H5Part.c 73.7 KB
Newer Older
gsell's avatar
gsell committed
1 2 3 4 5 6 7 8 9
/*! \mainpage H5Part: A Portable High Performance Parallel Data Interface to HDF5

Particle based simulations of accelerator beam-lines, especially in
six dimensional phase space, generate vast amounts of data. Even
though a subset of statistical information regarding phase space or
analysis needs to be preserved, reading and writing such enormous
restart files on massively parallel supercomputing systems remains
challenging. 

Kurt Stockinger's avatar
Kurt Stockinger committed
10
H5Part consists of Particles and Block structured Fields.
gsell's avatar
gsell committed
11

Kurt Stockinger's avatar
Kurt Stockinger committed
12
Developed by:
gsell's avatar
gsell committed
13

Kurt Stockinger's avatar
Kurt Stockinger committed
14 15 16 17 18 19 20 21 22
<UL>
<LI> Andreas Adelmann (PSI) </LI>
<LI> Achim Gsell (PSI) </LI>
<LI> Benedikt Oswald (PSI) </LI>

<LI> Wes Bethel (NERSC/LBNL)</LI>
<LI> John Shalf (NERSC/LBNL)</LI>
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
</UL>
gsell's avatar
gsell committed
23 24 25 26


Papers: 

Kurt Stockinger's avatar
Kurt Stockinger committed
27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
<UL>
<LI> A. Adelmann, R.D. Ryne, C. Siegerist, J. Shalf,"From Visualization to Data Mining with Large Data Sets," <i>
<a href="http://www.sns.gov/pac05">Particle Accelerator Conference (PAC05)</a></i>, Knoxville TN., May 16-20, 2005. (LBNL-57603)
<a href="http://vis.lbl.gov/Publications/2005/FPAT082.pdf">FPAT082.pdf</a>
</LI>


<LI> A. Adelmann, R.D. Ryne, J. Shalf, C. Siegerist,"H5Part: A Portable High Performance Parallel Data Interface for Particle Simulations," <i>
<a href="http://www.sns.gov/pac05">Particle Accelerator Conference (PAC05)</a></i>, Knoxville TN., May 16-20, 2005.
<a href="http://vis.lbl.gov/Publications/2005/FPAT083.pdf">FPAT083.pdf</a>
</LI>
</UL>

For further information contact: <a href="mailto:h5part@lists.psi.ch">h5part</a>

Last modified on April 19, 2007.

gsell's avatar
gsell committed
44 45
*/

gsell's avatar
gsell committed
46 47

/*!
gsell's avatar
gsell committed
48
  \defgroup h5part_c_api H5Part C API
gsell's avatar
gsell committed
49 50 51

*/
/*!
gsell's avatar
gsell committed
52
  \ingroup h5part_c_api
gsell's avatar
gsell committed
53 54 55
  \defgroup h5part_openclose	File Opening and Closing
*/
/*!
gsell's avatar
gsell committed
56
  \ingroup h5part_c_api
gsell's avatar
gsell committed
57 58 59
  \defgroup h5part_write	File Writing
*/  
/*!
gsell's avatar
gsell committed
60
  \ingroup h5part_c_api
gsell's avatar
gsell committed
61 62 63
  \defgroup h5part_read		File Reading
*/  
/*!
gsell's avatar
gsell committed
64
  \ingroup h5part_c_api
gsell's avatar
gsell committed
65 66 67
  \defgroup h5part_attrib	Reading and Writing Attributes
*/
/*!
gsell's avatar
gsell committed
68
  \ingroup h5part_c_api
gsell's avatar
gsell committed
69 70 71 72 73 74 75 76
  \defgroup h5part_errhandle	Error Handling
*/
/*!
  \internal
  \defgroup h5partkernel H5Part private functions 
*/


gsell's avatar
gsell committed
77 78 79 80 81 82 83 84
#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h>	/* va_arg - System dependent ?! */
#include <string.h>
#include <errno.h>
#include <fcntl.h>
#include <hdf5.h>

gsell's avatar
gsell committed
85 86 87 88 89 90 91 92
#ifndef WIN32
#include <unistd.h>
#else /* WIN32 */
#include <io.h>
#define open  _open
#define close _close
#endif /* WIN32 */

gsell's avatar
gsell committed
93 94 95 96 97 98 99 100
#include "H5PartTypes.h"
#include "H5Part.h"
#include "H5PartPrivate.h"
#include "H5PartErrors.h"

/********* Private Variable Declarations *************/

static unsigned			_debug = 0;
gsell's avatar
gsell committed
101
static h5part_int64_t		_h5part_errno = H5PART_SUCCESS;
gsell's avatar
gsell committed
102
static h5part_error_handler	_err_handler = H5PartReportErrorHandler;
103
static char *__funcname;
gsell's avatar
gsell committed
104 105 106 107 108 109 110 111 112 113 114 115 116

/********** Declaration of private functions ******/

static h5part_int64_t
_init(
	void
	);

static h5part_int64_t
_file_is_valid (
	const H5PartFile *f
	);

gsell's avatar
gsell committed
117 118 119
/*
  error handler for hdf5
*/
gsell's avatar
gsell committed
120 121
static herr_t
_h5_error_handler (
122 123 124
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	hid_t,
#endif
gsell's avatar
gsell committed
125 126 127 128 129
	void *
	);

/*========== File Opening/Closing ===============*/

gsell's avatar
gsell committed
130 131
static H5PartFile*
_H5Part_open_file (
gsell's avatar
gsell committed
132
	const char *filename,	/*!< [in] The name of the data file to open. */
133
	const char flags,	/*!< [in] The access mode for the file. */
gsell's avatar
gsell committed
134
	MPI_Comm comm,		/*!< [in] MPI communicator */
135 136 137 138
	int f_parallel,		/*!< [in] 0 for serial io otherwise parallel */
	h5part_int64_t align	/*!< [in] Number of bytes for setting alignment,
					  metadata block size, etc.
					  Set to 0 to disable. */
gsell's avatar
gsell committed
139
	) {
gsell's avatar
gsell committed
140 141 142 143
	if ( _init() < 0 ) {
		HANDLE_H5PART_INIT_ERR;
		return NULL;
	}
gsell's avatar
gsell committed
144
	_h5part_errno = H5PART_SUCCESS;
gsell's avatar
gsell committed
145 146 147 148 149 150 151 152
	H5PartFile *f = NULL;

	f = (H5PartFile*) malloc( sizeof (H5PartFile) );
	if( f == NULL ) {
		HANDLE_H5PART_NOMEM_ERR;
		goto error_cleanup;
	}
	memset (f, 0, sizeof (H5PartFile));
gsell's avatar
gsell committed
153 154 155 156 157 158 159 160

	f->groupname_step = strdup ( H5PART_GROUPNAME_STEP );
	if( f->groupname_step == NULL ) {
		HANDLE_H5PART_NOMEM_ERR;
		goto error_cleanup;
	}
	f->stepno_width = 0;

161 162 163 164 165 166 167
	f->xfer_prop = f->create_prop = H5P_DEFAULT;

	f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
	if (f->access_prop < 0) {
		HANDLE_H5P_CREATE_ERR;
		goto error_cleanup;
	}
gsell's avatar
gsell committed
168

gsell's avatar
gsell committed
169
	if ( f_parallel ) {
gsell's avatar
gsell committed
170
#ifdef PARALLEL_IO
gsell's avatar
gsell committed
171
		MPI_Info info = MPI_INFO_NULL;
172

gsell's avatar
gsell committed
173 174 175 176 177 178 179 180
		if (MPI_Comm_size (comm, &f->nprocs) != MPI_SUCCESS) {
			HANDLE_MPI_COMM_SIZE_ERR;
			goto error_cleanup;
		}
		if (MPI_Comm_rank (comm, &f->myproc) != MPI_SUCCESS) {
			HANDLE_MPI_COMM_RANK_ERR;
			goto error_cleanup;
		}
gsell's avatar
gsell committed
181

gsell's avatar
gsell committed
182 183
		f->pnparticles =
		  (h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
gsell's avatar
gsell committed
184 185 186 187
		if (f->pnparticles == NULL) {
			HANDLE_H5PART_NOMEM_ERR;
			goto error_cleanup;
		}
gsell's avatar
gsell committed
188

189 190 191 192 193 194 195 196 197
		/* select the HDF5 VFD */
		if (flags & H5PART_VFD_MPIPOSIX) {
			if (f->myproc == 0) {
				_H5Part_print_info ( "Selecting MPI-POSIX VFD" );
			}
			if (H5Pset_fapl_mpiposix ( f->access_prop, comm, 0 ) < 0) {
				HANDLE_H5P_SET_FAPL_ERR;
				goto error_cleanup;
			}
gsell's avatar
gsell committed
198
		}
199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
		else {
			if (f->myproc == 0) {
				_H5Part_print_info ( "Selecting MPI-IO VFD" );
			}
			if (H5Pset_fapl_mpio ( f->access_prop, comm, info ) < 0) {
				HANDLE_H5P_SET_FAPL_ERR;
				goto error_cleanup;
			}
			f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
			if (f->xfer_prop < 0) {
				HANDLE_H5P_CREATE_ERR;
				goto error_cleanup;
			}
			if (H5Pset_dxpl_mpio ( f->xfer_prop, H5FD_MPIO_COLLECTIVE ) < 0) {
				HANDLE_H5P_SET_DXPL_MPIO_ERR;
				goto error_cleanup;
			}
gsell's avatar
gsell committed
216
		}
gsell's avatar
gsell committed
217

