFStreams ()

static void	SetUsePersistentIFStreams (bool usepifs)

static bool	GetUseSynchronousReads ()

static void	SetUseSynchronousReads (bool usepsr)

static bool	GetUseDynamicSetSelection ()

static void	SetUseDynamicSetSelection (bool usedss)

static bool	GetNoFlushAfterWrite ()

static void	SetNoFlushAfterWrite (bool nfaw)

static bool	GetBarrierAfterLevel ()

static void	SetBarrierAfterLevel (bool bal)

static std::string	DirName (const std::string &filename)

static std::string	BaseName (const std::string &filename)

static void	Initialize ()

static void	Finalize ()

Static Public Member Functions inherited from amrex::VisMFBuffer
static Long	GetIOBufferSize ()

static void	SetIOBufferSize (Long iobuffersize)

static void	ClearBuffer (IO_Buffer &buf)

Additional Inherited Members
Static Protected Attributes inherited from amrex::VisMFBuffer
static Long	ioBufferSize
	-— the settable buffer size

Detailed Description

File I/O for FabArray<FArrayBox>. Wrapper class for reading/writing FabArray<FArrayBox> objects to disk in various "smart" ways.

Member Enumeration Documentation

◆ How

enum amrex::VisMF::How

How we write out FabArray<FArrayBox>s. These are deprecated, we always use NFiles. For OneFilePerCPU, set NFiles to NProcs.

Enumerator
OneFilePerCPU
NFiles

Constructor & Destructor Documentation

◆ VisMF() [1/3]

amrex::VisMF::VisMF ( std::string fafab_name )

explicit

Construct by reading in the on-disk VisMF of the specified name. The FABs in the on-disk FabArray are read on demand unless the entire FabArray is requested. The name here is the name of the FabArray not the name of the on-disk files.

◆ ~VisMF()

amrex::VisMF::~VisMF ( )

default

◆ VisMF() [2/3]

amrex::VisMF::VisMF ( const VisMF & )

delete

◆ VisMF() [3/3]

amrex::VisMF::VisMF ( VisMF && )

delete

Member Function Documentation

◆ AsyncWrite() [1/2]

void amrex::VisMF::AsyncWrite	(	const FabArray< FArrayBox > &	mf,
		const std::string &	mf_name,
		bool	valid_cells_only = `false`
	)

static

◆ AsyncWrite() [2/2]

void amrex::VisMF::AsyncWrite	(	FabArray< FArrayBox > &&	mf,
		const std::string &	mf_name,
		bool	valid_cells_only = `false`
	)

static

◆ BaseName()

std::string amrex::VisMF::BaseName ( const std::string & filename )

static

◆ boxArray()

const BoxArray & amrex::VisMF::boxArray ( ) const

The BoxArray of the on-disk FabArray<FArrayBox>.

◆ Check()

bool amrex::VisMF::Check ( const std::string & name )

static

Check if the multifab is ok, false is returned if not ok.

◆ clear() [1/3]

void amrex::VisMF::clear ( )

Delete()s all the FABs.

◆ clear() [2/3]

void amrex::VisMF::clear ( int fabIndex )

Delete()s the FAB at the specified index (all components).

◆ clear() [3/3]

void amrex::VisMF::clear	(	int	fabIndex,
		int	compIndex
	)

Delete()s the FAB at the specified index and component.

◆ CloseAllStreams()

void amrex::VisMF::CloseAllStreams ( )

static

◆ CloseStream()

void amrex::VisMF::CloseStream	(	const std::string &	fileName,
		bool	forceClose = `false`
	)

static

◆ DeleteStream()

void amrex::VisMF::DeleteStream ( const std::string & fileName )

static

◆ DirName()

std::string amrex::VisMF::DirName ( const std::string & filename )

static

◆ Exist()

bool amrex::VisMF::Exist ( const std::string & name )

static

Does FabArray exist?

◆ FileOffset()

Long amrex::VisMF::FileOffset ( std::ostream & os )

static

The file offset of the passed ostream.

◆ Finalize()

void amrex::VisMF::Finalize ( )

static

◆ GetBarrierAfterLevel()

static bool amrex::VisMF::GetBarrierAfterLevel ( )

inlinestatic

◆ GetCheckFilePositions()

static bool amrex::VisMF::GetCheckFilePositions ( )

inlinestatic

◆ GetFab()

const FArrayBox & amrex::VisMF::GetFab	(	int	fabIndex,
		int	compIndex
	)		const

The FAB at the specified index and component. Reads it from disk if necessary. This reads only the specified component.

