molpro::linalg::array::DistrArrayFile Class Reference

Distributed array storing the buffer on disk using temporary local files. More...

#include <DistrArrayFile.h>

Inheritance diagram for molpro::linalg::array::DistrArrayFile:

Collaboration diagram for molpro::linalg::array::DistrArrayFile:

Detailed Description

Distributed array storing the buffer on disk using temporary local files.

On construction, file and corresponding stream object are created and file is then closed. On destruction, file is deleted.

Warning

Only local operations will be currently supported, if RMA operations are requested, exception will be thrown.

Examples

LinearEigensystemDistrArrayExample.cpp, and OptimizeDistrArrayExample.cpp.

Public Member Functions
	DistrArrayFile ()=delete
	returns local array boundaries and size
	DistrArrayFile (const DistrArrayFile &source)
	Creates a copy of source, with its file in the directory of the file of source.
	DistrArrayFile (DistrArrayFile &&source)
	DistrArrayFile (size_t dimension, MPI_Comm comm=molpro::mpi::comm_global(), const std::string &directory=".")
	DistrArrayFile (std::unique_ptr< Distribution > distribution, MPI_Comm comm=molpro::mpi::comm_global(), const std::string &directory=".")
	DistrArrayFile (const DistrArray &source)
DistrArrayFile &	operator= (const DistrArrayFile &source)=delete
DistrArrayFile &	operator= (DistrArrayFile &&source) noexcept
	~DistrArrayFile () override
std::string	file_directory () const override
	The directory of the file holding this array, or an empty string if that is not known.
bool	compatible (const DistrArrayFile &source) const
void	erase () override
	Dummy.
value_type	at (index_type ind) const override
void	set (index_type ind, value_type val) override
	Writes value at a given index.
void	get (index_type lo, index_type hi, value_type *buf) const override
	Reads requested values.
std::vector< value_type >	get (index_type lo, index_type hi) const override
void	put (index_type lo, index_type hi, const value_type *data) override
	Writes requested values to file.
void	acc (index_type lo, index_type hi, const value_type *data) override
std::vector< value_type >	gather (const std::vector< index_type > &indices) const override
	gets elements with discontinuous indices from array. Blocking
void	scatter (const std::vector< index_type > &indices, const std::vector< value_type > &data) override
	array[indices[i]] = data[i] Puts vals of elements with discontinuous indices of array. Blocking.
void	scatter_acc (std::vector< index_type > &indices, const std::vector< value_type > &data) override
	array[indices[i]] += vals[i] Accumulates vals of elements into discontinuous indices of array. Atomic, blocking, with on-sided communication
std::vector< value_type >	vec () const override
	Copies the whole buffer into a vector. Blocking.
Public Member Functions inherited from molpro::linalg::array::DistrArrayDisk
const Distribution &	distribution () const override
	Access distribution of the array among processes.
value_type	dot (const DistrArrayDisk &y) const
void	set_buffer_size (size_t buffer_size)
size_t	disk_page_size () const override
std::unique_ptr< LocalBuffer >	local_buffer () override
	Not available: an array on disk is not held in memory.
std::unique_ptr< const LocalBuffer >	local_buffer () const override
	Not available: an array on disk is not held in memory.
value_type	dot (Span< const value_type > y) const
	Scalar product <this|y>. Collective, the result is available to each process.
virtual value_type	dot (const DistrArray &y) const
	Scalar product of two arrays. Collective. Throws error if any array is empty. Both arrays should be part of the same processor group (same communicator). The result is broadcast to each process.
virtual value_type	dot (const SparseArray &y) const
Public Member Functions inherited from molpro::linalg::array::DistrArray
virtual	~DistrArray ()=default
	DistrArray (const DistrArray &)=default
	DistrArray (DistrArray &&) noexcept=default
DistrArray &	operator= (const DistrArray &)=default
DistrArray &	operator= (DistrArray &&) noexcept=default
MPI_Comm	communicator () const
	return a copy of the communicator
virtual void	sync () const
	Synchronizes all process in this group and ensures any outstanding operations on the array have completed.
size_t	size () const
	total number of elements, same as overall dimension of array
