Private headers and defines for the PIO C interface. More...

#include <pio.h>
#include <bget.h>
#include <limits.h>
#include <math.h>

Classes
struct	mapsort
	Used to sort map points in the subset rearranger. More...

struct	pio_swapm_defaults
	swapm defaults. More...

Macros
#define	MPI_Offset long long

#define	LOG(e)

#define	max(a, b)

#define	min(a, b)

#define	MAX_GATHER_BLOCK_SIZE 0

#define	PIO_REQUEST_ALLOC_CHUNK 16

Typedefs
typedef struct mapsort	mapsort
	Used to sort map points in the subset rearranger. More...

typedef struct pio_swapm_defaults	pio_swapm_defaults
	swapm defaults. More...

Enumerations
enum	PIO_MSG { PIO_MSG_OPEN_FILE, PIO_MSG_CREATE_FILE, PIO_MSG_INQ_ATT, PIO_MSG_INQ_FORMAT, PIO_MSG_INQ_VARID, PIO_MSG_DEF_VAR, PIO_MSG_INQ_VAR, PIO_MSG_PUT_ATT_DOUBLE, PIO_MSG_PUT_ATT_INT, PIO_MSG_RENAME_ATT, PIO_MSG_DEL_ATT, PIO_MSG_INQ, PIO_MSG_GET_ATT_TEXT, PIO_MSG_GET_ATT_SHORT, PIO_MSG_PUT_ATT_LONG, PIO_MSG_REDEF, PIO_MSG_SET_FILL, PIO_MSG_ENDDEF, PIO_MSG_RENAME_VAR, PIO_MSG_PUT_ATT_SHORT, PIO_MSG_PUT_ATT_TEXT, PIO_MSG_INQ_ATTNAME, PIO_MSG_GET_ATT_ULONGLONG, PIO_MSG_GET_ATT_USHORT, PIO_MSG_PUT_ATT_ULONGLONG, PIO_MSG_GET_ATT_UINT, PIO_MSG_GET_ATT_LONGLONG, PIO_MSG_PUT_ATT_SCHAR, PIO_MSG_PUT_ATT_FLOAT, PIO_MSG_RENAME_DIM, PIO_MSG_GET_ATT_LONG, PIO_MSG_INQ_DIM, PIO_MSG_INQ_DIMID, PIO_MSG_PUT_ATT_USHORT, PIO_MSG_GET_ATT_FLOAT, PIO_MSG_SYNC, PIO_MSG_PUT_ATT_LONGLONG, PIO_MSG_PUT_ATT_UINT, PIO_MSG_GET_ATT_SCHAR, PIO_MSG_INQ_ATTID, PIO_MSG_DEF_DIM, PIO_MSG_GET_ATT_INT, PIO_MSG_GET_ATT_DOUBLE, PIO_MSG_PUT_ATT_UCHAR, PIO_MSG_GET_ATT_UCHAR, PIO_MSG_PUT_VARS_UCHAR, PIO_MSG_GET_VAR1_SCHAR, PIO_MSG_GET_VARS_ULONGLONG, PIO_MSG_GET_VARM_UCHAR, PIO_MSG_GET_VARM_SCHAR, PIO_MSG_GET_VARS_SHORT, PIO_MSG_GET_VAR_DOUBLE, PIO_MSG_GET_VARA_DOUBLE, PIO_MSG_GET_VAR_INT, PIO_MSG_GET_VAR_USHORT, PIO_MSG_PUT_VARS_USHORT, PIO_MSG_GET_VARA_TEXT, PIO_MSG_PUT_VARS_ULONGLONG, PIO_MSG_GET_VARA_INT, PIO_MSG_PUT_VARM, PIO_MSG_GET_VAR1_FLOAT, PIO_MSG_GET_VAR1_SHORT, PIO_MSG_GET_VARS_INT, PIO_MSG_PUT_VARS_UINT, PIO_MSG_GET_VAR_TEXT, PIO_MSG_GET_VARM_DOUBLE, PIO_MSG_PUT_VARM_UCHAR, PIO_MSG_PUT_VAR_USHORT, PIO_MSG_GET_VARS_SCHAR, PIO_MSG_GET_VARA_USHORT, PIO_MSG_PUT_VAR1_LONGLONG, PIO_MSG_PUT_VARA_UCHAR, PIO_MSG_PUT_VARM_SHORT, PIO_MSG_PUT_VAR1_LONG, PIO_MSG_PUT_VARS_LONG, PIO_MSG_GET_VAR1_USHORT, PIO_MSG_PUT_VAR_SHORT, PIO_MSG_PUT_VARA_INT, PIO_MSG_GET_VAR_FLOAT, PIO_MSG_PUT_VAR1_USHORT, PIO_MSG_PUT_VARA_TEXT, PIO_MSG_PUT_VARM_TEXT, PIO_MSG_GET_VARS_UCHAR, PIO_MSG_GET_VAR, PIO_MSG_PUT_VARM_USHORT, PIO_MSG_GET_VAR1_LONGLONG, PIO_MSG_GET_VARS_USHORT, PIO_MSG_GET_VAR_LONG, PIO_MSG_GET_VAR1_DOUBLE, PIO_MSG_PUT_VAR_ULONGLONG, PIO_MSG_PUT_VAR_INT, PIO_MSG_GET_VARA_UINT, PIO_MSG_PUT_VAR_LONGLONG, PIO_MSG_GET_VARS_LONGLONG, PIO_MSG_PUT_VAR_SCHAR, PIO_MSG_PUT_VAR_UINT, PIO_MSG_PUT_VAR, PIO_MSG_PUT_VARA_USHORT, PIO_MSG_GET_VAR_LONGLONG, PIO_MSG_GET_VARA_SHORT, PIO_MSG_PUT_VARS_SHORT, PIO_MSG_PUT_VARA_UINT, PIO_MSG_PUT_VARA_SCHAR, PIO_MSG_PUT_VARM_ULONGLONG, PIO_MSG_PUT_VAR1_UCHAR, PIO_MSG_PUT_VARM_INT, PIO_MSG_PUT_VARS_SCHAR, PIO_MSG_GET_VARA_LONG, PIO_MSG_PUT_VAR1, PIO_MSG_GET_VAR1_INT, PIO_MSG_GET_VAR1_ULONGLONG, PIO_MSG_GET_VAR_UCHAR, PIO_MSG_PUT_VARA_FLOAT, PIO_MSG_GET_VARA_UCHAR, PIO_MSG_GET_VARS_FLOAT, PIO_MSG_PUT_VAR1_FLOAT, PIO_MSG_PUT_VARM_FLOAT, PIO_MSG_PUT_VAR1_TEXT, PIO_MSG_PUT_VARS_TEXT, PIO_MSG_PUT_VARM_LONG, PIO_MSG_GET_VARS_LONG, PIO_MSG_PUT_VARS_DOUBLE, PIO_MSG_GET_VAR1, PIO_MSG_GET_VAR_UINT, PIO_MSG_PUT_VARA_LONGLONG, PIO_MSG_GET_VARA, PIO_MSG_PUT_VAR_DOUBLE, PIO_MSG_GET_VARA_SCHAR, PIO_MSG_PUT_VAR_FLOAT, PIO_MSG_GET_VAR1_UINT, PIO_MSG_GET_VARS_UINT, PIO_MSG_PUT_VAR1_ULONGLONG, PIO_MSG_PUT_VARM_UINT, PIO_MSG_PUT_VAR1_UINT, PIO_MSG_PUT_VAR1_INT, PIO_MSG_GET_VARA_FLOAT, PIO_MSG_GET_VARM_TEXT, PIO_MSG_PUT_VARS_FLOAT, PIO_MSG_GET_VAR1_TEXT, PIO_MSG_PUT_VARA_SHORT, PIO_MSG_PUT_VAR1_SCHAR, PIO_MSG_PUT_VARA_ULONGLONG, PIO_MSG_PUT_VARM_DOUBLE, PIO_MSG_GET_VARM_INT, PIO_MSG_PUT_VARA, PIO_MSG_PUT_VARA_LONG, PIO_MSG_GET_VARM_UINT, PIO_MSG_GET_VARM, PIO_MSG_PUT_VAR1_DOUBLE, PIO_MSG_GET_VARS_DOUBLE, PIO_MSG_GET_VARA_LONGLONG, PIO_MSG_GET_VAR_ULONGLONG, PIO_MSG_PUT_VARM_SCHAR, PIO_MSG_GET_VARA_ULONGLONG, PIO_MSG_GET_VAR_SHORT, PIO_MSG_GET_VARM_FLOAT, PIO_MSG_PUT_VAR_TEXT, PIO_MSG_PUT_VARS_INT, PIO_MSG_GET_VAR1_LONG, PIO_MSG_GET_VARM_LONG, PIO_MSG_GET_VARM_USHORT, PIO_MSG_PUT_VAR1_SHORT, PIO_MSG_PUT_VARS_LONGLONG, PIO_MSG_GET_VARM_LONGLONG, PIO_MSG_GET_VARS_TEXT, PIO_MSG_PUT_VARA_DOUBLE, PIO_MSG_PUT_VARS, PIO_MSG_PUT_VAR_UCHAR, PIO_MSG_GET_VAR1_UCHAR, PIO_MSG_PUT_VAR_LONG, PIO_MSG_GET_VARS, PIO_MSG_GET_VARM_SHORT, PIO_MSG_GET_VARM_ULONGLONG, PIO_MSG_PUT_VARM_LONGLONG, PIO_MSG_GET_VAR_SCHAR, PIO_MSG_GET_ATT_UBYTE, PIO_MSG_PUT_ATT_STRING, PIO_MSG_GET_ATT_STRING, PIO_MSG_PUT_ATT_UBYTE, PIO_MSG_INQ_VAR_FILL, PIO_MSG_DEF_VAR_FILL, PIO_MSG_DEF_VAR_DEFLATE, PIO_MSG_INQ_VAR_DEFLATE, PIO_MSG_INQ_VAR_SZIP, PIO_MSG_DEF_VAR_FLETCHER32, PIO_MSG_INQ_VAR_FLETCHER32, PIO_MSG_DEF_VAR_CHUNKING, PIO_MSG_INQ_VAR_CHUNKING, PIO_MSG_DEF_VAR_ENDIAN, PIO_MSG_INQ_VAR_ENDIAN, PIO_MSG_SET_CHUNK_CACHE, PIO_MSG_GET_CHUNK_CACHE, PIO_MSG_SET_VAR_CHUNK_CACHE, PIO_MSG_GET_VAR_CHUNK_CACHE, PIO_MSG_INITDECOMP_DOF, PIO_MSG_WRITEDARRAY, PIO_MSG_READDARRAY, PIO_MSG_SETERRORHANDLING, PIO_MSG_FREEDECOMP, PIO_MSG_CLOSE_FILE, PIO_MSG_DELETE_FILE, PIO_MSG_EXIT, PIO_MSG_GET_ATT, PIO_MSG_PUT_ATT, PIO_MSG_INQ_TYPE }
	These are the messages that can be sent over the intercomm when async is being used. More...