◆ GetGroupSets()

static bool amrex::VisMF::GetGroupSets ( )

inlinestatic

◆ GetHeaderVersion()

static VisMF::Header::Version amrex::VisMF::GetHeaderVersion ( )

inlinestatic

◆ GetMFFileInStreams()

static int amrex::VisMF::GetMFFileInStreams ( )

inlinestatic

◆ GetNoFlushAfterWrite()

static bool amrex::VisMF::GetNoFlushAfterWrite ( )

inlinestatic

◆ GetNOutFiles()

int amrex::VisMF::GetNOutFiles ( )

static

◆ GetSetBuf()

static bool amrex::VisMF::GetSetBuf ( )

inlinestatic

◆ GetUseDynamicSetSelection()

static bool amrex::VisMF::GetUseDynamicSetSelection ( )

inlinestatic

◆ GetUsePersistentIFStreams()

static bool amrex::VisMF::GetUsePersistentIFStreams ( )

inlinestatic

◆ GetUseSingleRead()

static bool amrex::VisMF::GetUseSingleRead ( )

inlinestatic

◆ GetUseSingleWrite()

static bool amrex::VisMF::GetUseSingleWrite ( )

inlinestatic

◆ GetUseSynchronousReads()

static bool amrex::VisMF::GetUseSynchronousReads ( )

inlinestatic

◆ GetVerbose()

static int amrex::VisMF::GetVerbose ( )

inlinestatic

◆ Initialize()

void amrex::VisMF::Initialize ( )

static

◆ max() [1/2]

Real amrex::VisMF::max	(	int	fabIndex,
		int	nComp
	)		const

The max of the FAB (in valid region) at specified index and component.

◆ max() [2/2]

Real amrex::VisMF::max ( int nComp ) const

The max of the FabArray (in valid region) at specified component.

◆ min() [1/2]

Real amrex::VisMF::min	(	int	fabIndex,
		int	nComp
	)		const

The min of the FAB (in valid region) at specified index and component.

◆ min() [2/2]

Real amrex::VisMF::min ( int nComp ) const

The min of the FabArray (in valid region) at specified component.

◆ nComp()

int amrex::VisMF::nComp ( ) const

The number of components in the on-disk FabArray<FArrayBox>.

◆ nGrow()

int amrex::VisMF::nGrow ( ) const

The grow factor of the on-disk FabArray<FArrayBox>.

◆ nGrowVect()

IntVect amrex::VisMF::nGrowVect ( ) const

◆ NoFabHeader()

bool amrex::VisMF::NoFabHeader ( const VisMF::Header & hdr )

static

◆ OpenStream()

std::ifstream * amrex::VisMF::OpenStream ( const std::string & fileName )

static

Open the stream if it is not already open Close the stream if not persistent or forced Close all open streams.

◆ operator=() [1/2]

VisMF & amrex::VisMF::operator= ( const VisMF & )

delete

◆ operator=() [2/2]

VisMF & amrex::VisMF::operator= ( VisMF && )

delete

◆ Read()

void amrex::VisMF::Read	(	FabArray< FArrayBox > &	mf,
		const std::string &	name,
		const char *	faHeader = `nullptr`,
		int	coordinatorProc = `ParallelDescriptor::IOProcessorNumber()`,
		int	allow_empty_mf = `0`
	)

static

Read a FabArray<FArrayBox> from disk written using VisMF::Write(). If the FabArray<FArrayBox> fafab has been fully defined, the BoxArray on the disk must match the BoxArray in fafab. If it is constructed with the default constructor, the BoxArray on the disk will be used and a new DistributionMapping will be made. A pre-read FabArray header can be passed in to avoid a read and broadcast.

◆ readFAB() [1/2]

FArrayBox * amrex::VisMF::readFAB	(	int	idx,
		const std::string &	mf_name
	)

Read the entire fab (all components).

◆ readFAB() [2/2]

FArrayBox * amrex::VisMF::readFAB	(	int	idx,
		int	icomp
	)

Read the specified fab component.

◆ ReadFAHeader()

void amrex::VisMF::ReadFAHeader	(	const std::string &	fafabName,
		Vector< char > &	header
	)

static

Read only the header of a FabArray, header will be resized here.

◆ RemoveFiles()

void amrex::VisMF::RemoveFiles	(	const std::string &	name,
		bool	verbose = `false`
	)

static

this will remove nfiles associated with name and the header

◆ SetBarrierAfterLevel()

static void amrex::VisMF::SetBarrierAfterLevel ( bool bal )

inlinestatic

◆ SetCheckFilePositions()

static void amrex::VisMF::SetCheckFilePositions ( bool cfp )

inlinestatic

◆ SetGroupSets()

static void amrex::VisMF::SetGroupSets ( bool groupsets )

inlinestatic

◆ SetHeaderVersion()

static void amrex::VisMF::SetHeaderVersion ( VisMF::Header::Version version )

inlinestatic

◆ SetMFFileInStreams()

void amrex::VisMF::SetMFFileInStreams	(	int	nstreams,
		MPI_Comm	comm = `ParallelDescriptor::Communicator()`
	)

