Classes
struct	write_buffers

Enumerations
enum	MPIIOOutputFields : unsigned int { MPIIO_OUT_NON = 0u , MPIIO_OUT_POS = 1u , MPIIO_OUT_VEL = 2u , MPIIO_OUT_TYP = 4u , MPIIO_OUT_BND = 8u }
	Constants which indicate what to output. More...

Functions
static bool	fatal_error (char const *msg, std::string const &fn="", std::string const &extra="")
	Fatal error handler.

static bool	fatal_error (char const msg, std::string const &fn, MPI_File fp, int errnum)
	Fatal error handler that closes an open file and queries the message associated with an MPI error code.

template<typename T >
static void	mpiio_dump_array (const std::string &fn, T const *arr, std::size_t len, std::size_t pref, MPI_Datatype MPI_T)
	Dump data `arr` of size `len` starting from prefix `pref` of type `T` using `MPI_T` as MPI datatype.

static unsigned long	mpi_calculate_file_offset (unsigned long n_items)
	Calculate the file offset on the local node.

static void	dump_info (std::string const &fn, unsigned fields, BondedInteractionsMap const &bonded_ias)
	Dump the fields and bond information.

void	mpi_mpiio_common_write (std::string const &prefix, unsigned fields, BondedInteractionsMap const &bonded_ias, ParticleRange const &particles, write_buffers &buffers)
	Parallel binary output using MPI-IO.

static unsigned long	get_num_elem (const std::string &fn, std::size_t elem_sz)
	Get the number of elements in a file by its file size and `elem_sz`.

template<typename T >
static void	mpiio_read_array (const std::string &fn, T *arr, std::size_t len, std::size_t pref, MPI_Datatype MPI_T)
	Read a previously dumped array of size `len` starting from prefix `pref` of type `T` using `MPI_T` as MPI datatype.

static unsigned	read_head (const std::string &fn, int rank)
	Read the header file and return the first value.

static std::tuple< unsigned long, unsigned long >	read_prefs (const std::string &fn, int rank, int size, unsigned long nglobalpart)
	Read the pref file.

void	mpi_mpiio_common_read (std::string const &prefix, unsigned fields, CellStructure &cell_structure)
	Parallel binary input using MPI-IO.

Enumeration Type Documentation

◆ MPIIOOutputFields

enum Mpiio::MPIIOOutputFields : unsigned int

Constants which indicate what to output.

To indicate the output of multiple fields, OR the corresponding values.

Enumerator
MPIIO_OUT_NON
MPIIO_OUT_POS
MPIIO_OUT_VEL
MPIIO_OUT_TYP
MPIIO_OUT_BND

Definition at line 41 of file core/io/mpiio/mpiio.hpp.

Function Documentation

◆ dump_info()

static void Mpiio::dump_info	(	std::string const &	fn,
		unsigned	fields,
		BondedInteractionsMap const &	bonded_ias
	)

static

Dump the fields and bond information.

To be called by the head node only.

Parameters

fn	The filename to write to
fields	The dumped fields
bonded_ias	The list of bonds

Definition at line 189 of file mpiio.cpp.

References BondedInteractionsMap::at(), BondedInteractionsMap::contains(), fatal_error(), BondedInteractionsMap::get_next_key(), number_of_partners(), and BondedInteractionsMap::size().

Referenced by mpi_mpiio_common_write().

◆ fatal_error() [1/2]

static bool Mpiio::fatal_error	(	char const *	msg,
		std::string const &	fn,
		MPI_File *	fp,
		int	errnum
	)

static

Fatal error handler that closes an open file and queries the message associated with an MPI error code.

On 1 MPI rank the error is recoverable and an exception is thrown. On more than 1 MPI rank the error is not recoverable.

Parameters

msg	Custom error message
fn	File path
fp	File handle
errnum	MPI error code

Definition at line 122 of file mpiio.cpp.

References fatal_error().

◆ fatal_error() [2/2]

static bool Mpiio::fatal_error	(	char const *	msg,
		std::string const &	fn = `""`,
		std::string const &	extra = `""`
	)

static

Fatal error handler.

On 1 MPI rank the error is recoverable and an exception is thrown. On more than 1 MPI rank the error is not recoverable.

Parameters

msg	Custom error message
fn	File path
extra	Extra context

Definition at line 92 of file mpiio.cpp.

References errexit().

Referenced by dump_info(), fatal_error(), get_num_elem(), mpi_mpiio_common_read(), mpiio_dump_array(), mpiio_read_array(), and read_head().

◆ get_num_elem()

static unsigned long Mpiio::get_num_elem	(	const std::string &	fn,
		std::size_t	elem_sz
	)

static

Get the number of elements in a file by its file size and elem_sz.

I.e. query the file size using stat(2) and divide it by elem_sz.

Parameters

fn	The filename
elem_sz	Size of a single element

Returns: The number of elements stored in the file

Definition at line 310 of file mpiio.cpp.

References fatal_error().

Referenced by mpi_mpiio_common_read().

◆ mpi_calculate_file_offset()

static unsigned long Mpiio::mpi_calculate_file_offset ( unsigned long n_items )

static

Calculate the file offset on the local node.