218 219 220 221 222 223 224 225 226 227 228 229 230
		if (flags & H5PART_FS_LUSTRE) {
			/* extend the btree size so that metadata pieces are
			 * close to the 1MB stripe width */
			if (f->myproc == 0) {
				_H5Part_print_info (
					"Setting HDF5 btree parameter to %d",
					H5PART_BTREE_IK );
				_H5Part_print_info (
					"Extending HDF5 btree size to %d bytes at rank 3",
					24+16*H5PART_BTREE_IK+40*(2*H5PART_BTREE_IK + 1) );
			}
			f->create_prop = H5Pcreate(H5P_FILE_CREATE);
			H5Pset_istore_k (f->create_prop, H5PART_BTREE_IK);
231
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
232 233 234 235 236 237 238 239 240 241 242
			/* defer metadata cache flushing until file close */
			H5AC_cache_config_t cache_config;
			cache_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
			H5Pget_mdc_config (f->access_prop, &cache_config);
			cache_config.set_initial_size = 1;
			cache_config.initial_size = 16 * 1024 * 1024;
			cache_config.evictions_enabled = 0;
			cache_config.incr_mode = H5C_incr__off;
			cache_config.flash_incr_mode = H5C_flash_incr__off;
			cache_config.decr_mode = H5C_decr__off;
			H5Pset_mdc_config (f->access_prop, &cache_config);
243 244 245 246
#elif
			_H5Part_print_info (
					"Unable to defer metadata write: need HDF5 1.8");
#endif
247
		}
248

249
		f->comm = comm;
gsell's avatar
gsell committed
250
#endif
gsell's avatar
gsell committed
251
	} else {
gsell's avatar
gsell committed
252
		f->comm = 0;
gsell's avatar
gsell committed
253 254
		f->nprocs = 1;
		f->myproc = 0;
gsell's avatar
gsell committed
255 256
		f->pnparticles = 
			(h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
gsell's avatar
gsell committed
257
	}
258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283

	if ( align != 0 ) {
		if (f->myproc == 0) {
			_H5Part_print_info ( "Setting HDF5 alignment to %ld bytes", align );
		}
		if (H5Pset_alignment ( f->access_prop, 0, align ) < 0) {
			HANDLE_H5P_SET_FAPL_ERR;
			goto error_cleanup;
		}
		if (f->myproc == 0) {
			_H5Part_print_info ( "Setting HDF5 meta block to %ld bytes", align );
		}
		if (H5Pset_meta_block_size ( f->access_prop, align ) < 0) {
			HANDLE_H5P_SET_FAPL_ERR;
			goto error_cleanup;
		}
		/*if (f->myproc == 0) {
			_H5Part_print_info ( "Setting HDF5 sieve buffer to %ld bytes", align );
		}
		if (H5Pset_sieve_buf_size ( f->access_prop, align ) < 0) {
			HANDLE_H5P_SET_FAPL_ERR;
			goto error_cleanup;
		}*/
	}

	if ( flags & H5PART_READ ) {
gsell's avatar
gsell committed
284 285
		f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
	}
286
	else if ( flags & H5PART_WRITE ){
gsell's avatar
gsell committed
287 288
		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
				     f->access_prop);
gsell's avatar
gsell committed
289
		f->empty = 1;
gsell's avatar
gsell committed
290
	}
291
	else if ( flags & H5PART_APPEND ) {
gsell's avatar
gsell committed
292 293 294 295
		int fd = open (filename, O_RDONLY, 0);
		if ( (fd == -1) && (errno == ENOENT) ) {
			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
					    f->create_prop, f->access_prop);
gsell's avatar
gsell committed
296
			f->empty = 1;
gsell's avatar
gsell committed
297 298 299 300 301 302 303 304 305 306
		}
		else if (fd != -1) {
			close (fd);
			f->file = H5Fopen (filename, H5F_ACC_RDWR,
					   f->access_prop);
			/*
			  The following function call returns an error,
			  if f->file < 0. But we can safely ignore this.
			*/
			f->timestep = _H5Part_get_num_objects_matching_pattern(
gsell's avatar
gsell committed
307
				f->file, "/", H5G_GROUP, f->groupname_step );
gsell's avatar
gsell committed
308 309 310 311 312 313 314 315 316 317 318 319 320
			if ( f->timestep < 0 ) goto error_cleanup;
		}
	}
	else {
		HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( flags );
		goto error_cleanup;
	}

	if (f->file < 0) {
		HANDLE_H5F_OPEN_ERR ( filename, flags );
		goto error_cleanup;
	}
	f->mode = flags;
gsell's avatar
gsell committed
321
	f->timegroup = -1;
gsell's avatar
gsell committed
322 323 324 325 326 327
	f->shape = 0;
	f->diskshape = H5S_ALL;
	f->memshape = H5S_ALL;
	f->viewstart = -1;
	f->viewend = -1;

gsell's avatar
gsell committed
328 329 330 331 332 333
	_H5Part_print_debug (
		"Proc[%d]: Opened file \"%s\" val=%lld",
		f->myproc,
		filename,
		(long long)(size_t)f );

gsell's avatar
gsell committed
334 335 336 337
	return f;

 error_cleanup:
	if (f != NULL ) {
gsell's avatar
gsell committed
338 339 340
		if (f->groupname_step) {
			free (f->groupname_step);
		}
gsell's avatar
gsell committed
341 342 343 344 345 346 347 348
		if (f->pnparticles != NULL) {
			free (f->pnparticles);
		}
		free (f);
	}
	return NULL;
}

gsell's avatar
gsell committed
349
#ifdef PARALLEL_IO
gsell's avatar
gsell committed
350
/*!
gsell's avatar
gsell committed
351
  \ingroup h5part_openclose
gsell's avatar
gsell committed
352

gsell's avatar
gsell committed
353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370
  Opens file with specified filename. 

  If you open with flag \c H5PART_WRITE, it will truncate any
  file with the specified filename and start writing to it. If 
  you open with \c H5PART_APPEND, then you can append new timesteps.
  If you open with \c H5PART_READ, then it will open the file
  readonly.

  The typical extension for these files is \c .h5.
  
  H5PartFile should be treated as an essentially opaque
  datastructure.  It acts as the file handle, but internally
  it maintains several key state variables associated with 
  the file.

  \return	File handle or \c NULL
 */
H5PartFile*
gsell's avatar
gsell committed
371
H5PartOpenFileParallel (
gsell's avatar
gsell committed
372
	const char *filename,	/*!< [in] The name of the data file to open. */
373
	const char flags,	/*!< [in] The access mode for the file. */
gsell's avatar
gsell committed
374
	MPI_Comm comm		/*!< [in] MPI communicator */
375 376 377 378 379
	) {

	SET_FNAME ( "H5PartOpenFileParallel" );

	int f_parallel = 1;	/* parallel i/o */
380
	h5part_int64_t align = 0; /* no alignment tuning */
381 382 383 384 385 386 387 388 389 390 391 392 393 394 395

	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
}

/*!
  \ingroup h5part_openclose

  Opens file with specified filename, and also specifices an alignment
  value used for HDF5 tuning parameters.

  \return	File handle or \c NULL
 */
H5PartFile*
H5PartOpenFileParallelAlign (
	const char *filename,	/*!< [in] The name of the data file to open. */
396
	const char flags,	/*!< [in] The access mode for the file. */
397 398 399 400
	MPI_Comm comm,		/*!< [in] MPI communicator */
	h5part_int64_t align	/*!< [in] Alignment size in bytes. */
	) {

401
	SET_FNAME ( "H5PartOpenFileParallelAlign" );
402

gsell's avatar
gsell committed
403
	int f_parallel = 1;	/* parallel i/o */
gsell's avatar
gsell committed
404

405
	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
gsell's avatar
gsell committed
406 407
}
#endif
gsell's avatar
gsell committed
408

gsell's avatar
gsell committed
409 410
/*!
  \ingroup  h5part_openclose
gsell's avatar
gsell committed
411

gsell's avatar
gsell committed
412
  Opens file with specified filename. 
gsell's avatar
gsell committed
413

gsell's avatar
gsell committed
414 415 416 417 418
  If you open with flag \c H5PART_WRITE, it will truncate any
  file with the specified filename and start writing to it. If 
  you open with \c H5PART_APPEND, then you can append new timesteps.
  If you open with \c H5PART_READ, then it will open the file
  readonly.
gsell's avatar
gsell committed
419

gsell's avatar
gsell committed
420 421 422 423 424 425
  The typical extension for these files is \c .h5.
  