bool	compatible (const DistrArray &other) const
	Checks that arrays are of the same dimensionality.
virtual void	zero ()
	Set all local elements to zero.
virtual void	error (const std::string &message) const
	stops application with an error
value_type	operator[] (index_type ind) const
util::ValueProxy< DistrArray >	operator[] (index_type ind)
virtual void	fill (value_type val)
virtual void	copy (const DistrArray &y)
virtual void	copy_patch (const DistrArray &y, index_type start, index_type end)
	Copies elements in a patch of y. If both arrays are empty than does nothing. If only one is empty, throws an error.
virtual void	axpy (value_type a, const DistrArray &y)
	this[:] += a * y[:]. Throws an error if any array is empty. Add a multiple of another array to this one. Blocking, collective.
virtual void	axpy (value_type a, const SparseArray &y)
void	copy (const SparseArray &y)
	this[:] = y[:], i.e. the elements of y, and zero elsewhere. Local, each process sets its local section.
virtual void	scal (value_type a)
virtual void	add (const DistrArray &y)
	Add another array to this. Local. Throws error if any array is empty.
virtual void	add (value_type a)
	Add a constant. Local.
virtual void	sub (const DistrArray &y)
	Subtract another array from this. Local. Throws error if any array is empty.
virtual void	sub (value_type a)
	Subtract a constant. Local.
virtual void	recip ()
	Take element-wise reciprocal of this. Local. No checks are made for zero values.
virtual void	times (const DistrArray &y)
	this[i] *= y[i]. Throws error if any array is empty.
virtual void	times (const DistrArray &y, const DistrArray &z)
	this[i] = y[i]*z[i]. Throws error if any array is empty.
void	copy (Span< const value_type > y)
void	axpy (value_type a, Span< const value_type > y)
	this[:] += a * y[:] over the local section. Local.
void	copy_to (Span< value_type > y) const
	y[:] = this[:]. Collective: each process copies its local section, and then y is replicated over all of them.
void	axpy_to (value_type a, Span< value_type > y) const
value_type	dot (Span< const value_type > y) const
	Scalar product <this|y>. Collective, the result is available to each process.
std::map< size_t, value_type >	select_max_dot (size_t n, Span< const value_type > y) const
	The n indices with the largest |this[i]*y[i]|. Collective.
void	divide (const DistrArray &y, const DistrArray &z, value_type shift=0, bool append=false, bool negative=false)
	this[i] = y[i]/(z[i]+shift). Collective. Throws error if any array is empty.
std::list< std::pair< index_type, value_type > >	min_n (int n) const
	returns n smallest elements in array x Collective operation, must be called by all processes in the group.
std::list< std::pair< index_type, value_type > >	max_n (int n) const
	returns n largest elements in array x Collective operation, must be called by all processes in the group.
std::list< std::pair< index_type, value_type > >	min_abs_n (int n) const
	returns n elements that are largest by absolute value in array x Collective operation, must be called by all processes in the group.
std::list< std::pair< index_type, value_type > >	max_abs_n (int n) const
	returns n elements that are largest by absolute value in array x Collective operation, must be called by all processes in the group.
std::vector< index_type >	min_loc_n (int n) const
	find the index of n smallest components in array x Collective operation, must be called by all processes in the group.
std::map< size_t, value_type >	select_max_dot (size_t n, const DistrArray &y) const
std::map< size_t, value_type >	select_max_dot (size_t n, const SparseArray &y) const
std::map< size_t, value_type >	select (size_t n, bool max=false, bool ignore_sign=false) const

Static Public Member Functions
static DistrArrayFile	CreateTempCopy (const DistrArray &source, const std::string &directory="")
	Creates a copy of source, with the same distribution and communicator, in a file which is erased on destruction.
static DistrArrayFile	CreateTempCopy (Span< const value_type > source, MPI_Comm comm, const std::string &directory=".")
	Creates a copy of a contiguous array in a file which is erased on destruction.
Static Public Member Functions inherited from molpro::linalg::array::DistrArrayDisk
static std::string	temp_copy_directory (const DistrArray &source, const std::string &directory)
	The directory for the file of a temporary copy of source.