Functions
void	pio_get_env (void)
	Get PIO environment variables. More...

int	pio_add_to_iodesc_list (io_desc_t *iodesc)

io_desc_t *	pio_get_iodesc_from_id (int ioid)

int	pio_delete_iodesc_from_list (int ioid)

file_desc_t *	pio_get_file_from_id (int ncid)

int	pio_delete_file_from_list (int ncid)

void	pio_add_to_file_list (file_desc_t *file)
	Add a new entry to the global list of open files. More...

void	pio_push_request (file_desc_t *file, int request)

iosystem_desc_t *	pio_get_iosystem_from_id (int iosysid)

int	pio_add_to_iosystem_list (iosystem_desc_t *ios)

int	check_netcdf (file_desc_t file, const int status, const char fname, const int line)
	Check the result of a netCDF API call. More...

int	iotype_error (const int iotype, const char *fname, const int line)

void	piodie (const char msg, const char fname, const int line)

void	pioassert (bool exp, const char msg, const char fname, const int line)

int	CalcStartandCount (const int basetype, const int ndims, const int gdims, const int num_io_procs, const int myiorank, PIO_Offset start, PIO_Offset *kount)

void	CheckMPIReturn (const int ierr, const char file[], const int line)
	Wrapper for MPI calls to print the Error string on error.

int	pio_fc_gather (void sendbuf, const int sendcnt, const MPI_Datatype sendtype, void recvbuf, const int recvcnt, const MPI_Datatype recvtype, const int root, MPI_Comm comm, const int flow_cntl)
	Provides the functionality of MPI_Gather with flow control options.

int	pio_fc_gatherv (void sendbuf, const int sendcnt, const MPI_Datatype sendtype, void recvbuf, const int recvcnts[], const int recvdispl[], const MPI_Datatype recvtype, const int root, MPI_Comm comm, const int flow_cntl)
	Provides the functionality of MPI_Gatherv with flow control options.

int	pio_swapm (void sndbuf, int sndlths[], int sdispls[], MPI_Datatype stypes[], void rcvbuf, int rcvlths[], int rdispls[], MPI_Datatype rtypes[], MPI_Comm comm, const bool handshake, bool isend, const int max_requests)
	Provides the functionality of MPI_Alltoallw with flow control options.

long long	lgcd_array (int nain, long long *ain)

void	PIO_Offset_size (MPI_Datatype dtype, int tsize)

PIO_Offset	GCDblocksize (const int arrlen, const PIO_Offset arr_in[])

int	subset_rearrange_create (const iosystem_desc_t ios, const int maplen, PIO_Offset compmap[], const int gsize[], const int ndim, io_desc_t *iodesc)

int	box_rearrange_create (const iosystem_desc_t ios, const int maplen, const PIO_Offset compmap[], const int gsize[], const int ndim, io_desc_t *iodesc)

int	rearrange_io2comp (const iosystem_desc_t ios, io_desc_t iodesc, void sbuf, void *rbuf)

int	rearrange_comp2io (const iosystem_desc_t ios, io_desc_t iodesc, void sbuf, void *rbuf, const int nvars)

int	calcdisplace (const int bsize, const int numblocks, const PIO_Offset map[], int displace[])

io_desc_t *	malloc_iodesc (const int piotype, const int ndims)

void	performance_tune_rearranger (iosystem_desc_t ios, io_desc_t *iodesc)

int	flush_output_buffer (file_desc_t *file, bool force, PIO_Offset addsize)
	Flush the output buffer. More...

void	compute_maxIObuffersize (MPI_Comm io_comm, io_desc_t *iodesc)

io_region *	alloc_region (const int ndims)

int	pio_delete_iosystem_from_list (int piosysid)
	Delete iosystem info from list. More...

int	gcd (int a, int b)

long long	lgcd (long long a, long long b)

int	gcd_array (int nain, int *ain)

void	free_region_list (io_region *top)

void	gindex_to_coord (const int ndims, const PIO_Offset gindex, const PIO_Offset gstride[], PIO_Offset *gcoord)

PIO_Offset	coord_to_lindex (const int ndims, const PIO_Offset lcoord[], const PIO_Offset count[])

int	ceil2 (const int i)
	Returns the smallest power of 2 greater than i.

int	pair (const int np, const int p, const int k)
	Given integers p and k between 0 and np-1, if (p+1)^k <= np-1 then return (p+1)^k else -1.