  H5PartFile should be treated as an essentially opaque
  datastructure.  It acts as the file handle, but internally
  it maintains several key state variables associated with 
  the file.
gsell's avatar
gsell committed
426

gsell's avatar
gsell committed
427 428
  \return	File handle or \c NULL
 */
gsell's avatar
gsell committed
429

gsell's avatar
gsell committed
430 431 432
H5PartFile*
H5PartOpenFile (
	const char *filename,	/*!< [in] The name of the data file to open. */
433
	const char flags	/*!< [in] The access mode for the file. */
gsell's avatar
gsell committed
434
	) {
gsell's avatar
gsell committed
435

gsell's avatar
gsell committed
436
	SET_FNAME ( "H5PartOpenFile" );
gsell's avatar
gsell committed
437

gsell's avatar
gsell committed
438 439
	MPI_Comm comm = 0;	/* dummy */
	int f_parallel = 0;	/* serial open */
440
	int align = 0;		/* no tuning parameters */
gsell's avatar
gsell committed
441

442 443 444 445 446 447 448 449 450 451 452 453 454 455
	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
}

/*!
  \ingroup h5part_openclose

  Opens file with specified filename, and also specifices an alignment
  value used for HDF5 tuning parameters.

  \return	File handle or \c NULL
 */
H5PartFile*
H5PartOpenFileAlign (
	const char *filename,	/*!< [in] The name of the data file to open. */
456
	const char flags,	/*!< [in] The access mode for the file. */
457 458 459 460 461 462 463 464
	h5part_int64_t align	/*!< [in] Alignment size in bytes. */
) {
	SET_FNAME ( "H5PartOpenFile" );

	MPI_Comm comm = 0;	/* dummy */
	int f_parallel = 0;	/* serial open */

	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
gsell's avatar
gsell committed
465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485
}

/*!
  Checks if a file was successfully opened.

  \return	\c H5PART_SUCCESS or error code
 */
static h5part_int64_t
_file_is_valid (
	const H5PartFile *f	/*!< filehandle  to check validity of */
	) {

	if( f == NULL )
		return H5PART_ERR_BADFD;
	else if(f->file > 0)
		return H5PART_SUCCESS;
	else
		return H5PART_ERR_BADFD;
}

/*!
gsell's avatar
gsell committed
486 487
  \ingroup h5part_openclose

gsell's avatar
gsell committed
488 489 490 491 492 493 494 495 496 497 498
  Closes an open file.

  \return	\c H5PART_SUCCESS or error code
*/
h5part_int64_t
H5PartCloseFile (
	H5PartFile *f		/*!< [in] filehandle of the file to close */
	) {

	SET_FNAME ( "H5PartCloseFile" );
	herr_t r = 0;
gsell's avatar
gsell committed
499
	_h5part_errno = H5PART_SUCCESS;
gsell's avatar
gsell committed
500 501 502 503 504 505 506 507 508

	CHECK_FILEHANDLE ( f );

	if ( f->block && f->close_block ) {
		(*f->close_block) ( f );
		f->block = NULL;
		f->close_block = NULL;
	}

509 510 511 512 513 514 515 516
#ifdef PARALLEL_IO
	if ( f->multiblock && f->close_multiblock ) {
		(*f->close_multiblock) ( f );
		f->multiblock = NULL;
		f->close_multiblock = NULL;
	}
#endif

gsell's avatar
gsell committed
517 518 519 520 521
	if( f->shape > 0 ) {
		r = H5Sclose( f->shape );
		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
		f->shape = 0;
	}
gsell's avatar
gsell committed
522
	if( f->timegroup >= 0 ) {
gsell's avatar
gsell committed
523 524
		r = H5Gclose( f->timegroup );
		if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
gsell's avatar
gsell committed
525
		f->timegroup = -1;
gsell's avatar
gsell committed
526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551
	}
	if( f->diskshape != H5S_ALL ) {
		r = H5Sclose( f->diskshape );
		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
		f->diskshape = 0;
	}
	if( f->xfer_prop != H5P_DEFAULT ) {
		r = H5Pclose( f->xfer_prop );
		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->xfer_prop" );
		f->xfer_prop = H5P_DEFAULT;
	}
	if( f->access_prop != H5P_DEFAULT ) {
		r = H5Pclose( f->access_prop );
		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->access_prop" );
		f->access_prop = H5P_DEFAULT;
	}  
	if( f->create_prop != H5P_DEFAULT ) {
		r = H5Pclose( f->create_prop );
		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->create_prop" );
		f->create_prop = H5P_DEFAULT;
	}
	if ( f->file ) {
		r = H5Fclose( f->file );
		if ( r < 0 ) HANDLE_H5F_CLOSE_ERR;
		f->file = 0;
	}
gsell's avatar
gsell committed
552 553 554
	if (f->groupname_step) {
		free (f->groupname_step);
	}
gsell's avatar
gsell committed
555 556 557 558 559
	if( f->pnparticles ) {
		free( f->pnparticles );
	}
	free( f );

gsell's avatar
gsell committed
560
	return _h5part_errno;
gsell's avatar
gsell committed
561 562 563
}

/*============== File Writing Functions ==================== */
gsell's avatar
gsell committed
564

gsell's avatar
gsell committed
565 566 567 568 569 570 571 572 573 574
h5part_int64_t
H5PartDefineStepName (
	H5PartFile *f,
	const char *name,
	const h5part_int64_t width
	) {
	f->groupname_step = strdup ( name );
	if( f->groupname_step == NULL ) {
		return HANDLE_H5PART_NOMEM_ERR;
	}
gsell's avatar
gsell committed
575
	f->stepno_width = (int)width;
gsell's avatar
gsell committed
576 577 578 579
	
	return H5PART_SUCCESS;
}

gsell's avatar
gsell committed
580
/*!
gsell's avatar
gsell committed
581 582
  \ingroup h5part_write

gsell's avatar
gsell committed
583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664
  Set number of particles for current time-step.

  This function's sole purpose is to prevent 
  needless creation of new HDF5 DataSpace handles if the number of 
  particles is invariant throughout the simulation. That's its only reason 
  for existence. After you call this subroutine, all subsequent 
  operations will assume this number of particles will be written.


  \return	\c H5PART_SUCCESS or error code
 */
h5part_int64_t
H5PartSetNumParticles (
	H5PartFile *f,			/*!< [in] Handle to open file */
	h5part_int64_t nparticles	/*!< [in] Number of particles */
	) {

	SET_FNAME ( "H5PartSetNumParticles" );
	int r;
#ifdef PARALLEL_IO
#ifdef HDF5V160
	hssize_t start[1];
#else
	hsize_t start[1];
#endif

	hsize_t stride[1];
	hsize_t count[1];
	hsize_t total;
	hsize_t dmax = H5S_UNLIMITED;
	register int i;
#endif

	CHECK_FILEHANDLE( f );

#ifndef PARALLEL_IO
	/*
	  if we are not using parallel-IO, there is enough information
	   to know that we can short circuit this routine.  However,
	   for parallel IO, this is going to cause problems because
	   we don't know if things have changed globally
	*/
	if ( f->nparticles == nparticles ) {
		return H5PART_SUCCESS;
	}
#endif
	if ( f->diskshape != H5S_ALL ) {
		r = H5Sclose( f->diskshape );
		if ( r < 0 ) return HANDLE_H5S_CLOSE_ERR;
		f->diskshape = H5S_ALL;
	}
	if(f->memshape != H5S_ALL) {
		r = H5Sclose( f->memshape );
		if ( r < 0 ) return HANDLE_H5S_CLOSE_ERR;
		f->memshape = H5S_ALL;
	}
	if( f->shape ) {
		r = H5Sclose(f->shape);
		if ( r < 0 ) return HANDLE_H5S_CLOSE_ERR;
	}
	f->nparticles =(hsize_t) nparticles;
#ifndef PARALLEL_IO
	f->shape = H5Screate_simple (1,
				     &(f->nparticles),
				     NULL);
	if ( f->shape < 0 ) HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );

#else /* PARALLEL_IO */
	/*
	  The Gameplan here is to declare the overall size of the on-disk
	  data structure the same way we do for the serial case.  But
	  then we must have additional "DataSpace" structures to define
	  our in-memory layout of our domain-decomposed portion of the particle
	  list as well as a "selection" of a subset of the on-disk 
	  data layout that will be written in parallel to mutually exclusive
	  regions by all of the processors during a parallel I/O operation.
	  These are f->shape, f->memshape and f->diskshape respectively.
	*/