Parameters

n_items Number of items on the local node.

Returns: The number of items on all nodes with lower rank.

Definition at line 175 of file mpiio.cpp.

Referenced by mpi_mpiio_common_read(), and mpi_mpiio_common_write().

◆ mpi_mpiio_common_read()

void Mpiio::mpi_mpiio_common_read	(	std::string const &	prefix,
		unsigned	fields,
		CellStructure &	cell_structure
	)

Parallel binary input using MPI-IO.

To be called by all MPI processes. Aborts ESPResSo if an error occurs. On 1 MPI rank, the error is converted to a runtime error and can be recovered.

Parameters

prefix	Filepath prefix.
fields	Specifier for which fields to read.
cell_structure	Bonds to serialize.

Definition at line 406 of file mpiio.cpp.

References CellStructure::add_particle(), fatal_error(), get_num_elem(), mpi_calculate_file_offset(), MPIIO_OUT_BND, MPIIO_OUT_POS, MPIIO_OUT_TYP, MPIIO_OUT_VEL, read_head(), read_prefs(), and CellStructure::remove_all_particles().

Referenced by ScriptInterface::MPIIO::MPIIOScript::do_call_method().

◆ mpi_mpiio_common_write()

void Mpiio::mpi_mpiio_common_write	(	std::string const &	prefix,
		unsigned	fields,
		BondedInteractionsMap const &	bonded_ias,
		ParticleRange const &	particles,
		write_buffers &	buffers
	)

Parallel binary output using MPI-IO.

To be called by all MPI processes. Aborts ESPResSo if an error occurs. On 1 MPI rank, the error is converted to a runtime error and can be recovered by removing any file that may have already been written.

Parameters

prefix	Filepath prefix.
fields	Specifier for which fields to dump.
bonded_ias	Bonds to serialize.
particles	Range of particles to serialize.
buffers	Write buffers.

Definition at line 214 of file mpiio.cpp.

References dump_info(), Mpiio::write_buffers::id, mpi_calculate_file_offset(), MPIIO_OUT_BND, MPIIO_OUT_POS, MPIIO_OUT_TYP, MPIIO_OUT_VEL, Mpiio::write_buffers::pos, ParticleRange::size(), Mpiio::write_buffers::type, and Mpiio::write_buffers::vel.

Referenced by ScriptInterface::MPIIO::MPIIOScript::do_call_method().

◆ mpiio_dump_array()

template<typename T >

static void Mpiio::mpiio_dump_array	(	const std::string &	fn,
		T const *	arr,
		std::size_t	len,
		std::size_t	pref,
		MPI_Datatype	MPI_T
	)

static

Dump data arr of size len starting from prefix pref of type T using MPI_T as MPI datatype.

Beware, that T and MPI_T have to match!

Parameters

fn	The file name to write to (must not already exist!)
arr	The array to dump
len	The number of elements to dump
pref	The prefix for this process
MPI_T	The MPI datatype corresponding to the template parameter `T`

Definition at line 148 of file mpiio.cpp.

References fatal_error().

◆ mpiio_read_array()

template<typename T >

static void Mpiio::mpiio_read_array	(	const std::string &	fn,
		T *	arr,
		std::size_t	len,
		std::size_t	pref,
		MPI_Datatype	MPI_T
	)

static

Read a previously dumped array of size len starting from prefix pref of type T using MPI_T as MPI datatype.

Beware, that T and MPI_T have to match!

Parameters

fn	The file name to read from
arr	The array to populate
len	The number of elements to read
pref	The prefix for this process
MPI_T	The MPI datatype corresponding to the template parameter `T`

Definition at line 334 of file mpiio.cpp.

References fatal_error().

◆ read_head()

static unsigned Mpiio::read_head	(	const std::string &	fn,
		int	rank
	)

static

Read the header file and return the first value.

To be called by all processes.

Parameters

fn	Filename of the head file
rank	The rank of the current process in `MPI_COMM_WORLD`

Definition at line 361 of file mpiio.cpp.

References fatal_error().

Referenced by mpi_mpiio_common_read().

◆ read_prefs()

static std::tuple< unsigned long, unsigned long > Mpiio::read_prefs	(	const std::string &	fn,
		int	rank,
		int	size,
		unsigned long	nglobalpart
	)

static

Read the pref file.

Needs to be called by all processes.

Parameters

fn	The file name of the prefs file
rank	The rank of the current process in `MPI_COMM_WORLD`
size	The size of `MPI_COMM_WORLD`
nglobalpart	The global amount of particles

Returns: The prefix and the local number of particles.

Definition at line 388 of file mpiio.cpp.

Referenced by mpi_mpiio_common_read().

Classes

Enumerations

Functions

Enumeration Type Documentation

◆ MPIIOOutputFields

Function Documentation

◆ dump_info()

◆ fatal_error() [1/2]

◆ fatal_error() [2/2]

◆ get_num_elem()

◆ mpi_calculate_file_offset()

◆ mpi_mpiio_common_read()

◆ mpi_mpiio_common_write()

◆ mpiio_dump_array()

◆ mpiio_read_array()

◆ read_head()

◆ read_prefs()