static

◆ SetNoFlushAfterWrite()

static void amrex::VisMF::SetNoFlushAfterWrite ( bool nfaw )

inlinestatic

◆ SetNOutFiles()

void amrex::VisMF::SetNOutFiles	(	int	noutfiles,
		MPI_Comm	comm = `ParallelDescriptor::Communicator()`
	)

static

◆ SetSetBuf()

static void amrex::VisMF::SetSetBuf ( bool setbuf )

inlinestatic

◆ SetUseDynamicSetSelection()

static void amrex::VisMF::SetUseDynamicSetSelection ( bool usedss )

inlinestatic

◆ SetUsePersistentIFStreams()

static void amrex::VisMF::SetUsePersistentIFStreams ( bool usepifs )

inlinestatic

◆ SetUseSingleRead()

static void amrex::VisMF::SetUseSingleRead ( bool usesingleread )

inlinestatic

◆ SetUseSingleWrite()

static void amrex::VisMF::SetUseSingleWrite ( bool usesinglewrite )

inlinestatic

◆ SetUseSynchronousReads()

static void amrex::VisMF::SetUseSynchronousReads ( bool usepsr )

inlinestatic

◆ SetVerbose()

static void amrex::VisMF::SetVerbose ( int v )

inlinestatic

◆ size()

int amrex::VisMF::size ( ) const

of FABs in the VisMF. Equal to # of Boxes in the BoxArray.

◆ Write()

Long amrex::VisMF::Write	(	const FabArray< FArrayBox > &	mf,
		const std::string &	name,
		VisMF::How	how = `NFiles`,
		bool	set_ghost = `false`
	)

static

Write a FabArray<FArrayBox> to disk in a "smart" way. Returns the total number of bytes written on this processor. If set_ghost is true, sets the ghost cells in the FabArray<FArrayBox> to one-half the average of the min and max over the valid region of each contained FAB.

◆ WriteOnlyHeader()

Long amrex::VisMF::WriteOnlyHeader	(	const FabArray< FArrayBox > &	mf,
		const std::string &	mf_name,
		VisMF::How	how = `NFiles`
	)

static

Write only the header-file corresponding to FabArray<FArrayBox> to disk without the corresponding FAB data. This writes BoxArray information (which might still be needed by data post-processing tools such as yt) when the FAB data is not needed. Returns the total number of bytes written on this processor.

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

/home/runner/work/amrex/amrex/Src/Base/AMReX_VisMF.H
/home/runner/work/amrex/amrex/Src/Base/AMReX_VisMF.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ How

Constructor & Destructor Documentation

◆ VisMF() [1/3]

◆ ~VisMF()

◆ VisMF() [2/3]

◆ VisMF() [3/3]

Member Function Documentation

◆ AsyncWrite() [1/2]

◆ AsyncWrite() [2/2]

◆ BaseName()

◆ boxArray()

◆ Check()

◆ clear() [1/3]

◆ clear() [2/3]

◆ clear() [3/3]

◆ CloseAllStreams()

◆ CloseStream()

◆ DeleteStream()

◆ DirName()

◆ Exist()

◆ FileOffset()

◆ Finalize()

◆ GetBarrierAfterLevel()

◆ GetCheckFilePositions()

◆ GetFab()

◆ GetGroupSets()

◆ GetHeaderVersion()

◆ GetMFFileInStreams()

◆ GetNoFlushAfterWrite()

◆ GetNOutFiles()

◆ GetSetBuf()

◆ GetUseDynamicSetSelection()

◆ GetUsePersistentIFStreams()

◆ GetUseSingleRead()

◆ GetUseSingleWrite()

◆ GetUseSynchronousReads()

◆ GetVerbose()

◆ Initialize()

◆ max() [1/2]

◆ max() [2/2]

◆ min() [1/2]

◆ min() [2/2]

◆ nComp()

◆ nGrow()

◆ nGrowVect()

◆ NoFabHeader()

◆ OpenStream()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ Read()

◆ readFAB() [1/2]

◆ readFAB() [2/2]

◆ ReadFAHeader()

◆ RemoveFiles()

◆ SetBarrierAfterLevel()

◆ SetCheckFilePositions()

◆ SetGroupSets()

◆ SetHeaderVersion()

◆ SetMFFileInStreams()

◆ SetNoFlushAfterWrite()

◆ SetNOutFiles()

◆ SetSetBuf()

◆ SetUseDynamicSetSelection()

◆ SetUsePersistentIFStreams()

◆ SetUseSingleRead()

◆ SetUseSingleWrite()

◆ SetUseSynchronousReads()

◆ SetVerbose()

◆ size()

of FABs in the VisMF. Equal to # of Boxes in the BoxArray.

◆ Write()

◆ WriteOnlyHeader()