DynProgr_PPU.c File Reference

PPU frontend to the alignment routines on the SPU. More...

#include <stdio.h>
#include <malloc.h>
#include <libspe2.h>
#include <sys/wait.h>
#include <sys/types.h>
#include <errno.h>
#include "DynProgr_SPE.h"
#include <string.h>
#include <stdbool.h>
#include <ctype.h>
#include <limits.h>
#include <time.h>
#include <math.h>
#include <float.h>
#include <assert.h>
#include "debug.h"
#include "swps3.h"
#include "matrix.h"
#include "DynProgr_scalar.h"
#include "DynProgr_PPU.h"
#include "DynProgr_PPU_profile.inc"

Include dependency graph for DynProgr_PPU.c:

Go to the source code of this file.

Defines

#define MAX(a, b)   (a>b?a:b)

#define MIN(a, b)   (a<b?a:b)

#define T   float

#define T   int16_t

#define T   int8_t

Functions

static int SPEAlign (const char *db, int dbLen, double *result)

static int SPECreateProfile (const char *query, int queryLen, const void *matrix, double min, double max)

Creates a profile in the SPE's memory.

static int SPEGetProfile (const SPEProfile *profile)

static int SPEInit (int dataType, int maxDbLen, Options *options)

Initializes a SPE.

static int SPEPutProfile (void *profile, int *blockSize)

static int submitSPECommand (SPECommand *command)

Sends a SPECommand to the SPE.

EXPORT double swps3_alignmentByteSPE (const SBMatrix matrix, const char *query, int queryLen, const char *db, int dbLen, Options *options)

EXPORT double swps3_alignmentFloatSPE (const SBMatrix matrix, const char *query, int queryLen, const char *db, int dbLen, Options *options)

EXPORT double swps3_alignmentProfileSPE (const char *db, int dbLen)

Profile must have been loaded before!

EXPORT double swps3_alignmentShortSPE (const SBMatrix matrix, const char *query, int queryLen, const char *db, int dbLen, Options *options)

EXPORT SPEProfile * swps3_createProfileBytePPU (const char *query, int queryLen, const SBMatrix matrix, int maxDbLen)

EXPORT SPEProfile * swps3_createProfileFloatPPU (const char *query, int queryLen, const SBMatrix matrix, int maxDbLen)

EXPORT SPEProfile * swps3_createProfileShortPPU (const char *query, int queryLen, const SBMatrix matrix, int maxDbLen)

EXPORT void swps3_freeProfilePPU (SPEProfile *profile)

EXPORT void swps3_loadProfileByte (SPEProfile *profile, int maxDbLen, Options *options)

EXPORT void swps3_loadProfileFloat (SPEProfile *profile, int maxDbLen, Options *options)

EXPORT void swps3_loadProfileShort (SPEProfile *profile, int maxDbLen, Options *options)

Variables

static spe_context_ptr_t spe_context = NULL

spe_program_handle_t spe_dynprogr_handle

Detailed Description

PPU frontend to the alignment routines on the SPU.

Definition in file DynProgr_PPU.c.

Define Documentation

#define MAX	(	a,
		b		)	(a>b?a:b)

Definition at line 57 of file DynProgr_PPU.c.

#define MIN	(	a,
		b		)	(a<b?a:b)

Definition at line 58 of file DynProgr_PPU.c.

#define T float

Definition at line 372 of file DynProgr_PPU.c.

#define T int16_t

Definition at line 372 of file DynProgr_PPU.c.

#define T int8_t

Definition at line 372 of file DynProgr_PPU.c.

Referenced by allocateProfile(), doCreateProfile(), dynProgrLocal(), dynProgrLocal2(), dynProgrLocalBlock(), swps3_createProfileAltivec(), swps3_dynProgrAltivec(), TcreateProfile(), and TdynProgLocal().

Function Documentation

static int SPEAlign	(	const char *	db,
		int	dbLen,
		double *	result
	)			`[static]`

Definition at line 196 of file DynProgr_PPU.c.

static int SPECreateProfile	(	const char *	query,
		int	queryLen,
		const void *	matrix,
		double	min,
		double	max
	)			`[static]`

Creates a profile in the SPE's memory.

Parameters:

	query	The query sequence.
	queryLen	The length of the query sequence.
	matrix	The scoring matrix with entries of the same type as specified in the SPEInit command.
	min	The highest value in the scoring matrix.
	max	The lowest value in the scoring matrix.

See also:: SPEInit()

Returns:: Nonzero on error.

Definition at line 154 of file DynProgr_PPU.c.

static int SPEGetProfile ( const SPEProfile * profile ) [static]

Definition at line 169 of file DynProgr_PPU.c.

static int SPEInit	(	int	dataType,
		int	maxDbLen,
		Options *	options
	)			`[static]`

Initializes a SPE.

Parameters:

	dataType	The data type for the computation. Must be one of SPE_ALIGNMENT_TYPE_DOUBLE, SPE_ALIGNMENT_TYPE_FLOAT, SPE_ALIGNMENT_TYPE_INT, SPE_ALIGNMENT_TYPE_SHORT, SPE_ALIGNMENT_TYPE_BYTE.
	maxDbLen	Maximal possible length of the database sequence.
	options	Program options.

Returns:: Nonzero on error.