	/*
	  acquire the number of particles to be written from each MPI process
	*/
665

gsell's avatar
gsell committed
666 667 668 669 670 671 672 673
	r = MPI_Allgather (
		&nparticles, 1, MPI_LONG_LONG,
		f->pnparticles, 1, MPI_LONG_LONG,
		f->comm);
	if ( r != MPI_SUCCESS) {
		return HANDLE_MPI_ALLGATHER_ERR;
	}
	if ( f->myproc == 0 ) {
gsell's avatar
gsell committed
674
		_H5Part_print_debug ( "Particle offsets:" );
gsell's avatar
gsell committed
675
		for(i=0;i<f->nprocs;i++) 
gsell's avatar
gsell committed
676 677
			_H5Part_print_debug ( "\tnp=%lld",
					      (long long) f->pnparticles[i] );
gsell's avatar
gsell committed
678 679 680 681 682 683 684 685 686 687
	}
	/* should I create a selection here? */

	/* compute start offsets */
	stride[0] = 1;
	start[0] = 0;
	for (i=0; i<f->myproc; i++) {
		start[0] += f->pnparticles[i];
	}
	
688
	/* compute total nparticles */
gsell's avatar
gsell committed
689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717
	total = 0;
	for (i=0; i < f->nprocs; i++) {
		total += f->pnparticles[i];
	}

	/* declare overall datasize */
	f->shape = H5Screate_simple (1, &total, &total);
	if (f->shape < 0) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total );


	/* declare overall data size  but then will select a subset */
	f->diskshape = H5Screate_simple (1, &total, &total);
	if (f->diskshape < 0) return HANDLE_H5S_CREATE_SIMPLE_ERR ( total );

	/* declare local memory datasize */
	f->memshape = H5Screate_simple (1, &(f->nparticles), &dmax);
	if (f->memshape < 0)
		return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );

	count[0] = nparticles;
	r = H5Sselect_hyperslab (
		f->diskshape,
		H5S_SELECT_SET,
		start,
		stride,
		count, NULL );
	if ( r < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;

	if ( f->timegroup < 0 ) {
gsell's avatar
gsell committed
718
		r = _H5Part_set_step ( f, 0 );
gsell's avatar
gsell committed
719
		if ( r < 0 ) return r;
gsell's avatar
gsell committed
720 721 722 723 724 725 726 727 728
		
	}
#endif
	return H5PART_SUCCESS;
}

static h5part_int64_t
_write_data (
	H5PartFile *f,		/*!< IN: Handle to open file */
gsell's avatar
gsell committed
729 730 731
	const char *name,	/*!< IN: Name to associate array with */
	const void *array,	/*!< IN: Array to commit to disk */
	const hid_t type	/*!< IN: Type of data */
gsell's avatar
gsell committed
732 733 734 735
	) {
	herr_t herr;
	hid_t dataset_id;

gsell's avatar
gsell committed
736
	_H5Part_print_debug ( "Create a dataset[%s] mounted on the "
gsell's avatar
gsell committed
737
			      "timestep %lld",
gsell's avatar
gsell committed
738
			      name, (long long)f->timestep );
gsell's avatar
gsell committed
739

740
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
741 742 743
	htri_t exists = H5Lexists ( f->timegroup, name, H5P_DEFAULT );
	if ( exists > 0 ) return HANDLE_H5D_EXISTS_ERR ( name, f->timestep );

744 745 746 747 748 749 750 751 752
	dataset_id = H5Dcreate2 ( 
		f->timegroup,
		name,
		type,
		f->shape,
		H5P_DEFAULT,
		H5P_DEFAULT,
		H5P_DEFAULT );
#else
gsell's avatar
gsell committed
753 754 755 756 757 758
	dataset_id = H5Dcreate ( 
		f->timegroup,
		name,
		type,
		f->shape,
		H5P_DEFAULT );
759
#endif
gsell's avatar
gsell committed
760 761 762
	if ( dataset_id < 0 )
		return HANDLE_H5D_CREATE_ERR ( name, f->timestep );

763 764 765 766 767 768 769 770 771
#ifdef COLLECTIVE_IO
	herr = H5Dwrite (
		dataset_id,
		type,
		f->memshape,
		f->diskshape,
		f->xfer_prop,
		array );
#else
gsell's avatar
gsell committed
772 773 774 775 776 777 778
	herr = H5Dwrite (
		dataset_id,
		type,
		f->memshape,
		f->diskshape,
		H5P_DEFAULT,
		array );
779 780
#endif

gsell's avatar
gsell committed
781 782 783 784 785
	if ( herr < 0 ) return HANDLE_H5D_WRITE_ERR ( name, f->timestep );

	herr = H5Dclose ( dataset_id );
	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;

gsell's avatar
gsell committed
786 787
	f->empty = 0;

gsell's avatar
gsell committed
788 789 790 791
	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
792 793
  \ingroup h5part_write

gsell's avatar
gsell committed
794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819
  Write array of 64 bit floating point data to file.

  After setting the number of particles with \c H5PartSetNumParticles() and
  the current timestep using \c H5PartSetStep(), you can start writing datasets
  into the file. Each dataset has a name associated with it (chosen by the
  user) in order to facilitate later retrieval. The name of the dataset is
  specified in the parameter \c name, which must be a null-terminated string.

  There are no restrictions on naming of datasets, but it is useful to arrive
  at some common naming convention when sharing data with other groups.

  The writing routines also implicitly store the datatype of the array so that
  the array can be reconstructed properly on other systems with incompatible
  type representations.

  All data that is written after setting the timestep is associated with that
  timestep. While the number of particles can change for each timestep, you
  cannot change the number of particles in the middle of a given timestep.

  The data is committed to disk before the routine returns.

  \return	\c H5PART_SUCCESS or error code
 */
h5part_int64_t
H5PartWriteDataFloat64 (
	H5PartFile *f,		/*!< [in] Handle to open file */
gsell's avatar
gsell committed
820 821
	const char *name,	/*!< [in] Name to associate array with */
	const h5part_float64_t *array	/*!< [in] Array to commit to disk */
gsell's avatar
gsell committed
822 823 824
	) {

	SET_FNAME ( "H5PartWriteDataFloat64" );
gsell's avatar
gsell committed
825
	h5part_int64_t herr;
gsell's avatar
gsell committed
826 827 828 829 830 831 832 833 834 835 836

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	herr = _write_data ( f, name, (void*)array, H5T_NATIVE_DOUBLE );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882
/*!
  \ingroup h5part_write

  Write array of 32 bit floating point data to file.

  After setting the number of particles with \c H5PartSetNumParticles() and
  the current timestep using \c H5PartSetStep(), you can start writing datasets
  into the file. Each dataset has a name associated with it (chosen by the
  user) in order to facilitate later retrieval. The name of the dataset is
  specified in the parameter \c name, which must be a null-terminated string.

  There are no restrictions on naming of datasets, but it is useful to arrive
  at some common naming convention when sharing data with other groups.

  The writing routines also implicitly store the datatype of the array so that
  the array can be reconstructed properly on other systems with incompatible
  type representations.

  All data that is written after setting the timestep is associated with that
  timestep. While the number of particles can change for each timestep, you
  cannot change the number of particles in the middle of a given timestep.

  The data is committed to disk before the routine returns.

  \return	\c H5PART_SUCCESS or error code
 */
h5part_int64_t
H5PartWriteDataFloat32 (
	H5PartFile *f,		/*!< [in] Handle to open file */
	const char *name,	/*!< [in] Name to associate array with */
	const h5part_float32_t *array	/*!< [in] Array to commit to disk */
	) {

	SET_FNAME ( "H5PartWriteDataFloat32" );
	h5part_int64_t herr;

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	herr = _write_data ( f, name, (void*)array, H5T_NATIVE_FLOAT );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

gsell's avatar
gsell committed
883
/*!
gsell's avatar
gsell committed
884 885
  \ingroup h5part_write

gsell's avatar
gsell committed
886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911
  Write array of 64 bit integer data to file.

  After setting the number of particles with \c H5PartSetNumParticles() and
  the current timestep using \c H5PartSetStep(), you can start writing datasets
  into the file. Each dataset has a name associated with it (chosen by the
  user) in order to facilitate later retrieval. The name of the dataset is
  specified in the parameter \c name, which must be a null-terminated string.

  There are no restrictions on naming of datasets, but it is useful to arrive
  at some common naming convention when sharing data with other groups.

  The writing routines also implicitly store the datatype of the array so that
  the array can be reconstructed properly on other systems with incompatible
  type representations.

  All data that is written after setting the timestep is associated with that
  timestep. While the number of particles can change for each timestep, you
  cannot change the number of particles in the middle of a given timestep.

  The data is committed to disk before the routine returns.

