H5Part.c 90.4 KB
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/*! \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. 

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H5Part consists of Particles and Block structured Fields.
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Developed by:
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<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>
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<LI> Mark Howison (NERSC/LBNL)</LI>
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</UL>
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Papers: 

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<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>


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<LI> A. Adelmann, R.D. Ryne, J. Shalf, C. Siegerist, "H5Part: A Portable High Performance Parallel Data Interface for Particle Simulations," <i>
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<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>

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*/

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/*!
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  \defgroup h5part_c_api H5Part C API
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*/
/*!
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  \ingroup h5part_c_api
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  \defgroup h5part_open 	File Opening and Closing
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*/
/*!
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  \ingroup h5part_c_api
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  \defgroup h5part_model	Setting up the Data Model
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*/  
/*!
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  \ingroup h5part_c_api
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  \defgroup h5part_data		Readind and Writing Datasets
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*/  
/*!
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  \ingroup h5part_c_api
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  \defgroup h5part_attrib	Reading and Writing Attributes
*/
/*!
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  \ingroup h5part_c_api
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  \defgroup h5part_errhandle	Error Handling
*/
/*!
  \internal
  \defgroup h5partkernel H5Part private functions 
*/


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#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>

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#ifndef WIN32
#include <unistd.h>
#else /* WIN32 */
#include <io.h>
#define open  _open
#define close _close
#endif /* WIN32 */

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#include "H5Part.h"
#include "H5PartPrivate.h"
#include "H5PartErrors.h"

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/********* Global Variable Declarations *************/
h5part_error_handler	_err_handler = H5PartReportErrorHandler;

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

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static unsigned			_is_root_proc = 0;
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static unsigned			_debug = H5PART_VERB_ERROR;
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static h5part_int64_t		_h5part_errno = H5PART_SUCCESS;
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static char *__funcname;
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/********** Declaration of private functions ******/

static h5part_int64_t
_init(
	void
	);

static h5part_int64_t
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_reset_view (
	H5PartFile *f
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	);

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/*
  error handler for hdf5
*/
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static herr_t
_h5_error_handler (
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#ifndef H5_USE_16_API
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	hid_t,
#endif
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	void *
	);

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static void
_vprint (
	FILE* f,
	const char *prefix,
	const char *fmt,
	va_list ap
	);

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

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static H5PartFile*
_H5Part_open_file (
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	const char *filename,	/*!< [in] The name of the data file to open. */
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	const char flags,	/*!< [in] The access mode for the file. */
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	MPI_Comm comm,		/*!< [in] MPI communicator */
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	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. */
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	) {
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	_h5part_errno = H5PART_SUCCESS;
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	H5PartFile *f = NULL;

	f = (H5PartFile*) malloc( sizeof (H5PartFile) );
	if( f == NULL ) {
		HANDLE_H5PART_NOMEM_ERR;
		goto error_cleanup;
	}
	memset (f, 0, sizeof (H5PartFile));
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	f->flags = flags;

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	/* set default step name */
	strncpy ( f->groupname_step, H5PART_GROUPNAME_STEP, H5PART_STEPNAME_LEN );
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	f->stepno_width = 0;

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	f->xfer_prop = f->dcreate_prop = f->fcreate_prop = H5P_DEFAULT;
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	f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
	if (f->access_prop < 0) {
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		HANDLE_H5P_CREATE_ERR;
		goto error_cleanup;
	}
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	if ( f_parallel ) {
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#ifdef PARALLEL_IO
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		MPI_Info info = MPI_INFO_NULL;
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		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;
		}
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		if ( f-> myproc == 0 ) _is_root_proc = 1;
		else _is_root_proc = 0;