Definition at line 129 of file DynProgr_PPU.c.

static int SPEPutProfile	(	void *	profile,
		int *	blockSize
	)			`[static]`

Definition at line 179 of file DynProgr_PPU.c.

static int submitSPECommand ( SPECommand * command ) [static]

Sends a SPECommand to the SPE.

Parameters:

command

A SPEcommand.

Returns:: Returns nonzero on error.

Definition at line 102 of file DynProgr_PPU.c.

EXPORT double swps3_alignmentByteSPE	(	const SBMatrix	matrix,
		const char *	query,
		int	queryLen,
		const char *	db,
		int	dbLen,
		Options *	options
	)

Definition at line 214 of file DynProgr_PPU.c.

Referenced by main().

EXPORT double swps3_alignmentFloatSPE	(	const SBMatrix	matrix,
		const char *	query,
		int	queryLen,
		const char *	db,
		int	dbLen,
		Options *	options
	)

Definition at line 276 of file DynProgr_PPU.c.

EXPORT double swps3_alignmentProfileSPE	(	const char *	db,
		int	dbLen
	)

Profile must have been loaded before!

Definition at line 311 of file DynProgr_PPU.c.

Referenced by main().

EXPORT double swps3_alignmentShortSPE	(	const SBMatrix	matrix,
		const char *	query,
		int	queryLen,
		const char *	db,
		int	dbLen,
		Options *	options
	)

Definition at line 244 of file DynProgr_PPU.c.

Referenced by main().

EXPORT SPEProfile* swps3_createProfileBytePPU	(	const char *	query,
		int	queryLen,
		const SBMatrix	matrix,
		int	maxDbLen
	)

Definition at line 356 of file DynProgr_PPU.c.

Referenced by main().

EXPORT SPEProfile* swps3_createProfileFloatPPU	(	const char *	query,
		int	queryLen,
		const SBMatrix	matrix,
		int	maxDbLen
	)

Definition at line 373 of file DynProgr_PPU.c.

Referenced by main().

EXPORT SPEProfile* swps3_createProfileShortPPU	(	const char *	query,
		int	queryLen,
		const SBMatrix	matrix,
		int	maxDbLen
	)

Definition at line 366 of file DynProgr_PPU.c.

Referenced by main().

EXPORT void swps3_freeProfilePPU ( SPEProfile * profile )

Definition at line 379 of file DynProgr_PPU.c.

References SPEProfile::addr.

Referenced by main().

EXPORT void swps3_loadProfileByte	(	SPEProfile *	profile,
		int	maxDbLen,
		Options *	options
	)

Definition at line 322 of file DynProgr_PPU.c.

Referenced by main().

EXPORT void swps3_loadProfileFloat	(	SPEProfile *	profile,
		int	maxDbLen,
		Options *	options
	)

Definition at line 344 of file DynProgr_PPU.c.

EXPORT void swps3_loadProfileShort	(	SPEProfile *	profile,
		int	maxDbLen,
		Options *	options
	)

Definition at line 333 of file DynProgr_PPU.c.

Referenced by main().

Variable Documentation

spe_context_ptr_t spe_context = NULL [static]

Definition at line 94 of file DynProgr_PPU.c.

spe_program_handle_t spe_dynprogr_handle

Generated on Thu Jun 5 12:44:40 2008 for swps3 by

1.5.4


Defines
#define	MAX(a, b) (a>b?a:b)
#define	MIN(a, b) (a<b?a:b)
#define	T float
#define	T int16_t
#define	T int8_t
Functions
static int	SPEAlign (const char db, int dbLen, double result)
static int	SPECreateProfile (const char query, int queryLen, const void matrix, double min, double max)
	Creates a profile in the SPE's memory.
static int	SPEGetProfile (const SPEProfile *profile)
static int	SPEInit (int dataType, int maxDbLen, Options *options)
	Initializes a SPE.
static int	SPEPutProfile (void profile, int blockSize)
static int	submitSPECommand (SPECommand *command)
	Sends a SPECommand to the SPE.
EXPORT double	swps3_alignmentByteSPE (const SBMatrix matrix, const char query, int queryLen, const char db, int dbLen, Options *options)
EXPORT double	swps3_alignmentFloatSPE (const SBMatrix matrix, const char query, int queryLen, const char db, int dbLen, Options *options)
EXPORT double	swps3_alignmentProfileSPE (const char *db, int dbLen)
	Profile must have been loaded before!
EXPORT double	swps3_alignmentShortSPE (const SBMatrix matrix, const char query, int queryLen, const char db, int dbLen, Options *options)
EXPORT SPEProfile *	swps3_createProfileBytePPU (const char *query, int queryLen, const SBMatrix matrix, int maxDbLen)
EXPORT SPEProfile *	swps3_createProfileFloatPPU (const char *query, int queryLen, const SBMatrix matrix, int maxDbLen)
EXPORT SPEProfile *	swps3_createProfileShortPPU (const char *query, int queryLen, const SBMatrix matrix, int maxDbLen)
EXPORT void	swps3_freeProfilePPU (SPEProfile *profile)
EXPORT void	swps3_loadProfileByte (SPEProfile profile, int maxDbLen, Options options)
EXPORT void	swps3_loadProfileFloat (SPEProfile profile, int maxDbLen, Options options)
EXPORT void	swps3_loadProfileShort (SPEProfile profile, int maxDbLen, Options options)
Variables
static spe_context_ptr_t	spe_context = NULL
spe_program_handle_t	spe_dynprogr_handle