  \return	\c H5PART_SUCCESS or error code
 */
h5part_int64_t
H5PartWriteDataInt64 (
	H5PartFile *f,		/*!< [in] Handle to open file */
gsell's avatar
gsell committed
912 913
	const char *name,	/*!< [in] Name to associate array with */
	const h5part_int64_t *array	/*!< [in] Array to commit to disk */
gsell's avatar
gsell committed
914 915
	) {

916
	SET_FNAME ( "H5PartWriteDataInt64" );
gsell's avatar
gsell committed
917

gsell's avatar
gsell committed
918
	h5part_int64_t herr;
gsell's avatar
gsell committed
919 920 921 922 923 924 925 926 927 928 929

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	herr = _write_data ( f, name, (void*)array, H5T_NATIVE_INT64 );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976
/*!
  \ingroup h5part_write

  Write array of 32 bit integer data to file.

  After setting the number of particles with \c H5PartSetNumParticles() and
  the current timestep using \c H5PartSetStep(), you can start writing datasets
  into the file. Each dataset has a name associated with it (chosen by the
  user) in order to facilitate later retrieval. The name of the dataset is
  specified in the parameter \c name, which must be a null-terminated string.

  There are no restrictions on naming of datasets, but it is useful to arrive
  at some common naming convention when sharing data with other groups.

  The writing routines also implicitly store the datatype of the array so that
  the array can be reconstructed properly on other systems with incompatible
  type representations.

  All data that is written after setting the timestep is associated with that
  timestep. While the number of particles can change for each timestep, you
  cannot change the number of particles in the middle of a given timestep.

  The data is committed to disk before the routine returns.

  \return	\c H5PART_SUCCESS or error code
 */
h5part_int64_t
H5PartWriteDataInt32 (
	H5PartFile *f,		/*!< [in] Handle to open file */
	const char *name,	/*!< [in] Name to associate array with */
	const h5part_int32_t *array	/*!< [in] Array to commit to disk */
	) {

	SET_FNAME ( "H5PartWriteDataInt32" );

	h5part_int64_t herr;

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	herr = _write_data ( f, name, (void*)array, H5T_NATIVE_INT32 );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

gsell's avatar
gsell committed
977 978 979
/********************** reading and writing attribute ************************/

/********************** private functions to handle attributes ***************/
gsell's avatar
gsell committed
980 981 982 983 984 985

/*!
  \ingroup h5partkernel
  @{
*/

gsell's avatar
gsell committed
986 987 988 989 990 991 992 993 994 995 996 997
/*!
   Normalize HDF5 type
*/
hid_t
_H5Part_normalize_h5_type (
	hid_t type
	) {
	H5T_class_t tclass = H5Tget_class ( type );
	int size = H5Tget_size ( type );

	switch ( tclass ){
	case H5T_INTEGER:
998 999 1000 1001 1002 1003 1004
	  if ( size==8 ) {
	    return H5T_NATIVE_INT64;
	  }
	  else if ( size==1 ) {
	    return H5T_NATIVE_CHAR;
	  }
	  break;
gsell's avatar
gsell committed
1005
	case H5T_FLOAT:
1006 1007 1008 1009 1010 1011 1012
	  if ( size==8 ) {
	    return H5T_NATIVE_DOUBLE;
	  }
	  else if ( size==4 ) {
	    return H5T_NATIVE_FLOAT;
	  }
	  break;
gsell's avatar
gsell committed
1013
	default:
1014
	  ; /* NOP */
gsell's avatar
gsell committed
1015
	}
gsell's avatar
gsell committed
1016
	_H5Part_print_warn ( "Unknown type %d", (int)type );
1017
	
gsell's avatar
gsell committed
1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034
	return -1;
}

h5part_int64_t
_H5Part_read_attrib (
	hid_t id,
	const char *attrib_name,
	void *attrib_value
	) {

	herr_t herr;
	hid_t attrib_id;
	hid_t space_id;
	hid_t type_id;
	hid_t mytype;
	hsize_t nelem;

1035 1036 1037 1038 1039 1040
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	if (! H5Aexists ( id, attrib_name )) {
	    _H5Part_print_warn ( "Attribute does not exist!" );
	}
	attrib_id = H5Aopen ( id, attrib_name, H5P_DEFAULT );
#else
gsell's avatar
gsell committed
1041
	attrib_id = H5Aopen_name ( id, attrib_name );
1042
#endif
gsell's avatar
gsell committed
1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087
	if ( attrib_id <= 0 ) return HANDLE_H5A_OPEN_NAME_ERR( attrib_name );

	mytype = H5Aget_type ( attrib_id );
	if ( mytype < 0 ) return HANDLE_H5A_GET_TYPE_ERR;

	space_id = H5Aget_space ( attrib_id );
	if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;

	nelem = H5Sget_simple_extent_npoints ( space_id );
	if ( nelem < 0 ) return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR;

	type_id = _H5Part_normalize_h5_type ( mytype );

	herr = H5Aread (attrib_id, type_id, attrib_value );
	if ( herr < 0 ) return HANDLE_H5A_READ_ERR;

	herr = H5Sclose ( space_id );
	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;

	herr = H5Tclose ( mytype );
	if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;

	herr = H5Aclose ( attrib_id );
	if ( herr < 0 ) return HANDLE_H5A_CLOSE_ERR;

	return H5PART_SUCCESS;
}

h5part_int64_t
_H5Part_write_attrib (
	hid_t id,
	const char *attrib_name,
	const hid_t attrib_type,
	const void *attrib_value,
	const hsize_t attrib_nelem
	) {

	herr_t herr;
	hid_t space_id;
	hid_t attrib_id;

	space_id = H5Screate_simple (1, &attrib_nelem, NULL);
	if ( space_id < 0 )
		return HANDLE_H5S_CREATE_SIMPLE_ERR ( attrib_nelem );

1088 1089 1090 1091 1092 1093 1094 1095 1096
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	attrib_id = H5Acreate2 ( 
		id,
		attrib_name,
		attrib_type,
		space_id,
		H5P_DEFAULT,
		H5P_DEFAULT );
#else
gsell's avatar
gsell committed
1097 1098 1099 1100 1101 1102
	attrib_id = H5Acreate ( 
		id,
		attrib_name,
		attrib_type,
		space_id,
		H5P_DEFAULT );
1103
#endif
gsell's avatar
gsell committed
1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132
	if ( attrib_id < 0 ) return HANDLE_H5A_CREATE_ERR ( attrib_name );

	herr = H5Awrite ( attrib_id, attrib_type, attrib_value);
	if ( herr < 0 ) return HANDLE_H5A_WRITE_ERR ( attrib_name );

	herr = H5Aclose ( attrib_id );
	if ( herr < 0 ) return HANDLE_H5A_CLOSE_ERR;

	herr = H5Sclose ( space_id );
	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;

	return H5PART_SUCCESS;
}

h5part_int64_t
_H5Part_get_attrib_info (
	hid_t id,
	const h5part_int64_t attrib_idx,
	char *attrib_name,
	const h5part_int64_t len_attrib_name,
	h5part_int64_t *attrib_type,
	h5part_int64_t *attrib_nelem
	) {

	herr_t herr;
	hid_t attrib_id;
	hid_t mytype;
	hid_t space_id;

gsell's avatar
gsell committed
1133
	attrib_id = H5Aopen_idx ( id, (unsigned int)attrib_idx );
gsell's avatar
gsell committed
1134 1135 1136
	if ( attrib_id < 0 ) return HANDLE_H5A_OPEN_IDX_ERR ( attrib_idx );

	if ( attrib_nelem ) {
gsell's avatar
gsell committed
1137 1138 1139
		space_id =  H5Aget_space ( attrib_id );
		if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;

gsell's avatar
gsell committed
1140 1141 1142
		*attrib_nelem = H5Sget_simple_extent_npoints ( space_id );
		if ( *attrib_nelem < 0 )
			return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR;
gsell's avatar
gsell committed
1143 1144 1145

		herr = H5Sclose ( space_id );
		if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
gsell's avatar
gsell committed
1146 1147 1148 1149
	}
	if ( attrib_name ) {
		herr = H5Aget_name (
			attrib_id,
gsell's avatar
gsell committed
1150
			(size_t)len_attrib_name,
gsell's avatar
gsell committed
1151 1152 1153 1154
			attrib_name );
		if ( herr < 0 ) return HANDLE_H5A_GET_NAME_ERR;
	}
	if ( attrib_type ) {
gsell's avatar
gsell committed
1155 1156
		mytype = H5Aget_type ( attrib_id );
		if ( mytype < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
gsell's avatar
gsell committed
1157

gsell's avatar
gsell committed
1158
		*attrib_type = _H5Part_normalize_h5_type ( mytype );
gsell's avatar
gsell committed
1159

gsell's avatar
gsell committed
1160 1161 1162
		herr = H5Tclose ( mytype );
		if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
	}
gsell's avatar
gsell committed
1163 1164 1165 1166 1167 1168 1169 1170 1171
	herr = H5Aclose ( attrib_id);
	if ( herr < 0 ) return HANDLE_H5A_CLOSE_ERR;

	return H5PART_SUCCESS;
}

/********************** attribute API ****************************************/

/*!
gsell's avatar
gsell committed
1172 1173
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196
  Writes a string attribute bound to a file.