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		f->pnparticles =
		  (h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
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		if (f->pnparticles == NULL) {
			HANDLE_H5PART_NOMEM_ERR;
			goto error_cleanup;
		}
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		/* optional lustre optimizations */
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		if ( flags & H5PART_FS_LUSTRE )
		{
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			/* extend the btree size so that metadata pieces are
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		 	* close to the alignment value */
			if ( align > 0 )
			{
				unsigned int btree_ik = (align - 4096) / 96;
				unsigned int btree_bytes = 64 + 96*btree_ik;
				if ( btree_bytes > align ) {
					HANDLE_H5PART_INVALID_ERR(
						"btree_ik", btree_ik );
					goto error_cleanup;
				}
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				_H5Part_print_info (
					"Setting HDF5 btree parameter to %u",
					btree_ik );
				_H5Part_print_info (
					"Extending HDF5 btree size to %u "
					"bytes at rank 3", btree_bytes );
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				f->fcreate_prop = H5Pcreate(H5P_FILE_CREATE);
				if ( f->fcreate_prop < 0 ) {
					HANDLE_H5P_CREATE_ERR;
					goto error_cleanup;
				}
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				H5Pset_istore_k (f->fcreate_prop, btree_ik);
			}
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#ifdef H5PART_HAVE_HDF5_18
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			/* defer metadata cache flushing until file close */
			H5AC_cache_config_t cache_config;
			cache_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
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			H5Pget_mdc_config (f->access_prop, &cache_config);
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			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;
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			H5Pset_mdc_config (f->access_prop, &cache_config);
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#else // H5_USE_16_API
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			_H5Part_print_warn (
				"Unable to defer metadata write: need HDF5 1.8");
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#endif // H5_USE_16_API
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		}
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		/* select the HDF5 VFD */
		if (flags & H5PART_VFD_MPIPOSIX) {
			_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;
			}
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		} else if (flags & H5PART_VFD_CORE) {
			_H5Part_print_info ( "Selecting CORE VFD" );
			if (H5Pset_fapl_core ( f->access_prop, comm, 0 ) < 0) {
				HANDLE_H5P_SET_FAPL_ERR;
				goto error_cleanup;
			}
		} else {
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			_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;
			}
			if (flags & H5PART_VFD_MPIIO_IND) {
				_H5Part_print_info ( "Using independent mode" );
			} else {
				_H5Part_print_info ( "Using collective mode" );
				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;
				}
			}
		}

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		f->comm = comm;
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#endif // PARALLEL_IO
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	} else {
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		_is_root_proc = 1;
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		f->comm = 0;
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		f->nprocs = 1;
		f->myproc = 0;
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		f->pnparticles = 
			(h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
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	}
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	if ( align != 0 ) {
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		_H5Part_print_info (
			"Setting HDF5 alignment to %ld bytes",
			align );
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		if (H5Pset_alignment ( f->access_prop, 0, align ) < 0) {
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			HANDLE_H5P_SET_FAPL_ERR;
			goto error_cleanup;
		}
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		_H5Part_print_info (
			"Setting HDF5 meta block to %ld bytes",
			align );
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		if (H5Pset_meta_block_size ( f->access_prop, align ) < 0) {
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			HANDLE_H5P_SET_FAPL_ERR;
			goto error_cleanup;
		}
	}

	if ( flags & H5PART_READ ) {
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		f->file = H5Fopen(filename, H5F_ACC_RDONLY, f->access_prop);
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	}
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	else if ( flags & H5PART_WRITE ){
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		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->fcreate_prop,
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				f->access_prop);
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		f->empty = 1;
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	}
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	else if ( flags & H5PART_APPEND ) {
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		int fd = open(filename, O_RDONLY, 0);
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		if ( (fd == -1) && (errno == ENOENT) ) {
			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
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					f->fcreate_prop, f->access_prop);
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			f->empty = 1;
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		}
		else if (fd != -1) {
			close (fd);
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			f->file = H5Fopen(
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				filename, H5F_ACC_RDWR, f->access_prop);
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			/*
			  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(
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				f->file, "/", H5G_GROUP, f->groupname_step );
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			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;
	}
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	f->nparticles = 0;
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	f->timegroup = -1;
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	f->shape = H5S_ALL;
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	f->diskshape = H5S_ALL;
	f->memshape = H5S_ALL;
	f->viewstart = -1;
	f->viewend = -1;
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	f->viewindexed = 0;
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	f->throttle = 0;
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	_H5Part_print_debug (
		"Proc[%d]: Opened file \"%s\" val=%lld",
		f->myproc,
		filename,
		(long long)(size_t)f );

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	return f;

 error_cleanup:
	if (f != NULL ) {
		if (f->pnparticles != NULL) {
			free (f->pnparticles);
		}
		free (f);
	}
	return NULL;
}

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#ifdef PARALLEL_IO
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/*!
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  \ingroup h5part_open
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  Opens file with specified filename. 