Friends
void	swap (DistrArrayFile &x, DistrArrayFile &y) noexcept

Additional Inherited Members
Public Types inherited from molpro::linalg::array::DistrArrayDisk
using	disk_array = void
	a compile time tag that this is a distributed disk array
Public Types inherited from molpro::linalg::array::DistrArray
using	distributed_array = void
	a compile time tag that this is a distributed array
using	value_type = double
using	index_type = size_t
using	SparseArray = std::map< index_type, double >
using	Distribution = util::Distribution< index_type >
Protected Member Functions inherited from molpro::linalg::array::DistrArrayDisk
	DistrArrayDisk (std::unique_ptr< Distribution > distr, MPI_Comm commun)
	DistrArrayDisk ()
	DistrArrayDisk (const DistrArray &source)
	DistrArrayDisk (DistrArrayDisk &&source) noexcept
	~DistrArrayDisk () override
	DistrArray (size_t dimension, MPI_Comm commun)
	Initializes array without allocating any memory.
	DistrArray ()=default
	DistrArray (const DistrArray &)=default
	DistrArray (DistrArray &&) noexcept=default
Protected Member Functions inherited from molpro::linalg::array::DistrArray
	DistrArray (size_t dimension, MPI_Comm commun)
	Initializes array without allocating any memory.
	DistrArray ()=default
void	check_compatible (Span< const value_type > y, const std::string &name) const
	Stops with an error unless the contiguous array y has as many elements as this.
virtual void	_divide (const DistrArray &y, const DistrArray &z, value_type shift, bool append, bool negative)
Protected Attributes inherited from molpro::linalg::array::DistrArrayDisk
bool	m_allocated = false
	Flags that the memory view buffer has been allocated.
std::unique_ptr< Distribution >	m_distribution
	describes distribution of array among processes
size_t	m_buffer_size = 8192
	buffer size for paged access via BufferManager
Protected Attributes inherited from molpro::linalg::array::DistrArray
index_type	m_dimension = 0
	number of elements in the array
MPI_Comm	m_communicator

Constructor & Destructor Documentation

DistrArrayFile() [1/6]

molpro::linalg::array::DistrArrayFile::DistrArrayFile ( )

delete

returns local array boundaries and size

DistrArrayFile() [2/6]

molpro::linalg::array::DistrArrayFile::DistrArrayFile

(

const DistrArrayFile &

source

)

Creates a copy of source, with its file in the directory of the file of source.

DistrArrayFile() [3/6]

molpro::linalg::array::DistrArrayFile::DistrArrayFile

(

DistrArrayFile &&

source

)

DistrArrayFile() [4/6]

molpro::linalg::array::DistrArrayFile::DistrArrayFile ( size_t  dimension, MPI_Comm  comm = molpro::mpi::comm_global(), const std::string &  directory = "."  )

explicit

DistrArrayFile() [5/6]

molpro::linalg::array::DistrArrayFile::DistrArrayFile ( std::unique_ptr< Distribution >  distribution, MPI_Comm  comm = molpro::mpi::comm_global(), const std::string &  directory = "."  )

explicit

DistrArrayFile() [6/6]

molpro::linalg::array::DistrArrayFile::DistrArrayFile ( const DistrArray &  source )

explicit

Creates a copy of source, with its file next to that of source if it is a disk array, otherwise in the current directory

~DistrArrayFile()

molpro::linalg::array::DistrArrayFile::~DistrArrayFile ( )

override

Member Function Documentation

acc()

void molpro::linalg::array::DistrArrayFile::acc ( DistrArray::index_type  lo, DistrArray::index_type  hi, const value_type *  data  )

overridevirtual

Warning

below functions have to be implemented being pure virtuals, but will return exceptions taken we don't do collectives here

Implements molpro::linalg::array::DistrArray.

at()

DistrArray::value_type molpro::linalg::array::DistrArrayFile::at ( DistrArray::index_type  ind ) const

overridevirtual

Returns

element at given index

Implements molpro::linalg::array::DistrArray.

compatible()

bool molpro::linalg::array::DistrArrayFile::compatible

(

const DistrArrayFile &

source

)

const

CreateTempCopy() [1/2]

DistrArrayFile molpro::linalg::array::DistrArrayFile::CreateTempCopy ( const DistrArray &  source, const std::string &  directory = ""  )

static

Creates a copy of source, with the same distribution and communicator, in a file which is erased on destruction.