  This function creates a new attribute \c name with the string \c value as
  content. The attribute is bound to the file associated with the file handle 
  \c f.

  If the attribute already exists an error will be returned. There
  is currently no way to change the content of an existing attribute.

  \return	\c H5PART_SUCCESS or error code   
*/
h5part_int64_t
H5PartWriteFileAttribString (
	H5PartFile *f,		/*!< [in] Handle to open file */
	const char *attrib_name,/*!< [in] Name of attribute to create */
	const char *attrib_value/*!< [in] Value of attribute */ 
	) {

	SET_FNAME ( "H5PartWriteFileAttribString" );

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );

1197 1198 1199
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	hid_t group_id = H5Gopen2(f->file,"/",H5P_DEFAULT);
#else
gsell's avatar
gsell committed
1200
	hid_t group_id = H5Gopen(f->file,"/");
1201
#endif
gsell's avatar
gsell committed
1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218
	if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" );

	h5part_int64_t herr = _H5Part_write_attrib (
		group_id,
		attrib_name,
		H5T_NATIVE_CHAR,
		attrib_value,
		strlen ( attrib_value ) + 1 );
	if ( herr < 0 ) return herr;

	herr = H5Gclose ( group_id );
	if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1219 1220
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231
  Writes a string attribute bound to the current time-step.

  If the attribute already exists an error will be returned. There
  is currently no way to change the content of an existing attribute.

  \return	\c H5PART_SUCCESS or error code   
*/

h5part_int64_t
H5PartWriteStepAttribString (
	H5PartFile *f,		/*!< [in] Handle to open file */
1232 1233
	const char *name,	/*!< [in] Name of attribute to create */
	const char *value	/*!< [in] Value of attribute */ 
gsell's avatar
gsell committed
1234 1235 1236 1237 1238 1239 1240 1241 1242 1243
	) {

	SET_FNAME ( "H5PartWriteStepAttribString" );

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	h5part_int64_t herr = _H5Part_write_attrib (
		f->timegroup,
1244
		name,
gsell's avatar
gsell committed
1245
		H5T_NATIVE_CHAR,
1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317
		value,
		strlen ( value ) + 1 );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
  \ingroup h5part_attrib

  Writes an int32 attribute bound to the current time-step.

  If the attribute already exists an error will be returned. There
  is currently no way to change the content of an existing attribute.

  \return	\c H5PART_SUCCESS or error code   
*/

h5part_int64_t
H5PartWriteStepAttribInt32 (
	H5PartFile *f,			/*!< [in] Handle to open file */
	const char *name,		/*!< [in] Name of attribute to create */
	const h5part_int32_t value	/*!< [in] Value of attribute */ 
	) {

	SET_FNAME ( "H5PartWriteStepAttribInt32" );

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	h5part_int64_t herr = _H5Part_write_attrib (
		f->timegroup,
		name,
		H5T_NATIVE_INT32,
		&value,
		1 );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
  \ingroup h5part_attrib

  Writes a float32 attribute bound to the current time-step.

  If the attribute already exists an error will be returned. There
  is currently no way to change the content of an existing attribute.

  \return	\c H5PART_SUCCESS or error code   
*/

h5part_int64_t
H5PartWriteStepAttribFloat32 (
	H5PartFile *f,			/*!< [in] Handle to open file */
	const char *name,		/*!< [in] Name of attribute to create */
	const h5part_float32_t value	/*!< [in] Value of attribute */ 
	) {

	SET_FNAME ( "H5PartWriteStepAttribFloat32" );

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	h5part_int64_t herr = _H5Part_write_attrib (
		f->timegroup,
		name,
		H5T_NATIVE_FLOAT,
		&value,
		1 );
gsell's avatar
gsell committed
1318 1319 1320 1321 1322 1323
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1324 1325
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352
  Writes a attribute bound to the current time-step.

  This function creates a new attribute \c name with the string \c value as
  content. The attribute is bound to the current time step in the file given
  by the file handle \c f.

  The value of the attribute is given the parameter \c type, which must be one
  of \c H5T_NATIVE_DOUBLE, \c H5T_NATIVE_INT64 of \c H5T_NATIVE_CHAR, the array
  \c value and the number of elements \c nelem in the array.

  If the attribute already exists an error will be returned. There
  is currently no way to change the content of an existing attribute.

  \return	\c H5PART_SUCCESS or error code   
*/

h5part_int64_t
H5PartWriteStepAttrib (
	H5PartFile *f,			/*!< [in] Handle to open file */
	const char *attrib_name,	/*!< [in] Name of attribute */
	const h5part_int64_t attrib_type,/*!< [in] Type of value. */
	const void *attrib_value,	/*!< [in] Value of attribute */ 
	const h5part_int64_t attrib_nelem/*!< [in] Number of elements */
	){

	SET_FNAME ( "H5PartWriteStepAttrib" );

gsell's avatar
gsell committed
1353
	h5part_int64_t herr;
gsell's avatar
gsell committed
1354 1355 1356 1357 1358 1359 1360 1361

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE( f );
	CHECK_TIMEGROUP( f );

	herr = _H5Part_write_attrib (
		f->timegroup,
		attrib_name,
gsell's avatar
gsell committed
1362
		(const hid_t)attrib_type,
gsell's avatar
gsell committed
1363 1364 1365 1366 1367 1368 1369 1370
		attrib_value,
		attrib_nelem );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1371 1372
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399
  Writes a attribute bound to a file.

  This function creates a new attribute \c name with the string \c value as
  content. The attribute is bound to the file file given by the file handle
  \c f.

  The value of the attribute is given the parameter \c type, which must be one
  of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64 of H5T_NATIVE_CHAR, the array \c value
  and the number of elements \c nelem in the array.

  If the attribute already exists an error will be returned. There
  is currently no way to change the content of an existing attribute.

  \return	\c H5PART_SUCCESS or error code   
*/

h5part_int64_t
H5PartWriteFileAttrib (
	H5PartFile *f,			/*!< [in] Handle to open file */
	const char *attrib_name,	/*!< [in] Name of attribute */
	const h5part_int64_t attrib_type,/*!< [in] Type of value. */
	const void *attrib_value,	/*!< [in] Value of attribute */ 
	const h5part_int64_t attrib_nelem/*!< [in] Number of elements */
	) {

	SET_FNAME ( "H5PartWriteFileAttrib" );

gsell's avatar
gsell committed
1400
	h5part_int64_t herr;
gsell's avatar
gsell committed
1401 1402 1403 1404 1405
	hid_t group_id;

	CHECK_FILEHANDLE ( f );
	CHECK_WRITABLE_MODE ( f );

1406 1407 1408
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	group_id = H5Gopen2(f->file,"/",H5P_DEFAULT);
#else
gsell's avatar
gsell committed
1409
	group_id = H5Gopen(f->file,"/");
1410
#endif
gsell's avatar
gsell committed
1411 1412
	if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" );

gsell's avatar
gsell committed
1413
	herr = _H5Part_write_attrib (
gsell's avatar
gsell committed
1414 1415
		group_id,
		attrib_name,
gsell's avatar
gsell committed
1416
		(const hid_t)attrib_type,
gsell's avatar
gsell committed
1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427
		attrib_value,
		attrib_nelem );
	if ( herr < 0 ) return herr;

	herr = H5Gclose ( group_id );
	if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1428 1429
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450
  Gets the number of attributes bound to the current step.

  \return	Number of attributes bound to current time step or error code.
*/
h5part_int64_t
H5PartGetNumStepAttribs (
	H5PartFile *f			/*!< [in] Handle to open file */
	) {

	SET_FNAME ( "H5PartGetNumStepAttribs" );
	h5part_int64_t nattribs;

	CHECK_FILEHANDLE ( f );

	nattribs = H5Aget_num_attrs(f->timegroup);
	if ( nattribs < 0 ) HANDLE_H5A_GET_NUM_ATTRS_ERR;

	return nattribs;
}

/*!
gsell's avatar
gsell committed
1451 1452
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467
  Gets the number of attributes bound to the file.

  \return	Number of attributes bound to file \c f or error code.
*/
h5part_int64_t
H5PartGetNumFileAttribs (
	H5PartFile *f			/*!< [in] Handle to open file */
	) {

	SET_FNAME ( "H5PartGetNumFileAttribs" );
	herr_t herr;
	h5part_int64_t nattribs;

	CHECK_FILEHANDLE ( f );

1468 1469 1470
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	hid_t group_id = H5Gopen2 ( f->file, "/", H5P_DEFAULT );
#else
gsell's avatar
gsell committed
1471
	hid_t group_id = H5Gopen ( f->file, "/" );
1472
#endif
gsell's avatar
gsell committed
1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483
	if ( group_id < 0 ) HANDLE_H5G_OPEN_ERR ( "/" );

	nattribs = H5Aget_num_attrs ( group_id );
	if ( nattribs < 0 ) HANDLE_H5A_GET_NUM_ATTRS_ERR;

	herr = H5Gclose ( group_id );
	if ( herr < 0 ) HANDLE_H5G_CLOSE_ERR;
	return nattribs;
}

/*!
gsell's avatar
gsell committed
1484 1485
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500
  Gets the name, type and number of elements of the step attribute
  specified by its index.