int	define_iodesc_datatypes (const iosystem_desc_t ios, io_desc_t *iodesc)

int	create_mpi_datatypes (const MPI_Datatype basetype, const int msgcnt, const PIO_Offset dlen, const PIO_Offset mindex[], const int mcount[], int *mfrom, MPI_Datatype mtype[])

int	compare_offsets (const void a, const void b)

void	print_trace (FILE *fp)

void	cn_buffer_report (iosystem_desc_t ios, bool collective)
	Print out info about the buffer for debug purposes. More...

void	compute_buffer_init (iosystem_desc_t ios)
	Initialize the compute buffer to size PIO_CNBUFFER_LIMIT. More...

void	free_cn_buffer_pool (iosystem_desc_t ios)
	Free the buffer pool. More...

void	flush_buffer (int ncid, wmulti_buffer *wmb, bool flushtodisk)
	Flush the buffer. More...

void	piomemerror (iosystem_desc_t ios, size_t req, char *fname, const int line)

void	compute_maxaggregate_bytes (const iosystem_desc_t ios, io_desc_t *iodesc)
	Compute the maximum aggregate number of bytes. More...

int	check_mpi (file_desc_t file, const int mpierr, const char filename, const int line)
	Handle MPI errors. More...

Variables
PIO_Offset	PIO_BUFFER_SIZE_LIMIT

bool	PIO_Save_Decomps

Detailed Description

Private headers and defines for the PIO C interface.

Author: Jim Edwards

Date: 2014

See also: http://code.google.com/p/parallelio/

Macro Definition Documentation

§ max

#define max	(	a,
		b
	)

Value:

({ __typeof__ (a) _a = (a);         \
    __typeof__ (b) _b = (b);        \
    _a > _b ? _a : _b; })

§ min

#define min	(	a,
		b
	)

Value:

({ __typeof__ (a) _a = (a);         \
    __typeof__ (b) _b = (b);        \
    _a < _b ? _a : _b; })

Typedef Documentation

§ mapsort

typedef struct mapsort mapsort

Used to sort map points in the subset rearranger.

§ pio_swapm_defaults

typedef struct pio_swapm_defaults pio_swapm_defaults

swapm defaults.

Enumeration Type Documentation

§ PIO_MSG

enum PIO_MSG

These are the messages that can be sent over the intercomm when async is being used.

Function Documentation

§ box_rearrange_create()

int box_rearrange_create	(	const iosystem_desc_t	ios,
		const int	maplen,
		const PIO_Offset	compmap[],
		const int	gsize[],
		const int	ndims,
		io_desc_t *	iodesc
	)

§ check_mpi()

int check_mpi	(	file_desc_t *	file,
		const int	mpierr,
		const char *	filename,
		const int	line
	)

Handle MPI errors.

An error message is sent to stderr, then the check_netcdf() function is called with PIO_EIO.

Parameters

file	pointer to the file_desc_t info. May be NULL, in which case check_netcdf() is not called.
mpierr	the MPI return code to handle
filename	the name of the code file where error occured.
line	the line of code where error occured.

Returns: PIO_NOERR for no error, otherwise PIO_EIO.

§ check_netcdf()

int check_netcdf	(	file_desc_t *	file,
		int	status,
		const char *	fname,
		const int	line
	)

Check the result of a netCDF API call.

Parameters

file	pointer to the PIO structure describing this file.
status	the return value from the netCDF call.
fname	the name of the code file.
line	the line number of the netCDF call in the code.

Returns: the error code

§ cn_buffer_report()

void cn_buffer_report	(	iosystem_desc_t	ios,
		bool	collective
	)

Print out info about the buffer for debug purposes.

Parameters

ios	the IO system structure
collective	true if collective report is desired

§ compare_offsets()

int compare_offsets	(	const void *	a,
		const void *	b
	)

§ compute_buffer_init()

void compute_buffer_init ( iosystem_desc_t ios )

Initialize the compute buffer to size PIO_CNBUFFER_LIMIT.

This routine initializes the compute buffer pool if the bget memory management is used. If malloc is used (that is, PIO_USE_MALLOC is non zero), this function does nothing.