Parameters

source	array to be copied
directory	directory for the file. If empty, the directory of the file of source is used if it is a disk array, otherwise the current directory.

CreateTempCopy() [2/2]

DistrArrayFile molpro::linalg::array::DistrArrayFile::CreateTempCopy ( Span< const value_type >  source, MPI_Comm  comm, const std::string &  directory = "."  )

static

Creates a copy of a contiguous array in a file which is erased on destruction.

Parameters

source	all elements of the array, the same on every process of comm
comm	the processes over which the new array is distributed
directory	directory for the file

erase()

void molpro::linalg::array::DistrArrayFile::erase ( )

inlineoverridevirtual

Dummy.

Implements molpro::linalg::array::DistrArrayDisk.

file_directory()

std::string molpro::linalg::array::DistrArrayFile::file_directory ( ) const

inlineoverridevirtual

The directory of the file holding this array, or an empty string if that is not known.

Reimplemented from molpro::linalg::array::DistrArrayDisk.

gather()

std::vector< DistrArrayFile::value_type > molpro::linalg::array::DistrArrayFile::gather ( const std::vector< index_type > &  indices ) const

overridevirtual

gets elements with discontinuous indices from array. Blocking

Returns

res[i] = array[indices[i]]

Implements molpro::linalg::array::DistrArray.

get() [1/2]

std::vector< DistrArrayFile::value_type > molpro::linalg::array::DistrArrayFile::get ( DistrArray::index_type  lo, DistrArray::index_type  hi  ) const

overridevirtual

Returns

a vector of values read from file

Implements molpro::linalg::array::DistrArray.

get() [2/2]

void molpro::linalg::array::DistrArrayFile::get ( DistrArray::index_type  lo, DistrArray::index_type  hi, DistrArray::value_type *  buf  ) const

overridevirtual

Reads requested values.

Implements molpro::linalg::array::DistrArray.

operator=() [1/2]

DistrArrayFile & molpro::linalg::array::DistrArrayFile::operator= ( const DistrArrayFile &  source )

delete

operator=() [2/2]

DistrArrayFile & molpro::linalg::array::DistrArrayFile::operator= ( DistrArrayFile &&  source )

noexcept

put()

void molpro::linalg::array::DistrArrayFile::put ( DistrArray::index_type  lo, DistrArray::index_type  hi, const value_type *  data  )

overridevirtual

Writes requested values to file.

Implements molpro::linalg::array::DistrArray.

scatter()

void molpro::linalg::array::DistrArrayFile::scatter ( const std::vector< index_type > &  indices, const std::vector< value_type > &  data  )

overridevirtual

array[indices[i]] = data[i] Puts vals of elements with discontinuous indices of array. Blocking.

Implements molpro::linalg::array::DistrArray.

scatter_acc()

void molpro::linalg::array::DistrArrayFile::scatter_acc ( std::vector< index_type > &  indices, const std::vector< value_type > &  data  )

overridevirtual

array[indices[i]] += vals[i] Accumulates vals of elements into discontinuous indices of array. Atomic, blocking, with on-sided communication

Implements molpro::linalg::array::DistrArray.

set()

void molpro::linalg::array::DistrArrayFile::set ( DistrArray::index_type  ind, DistrArray::value_type  val  )

overridevirtual

Writes value at a given index.

Implements molpro::linalg::array::DistrArray.

vec()

std::vector< DistrArrayFile::value_type > molpro::linalg::array::DistrArrayFile::vec ( ) const

overridevirtual

Copies the whole buffer into a vector. Blocking.

Note

This is only meant for debugging small arrays!

Implements molpro::linalg::array::DistrArray.

Friends And Related Symbol Documentation

swap

void swap ( DistrArrayFile &  x, DistrArrayFile &  y  )

friend