  This function can be used to retrieve all attributes bound to the
  current time-step by looping from \c 0 to the number of attribute
  minus one.  The number of attributes bound to the current
  time-step can be queried by calling the function
  \c H5PartGetNumStepAttribs().

  \return	\c H5PART_SUCCESS or error code 
*/
h5part_int64_t
H5PartGetStepAttribInfo (
	H5PartFile *f,			/*!< [in]  Handle to open file */
	const h5part_int64_t attrib_idx,/*!< [in]  Index of attribute to
1501
						   get infos about */
gsell's avatar
gsell committed
1502 1503 1504 1505 1506 1507 1508 1509
	char *attrib_name,		/*!< [out] Name of attribute */
	const h5part_int64_t len_of_attrib_name,
					/*!< [in]  length of buffer \c name */
	h5part_int64_t *attrib_type,	/*!< [out] Type of value. */
	h5part_int64_t *attrib_nelem	/*!< [out] Number of elements */
	) {
	
	SET_FNAME ( "H5PartGetStepAttribInfo" );
gsell's avatar
gsell committed
1510
	h5part_int64_t herr;
gsell's avatar
gsell committed
1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526

	CHECK_FILEHANDLE( f );

	herr = _H5Part_get_attrib_info (
		f->timegroup,
		attrib_idx,
		attrib_name,
		len_of_attrib_name,
		attrib_type,
		attrib_nelem );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1527 1528
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543
  Gets the name, type and number of elements of the file attribute
  specified by its index.

  This function can be used to retrieve all attributes bound to the
  file \c f by looping from \c 0 to the number of attribute minus
  one.  The number of attributes bound to file \c f can be queried
  by calling the function \c H5PartGetNumFileAttribs().

  \return	\c H5PART_SUCCESS or error code 
*/

h5part_int64_t
H5PartGetFileAttribInfo (
	H5PartFile *f,			/*!< [in]  Handle to open file */
	const h5part_int64_t attrib_idx,/*!< [in]  Index of attribute to get
1544
						   infos about */
gsell's avatar
gsell committed
1545 1546 1547 1548 1549 1550 1551 1552 1553
	char *attrib_name,		/*!< [out] Name of attribute */
	const h5part_int64_t len_of_attrib_name,
					/*!< [in]  length of buffer \c name */
	h5part_int64_t *attrib_type,	/*!< [out] Type of value. */
	h5part_int64_t *attrib_nelem	/*!< [out] Number of elements */
	) {

	SET_FNAME ( "H5PartGetFileAttribInfo" );
	hid_t group_id;
gsell's avatar
gsell committed
1554
	h5part_int64_t herr;
gsell's avatar
gsell committed
1555 1556 1557

	CHECK_FILEHANDLE( f );

1558 1559 1560
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	group_id = H5Gopen2(f->file,"/",H5P_DEFAULT);
#else
gsell's avatar
gsell committed
1561
	group_id = H5Gopen(f->file,"/");
1562
#endif
gsell's avatar
gsell committed
1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580
	if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" );

	herr = _H5Part_get_attrib_info (
		group_id,
		attrib_idx,
		attrib_name,
		len_of_attrib_name,
		attrib_type,
		attrib_nelem );
	if ( herr < 0 ) return herr;

	herr = H5Gclose ( group_id );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1581 1582
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1583 1584 1585 1586 1587 1588 1589
  Reads an attribute bound to current time-step.

  \return \c H5PART_SUCCESS or error code 
*/
h5part_int64_t
H5PartReadStepAttrib (
	H5PartFile *f,			/*!< [in]  Handle to open file */
gsell's avatar
gsell committed
1590
	const char *attrib_name,	/*!< [in] Name of attribute to read */
gsell's avatar
gsell committed
1591 1592 1593 1594 1595
	void *attrib_value		/*!< [out] Value of attribute */
	) {

	SET_FNAME ( "H5PartReadStepAttrib" );

gsell's avatar
gsell committed
1596
	h5part_int64_t herr;
gsell's avatar
gsell committed
1597 1598 1599 1600 1601 1602 1603 1604 1605 1606

	CHECK_FILEHANDLE( f );

	herr = _H5Part_read_attrib ( f->timegroup, attrib_name, attrib_value );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
gsell's avatar
gsell committed
1607 1608
  \ingroup h5part_attrib

gsell's avatar
gsell committed
1609 1610 1611 1612 1613 1614 1615
  Reads an attribute bound to file \c f.

  \return \c H5PART_SUCCESS or error code 
*/
h5part_int64_t
H5PartReadFileAttrib ( 
	H5PartFile *f,
gsell's avatar
gsell committed
1616
	const char *attrib_name,
gsell's avatar
gsell committed
1617 1618 1619 1620 1621 1622
	void *attrib_value
	) {

	SET_FNAME ( "H5PartReadFileAttrib" );

	hid_t group_id;
gsell's avatar
gsell committed
1623
	h5part_int64_t herr;
gsell's avatar
gsell committed
1624 1625 1626

	CHECK_FILEHANDLE( f );

1627 1628 1629
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	group_id = H5Gopen2(f->file,"/",H5P_DEFAULT);
#else
gsell's avatar
gsell committed
1630
	group_id = H5Gopen(f->file,"/");
1631
#endif
gsell's avatar
gsell committed
1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655
	if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" );

	herr = _H5Part_read_attrib ( group_id, attrib_name, attrib_value );
	if ( herr < 0 ) return herr;

	herr = H5Gclose ( group_id );
	if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;

	return H5PART_SUCCESS;
}


/*================== File Reading Routines =================*/
/*
  H5PartSetStep:


  So you use this to random-access the file for a particular timestep.
  Failure to explicitly set the timestep on each read will leave you
  stuck on the same timestep for *all* of your reads.  That is to say
  the writes auto-advance the file pointer, but the reads do not
  (they require explicit advancing by selecting a particular timestep).
*/

gsell's avatar
gsell committed
1656
h5part_int64_t
gsell's avatar
gsell committed
1657
_H5Part_set_step (
gsell's avatar
gsell committed
1658 1659 1660 1661 1662 1663
	H5PartFile *f,			/*!< [in]  Handle to open file */
	const h5part_int64_t step	/*!< [in]  Time-step to set. */
	) {

	char name[128];

1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676
	/* Work around sprintf bug on older systems */
	if (f->stepno_width == 0 && step == 0) {
	    sprintf (
		    name,
		    "%s#%0*lld",
		    f->groupname_step, 1, (long long) step );
	}
	else {
	    sprintf (
		    name,
		    "%s#%0*lld",
		    f->groupname_step, f->stepno_width, (long long) step );
	}
1677

1678
	if ( (!(f->mode & H5PART_READ)) && _H5Part_have_group ( f->file, name ) ) {
gsell's avatar
gsell committed
1679 1680 1681 1682
		return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
	}

	if ( f->timegroup >= 0 ) {
1683
		herr_t herr = H5Gclose ( f->timegroup );
gsell's avatar
gsell committed
1684 1685 1686 1687 1688
		if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;
	}
	f->timegroup = -1;
	f->timestep = step;

1689
	if( f->mode & H5PART_READ ) {
1690
		_H5Part_print_debug (
gsell's avatar
gsell committed
1691 1692 1693 1694 1695
			"Proc[%d]: Set step to #%lld for file %lld",
			f->myproc,
			(long long)step,
			(long long)(size_t) f );

1696 1697 1698
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
		f->timegroup = H5Gopen2 ( f->file, name, H5P_DEFAULT ); 
#else
gsell's avatar
gsell committed
1699
		f->timegroup = H5Gopen ( f->file, name ); 
1700
#endif
gsell's avatar
gsell committed
1701 1702 1703 1704 1705 1706 1707 1708 1709
		if ( f->timegroup < 0 ) return HANDLE_H5G_OPEN_ERR( name );
	}
	else {
		_H5Part_print_debug (
			"Proc[%d]: Create step #%lld for file %lld", 
			f->myproc,
			(long long)step,
			(long long)(size_t) f );

1710 1711 1712 1713 1714 1715 1716 1717
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
		f->timegroup = H5Gcreate2 (
			f->file,
			name,
			0,
			H5P_DEFAULT,
			H5P_DEFAULT );
#else
gsell's avatar
gsell committed
1718
		f->timegroup = H5Gcreate ( f->file, name, 0 );
1719
#endif
gsell's avatar
gsell committed
1720 1721 1722 1723 1724 1725
		if ( f->timegroup < 0 ) return HANDLE_H5G_CREATE_ERR ( name );
	}

	return H5PART_SUCCESS;
}

gsell's avatar
gsell committed
1726
/*!
gsell's avatar
gsell committed
1727 1728
  \ingroup h5part_read

gsell's avatar
gsell committed
1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744
  Set the current time-step.