Parameters

ios	the iosystem descriptor which will use the new buffer

§ compute_maxaggregate_bytes()

void compute_maxaggregate_bytes	(	const iosystem_desc_t	ios,
		io_desc_t *	iodesc
	)

Compute the maximum aggregate number of bytes.

Parameters

ios	the IO system structure
iodesc	a pointer to the defined iodescriptor for the buffer

§ compute_maxIObuffersize()

void compute_maxIObuffersize	(	MPI_Comm	io_comm,
		io_desc_t *	iodesc
	)

§ coord_to_lindex()

PIO_Offset coord_to_lindex	(	const int	ndims,
		const PIO_Offset	lcoord[],
		const PIO_Offset	count[]
	)

§ create_mpi_datatypes()

int create_mpi_datatypes	(	const MPI_Datatype	basetype,
		const int	msgcnt,
		const PIO_Offset	dlen,
		const PIO_Offset	mindex[],
		const int	mcount[],
		int *	mfrom,
		MPI_Datatype	mtype[]
	)

§ define_iodesc_datatypes()

int define_iodesc_datatypes	(	const iosystem_desc_t	ios,
		io_desc_t *	iodesc
	)

§ flush_buffer()

void flush_buffer	(	int	ncid,
		wmulti_buffer *	wmb,
		bool	flushtodisk
	)

Flush the buffer.

Parameters

ncid	identifies the netCDF file
wmb
flushtodisk

§ flush_output_buffer()

int flush_output_buffer	(	file_desc_t *	file,
		bool	force,
		PIO_Offset	addsize
	)

Flush the output buffer.

This is only relevant for files opened with pnetcdf.

Parameters

file	a pointer to the open file descriptor for the file that will be written to
force	true to force the flushing of the buffer
addsize	additional size to add to buffer (in bytes)

Returns: 0 for success, error code otherwise.

§ free_cn_buffer_pool()

void free_cn_buffer_pool ( iosystem_desc_t ios )

Free the buffer pool.

If malloc is used (that is, PIO_USE_MALLOC is non zero), this function does nothing.

Parameters

ios	the IO system structure

§ pio_add_to_file_list()

void pio_add_to_file_list ( file_desc_t * file )

Add a new entry to the global list of open files.

Parameters

file	pointer to the file_desc_t struct for the new file.

§ pio_delete_iosystem_from_list()

int pio_delete_iosystem_from_list ( int piosysid )

Delete iosystem info from list.

§ pio_get_env()

void pio_get_env ( void )

Get PIO environment variables.

§ rearrange_comp2io()

int rearrange_comp2io	(	const iosystem_desc_t	ios,
		io_desc_t *	iodesc,
		void *	sbuf,
		void *	rbuf,
		const int	nvars
	)

§ rearrange_io2comp()

int rearrange_io2comp	(	const iosystem_desc_t	ios,
		io_desc_t *	iodesc,
		void *	sbuf,
		void *	rbuf
	)

§ subset_rearrange_create()

int subset_rearrange_create	(	const iosystem_desc_t	ios,
		const int	maplen,
		PIO_Offset	compmap[],
		const int	gsize[],
		const int	ndims,
		io_desc_t *	iodesc
	)

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Macro Definition Documentation

§ max

§ min

Typedef Documentation

§ mapsort

§ pio_swapm_defaults

Enumeration Type Documentation

§ PIO_MSG

Function Documentation

§ box_rearrange_create()

§ check_mpi()

§ check_netcdf()

§ cn_buffer_report()

§ compare_offsets()

§ compute_buffer_init()

§ compute_maxaggregate_bytes()

§ compute_maxIObuffersize()

§ coord_to_lindex()

§ create_mpi_datatypes()

§ define_iodesc_datatypes()

§ flush_buffer()

§ flush_output_buffer()

§ free_cn_buffer_pool()

§ pio_add_to_file_list()

§ pio_delete_iosystem_from_list()

§ pio_get_env()

§ rearrange_comp2io()

§ rearrange_io2comp()

§ subset_rearrange_create()