  When writing data to a file the current time step must be set first
  (even if there is only one). In write-mode this function creates a new
  time-step! You are not allowed to step to an already existing time-step.
  This prevents you from overwriting existing data. Another consequence is,
  that you \b must write all data before going to the next time-step.

  In read-mode you can use this function to random-access the file for a
  particular timestep.

  \return \c H5PART_SUCCESS or error code 
*/
h5part_int64_t
H5PartSetStep (
	H5PartFile *f,			/*!< [in]  Handle to open file */
gsell's avatar
gsell committed
1745
	const h5part_int64_t step	/*!< [in]  Time-step to set. */
gsell's avatar
gsell committed
1746 1747 1748 1749 1750 1751
	) {

	SET_FNAME ( "H5PartSetStep" );

	CHECK_FILEHANDLE ( f );

gsell's avatar
gsell committed
1752
	return _H5Part_set_step ( f, step );
gsell's avatar
gsell committed
1753 1754 1755 1756
}

/********************** query file structure *********************************/

1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773
/*!
  \ingroup h5part_kernel

  Test whether a group named \c name exists at location \c id.
*/
h5part_int64_t
_H5Part_have_group (
	const hid_t id,
	const char *name
	) {
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
	return (H5Lexists( id, name, H5P_DEFAULT ) ? 1 : 0);
#else
	return (H5Gget_objinfo( id, name, 1, NULL ) >= 0 ? 1 : 0);
#endif
}

gsell's avatar
gsell committed
1774 1775
/*!
  \ingroup h5part_kernel
gsell's avatar
gsell committed
1776

gsell's avatar
gsell committed
1777 1778
  Iterator for \c H5Giterate().
*/
gsell's avatar
gsell committed
1779 1780 1781 1782 1783 1784 1785
herr_t
_H5Part_iteration_operator (
	hid_t group_id,		/*!< [in]  group id */
	const char *member_name,/*!< [in]  group name */
	void *operator_data	/*!< [in,out] data passed to the iterator */
	) {

gsell's avatar
gsell committed
1786
	struct _iter_op_data *data = (struct _iter_op_data*)operator_data;
gsell's avatar
gsell committed
1787 1788
	herr_t herr;

gsell's avatar
gsell committed
1789
	if ( data->type != H5G_UNKNOWN ) {
1790 1791
#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 8
                H5O_info_t objinfo;
1792
		herr = H5Oget_info ( group_id, &objinfo );
1793 1794 1795
		if ( herr < 0 ) return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name );
#else
	        H5G_stat_t objinfo;
gsell's avatar
gsell committed
1796
		herr = H5Gget_objinfo ( group_id, member_name, 1, &objinfo );
gsell's avatar
gsell committed
1797
		if ( herr < 0 ) return (herr_t)HANDLE_H5G_GET_OBJINFO_ERR ( member_name );
1798
#endif
gsell's avatar
gsell committed
1799 1800 1801
		if ( objinfo.type != data->type )
			return 0;/* don't count, continue iteration */
	}
gsell's avatar
gsell committed
1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819

	if ( data->name && (data->stop_idx == data->count) ) {
		memset ( data->name, 0, data->len );
		strncpy ( data->name, member_name, data->len-1 );
		
		return 1;	/* stop iteration */
	}
	/*
	  count only if pattern is NULL or member name matches
	*/
	if ( !data->pattern ||
	     (strncmp (member_name, data->pattern, strlen(data->pattern)) == 0)
	      ) {
		data->count++;
	}
	return 0;		/* continue iteration */
}

gsell's avatar
gsell committed
1820 1821 1822 1823 1824
/*!
  \ingroup h5part_kernel

  Iterator for \c H5Giterate().
*/
gsell's avatar
gsell committed
1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838
h5part_int64_t
_H5Part_get_num_objects (
	hid_t group_id,
	const char *group_name,
	const hid_t type
	) {

	return _H5Part_get_num_objects_matching_pattern (
		group_id,
		group_name,
		type,
		NULL );
}

gsell's avatar
gsell committed
1839 1840 1841 1842 1843
/*!
  \ingroup h5part_kernel

  Iterator for \c H5Giterate().
*/
gsell's avatar
gsell committed
1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866
h5part_int64_t
_H5Part_get_num_objects_matching_pattern (
	hid_t group_id,
	const char *group_name,
	const hid_t type,
	char * const pattern
	) {

	h5part_int64_t herr;
	int idx = 0;
	struct _iter_op_data data;

	memset ( &data, 0, sizeof ( data ) );
	data.type = type;
	data.pattern = pattern;

	herr = H5Giterate ( group_id, group_name, &idx,
			    _H5Part_iteration_operator, &data );
	if ( herr < 0 ) return herr;
	
	return data.count;
}

gsell's avatar
gsell committed
1867 1868 1869 1870 1871
/*!
  \ingroup h5part_kernel

  Iterator for \c H5Giterate().
*/
gsell's avatar
gsell committed
1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886
h5part_int64_t
_H5Part_get_object_name (
	hid_t group_id,
	const char *group_name,
	const hid_t type,
	const h5part_int64_t idx,
	char *obj_name,
	const h5part_int64_t len_obj_name
	) {

	herr_t herr;
	struct _iter_op_data data;
	int iterator_idx = 0;

	memset ( &data, 0, sizeof ( data ) );
gsell's avatar
gsell committed
1887
	data.stop_idx = (hid_t)idx;
gsell's avatar
gsell committed
1888 1889
	data.type = type;
	data.name = obj_name;
gsell's avatar
gsell committed
1890
	data.len = (size_t)len_obj_name;
gsell's avatar
gsell committed
1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902

	herr = H5Giterate ( group_id, group_name, &iterator_idx,
			    _H5Part_iteration_operator,
			    &data );
	if ( herr < 0 ) return (h5part_int64_t)herr;

	if ( herr == 0 ) HANDLE_H5PART_NOENTRY_ERR( group_name,
						    type, idx );

	return H5PART_SUCCESS;
}

gsell's avatar
gsell committed
1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923
/*!
  \ingroup h5part_read

  Query whether a particular step already exists in the file
  \c f.

  It works for both reading and writing of files

  \return      true or false
*/
h5part_int64_t
H5PartHasStep (
	H5PartFile *f,		/*!< [in]  Handle to open file */
	h5part_int64_t step	/*!< [in]  Step number to query */
	) {
  
	SET_FNAME ( "H5PartHasStep" );

	CHECK_FILEHANDLE( f );

	char name[128];
1924 1925 1926 1927 1928 1929 1930 1931
	/* Work around sprintf bug on older systems */
	if (f->stepno_width == 0 && step == 0) {
	    sprintf ( name, "%s#%0*lld", f->groupname_step, 1, (long long) step );
	}
	else {
	    sprintf ( name, "%s#%0*lld", f->groupname_step, f->stepno_width, (long long) step );
	}
        return _H5Part_have_group ( f->file, name );
gsell's avatar
gsell committed
1932 1933 1934
}


gsell's avatar
gsell committed
1935
/*!
gsell's avatar
gsell committed
1936 1937
  \ingroup h5part_read

gsell's avatar
gsell committed
1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957
  Get the number of time-steps that are currently stored in the file
  \c f.

  It works for both reading and writing of files, but is probably
  only typically used when you are reading.

  \return	number of time-steps or error code
*/
h5part_int64_t
H5PartGetNumSteps (
	H5PartFile *f			/*!< [in]  Handle to open file */
	) {

	SET_FNAME ( "H5PartGetNumSteps" );

	CHECK_FILEHANDLE( f );

	return _H5Part_get_num_objects_matching_pattern (
		f->file,
		"/",
gsell's avatar
gsell committed
1958
		H5G_UNKNOWN,
gsell's avatar
gsell committed
1959
		f->groupname_step );
gsell's avatar
gsell committed
1960 1961 1962
}

/*!
gsell's avatar
gsell committed
1963 1964
  \ingroup h5part_read

gsell's avatar
gsell committed
1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980
  Get the number of datasets that are stored at the current time-step.

  \return	number of datasets in current timestep or error code
*/

h5part_int64_t
H5PartGetNumDatasets (
	H5PartFile *f			/*!< [in]  Handle to open file */
	) {

	SET_FNAME ( "H5PartGetNumDatasets" );

	char stepname[128];

	CHECK_FILEHANDLE( f );

1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993
	/* Work around sprintf bug on older systems */
	if (f->stepno_width == 0 && f->timestep == 0) {
	    sprintf (
		    stepname,
		    "%s#%0*lld",
		    f->groupname_step, 1, (long long) f->timestep );
	}
	else {
	    sprintf (
		    stepname,
		    "%s#%0*lld",
		    f->groupname_step, f->stepno_width, (long long) f->timestep );
	}
gsell's avatar
gsell committed
1994 1995 1996 1997