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  Flags are bit values that can be combined with the bit operator \c |
  and include:
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  - \c H5PART_WRITE - truncate file and open for writing
  - \c H5PART_APPEND - open file for writing without truncating
  - \c H5PART_READ - open file read-only
  - \c H5PART_FS_LUSTRE - enable optimizations for the Lustre file system
  - \c H5PART_VFD_MPIPOSIX - use the HDF5 MPI-POSIX virtual file driver
  - \c H5PART_VFD_MPIO_IND - use MPI-IO in indepedent mode

  The typical file extension is \c .h5.
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  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*
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H5PartOpenFileParallel (
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	const char *filename,	/*!< [in] The name of the data file to open. */
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	const char flags,	/*!< [in] The access mode for the file. */
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	MPI_Comm comm		/*!< [in] MPI communicator */
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	) {
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	INIT
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	SET_FNAME ( "H5PartOpenFileParallel" );

	int f_parallel = 1;	/* parallel i/o */
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	h5part_int64_t align = 0; /* no alignment tuning */
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	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
}

/*!
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  \ingroup h5part_open
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  Opens file with specified filename, and also specifices an alignment
  value used for HDF5 tuning parameters.

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  Flags are bit values that can be combined with the bit operator \c |
  and include:

  - \c H5PART_WRITE - truncate file and open for writing
  - \c H5PART_APPEND - open file for writing without truncating
  - \c H5PART_READ - open file read-only
  - \c H5PART_FS_LUSTRE - enable optimizations for the Lustre file system
  - \c H5PART_VFD_MPIPOSIX - use the HDF5 MPI-POSIX virtual file driver
  - \c H5PART_VFD_MPIO_IND - use MPI-IO in indepedent mode

  The typical file extension 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.

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  \return	File handle or \c NULL
 */
H5PartFile*
H5PartOpenFileParallelAlign (
	const char *filename,	/*!< [in] The name of the data file to open. */
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	const char flags,	/*!< [in] The access mode for the file. */
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	MPI_Comm comm,		/*!< [in] MPI communicator */
	h5part_int64_t align	/*!< [in] Alignment size in bytes. */
	) {
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	INIT
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	SET_FNAME ( "H5PartOpenFileParallelAlign" );
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	int f_parallel = 1;	/* parallel i/o */
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	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
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}
#endif
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/*!
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  \ingroup  h5part_open
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  Opens file with specified filename. 
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  Flags are bit values that can be combined with the bit operator \c |
  and include:

  - \c H5PART_WRITE - truncate file and open for writing
  - \c H5PART_APPEND - open file for writing without truncating
  - \c H5PART_READ - open file read-only
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  The typical file extension is \c .h5.
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  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.
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  \return	File handle or \c NULL
 */
H5PartFile*
H5PartOpenFile (
	const char *filename,	/*!< [in] The name of the data file to open. */
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	const char flags	/*!< [in] The access mode for the file. */
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	) {
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	INIT
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	SET_FNAME ( "H5PartOpenFile" );
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	MPI_Comm comm = 0;	/* dummy */
	int f_parallel = 0;	/* serial open */
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	int align = 0;		/* no tuning parameters */
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	return _H5Part_open_file ( filename, flags, comm, f_parallel, align );
}

/*!
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  \ingroup h5part_open
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  Opens file with specified filename, and also specifices an alignment
  value used for HDF5 tuning parameters.

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  Flags are bit values that can be combined with the bit operator \c |
  and include:

  - \c H5PART_WRITE - truncate file and open for writing
  - \c H5PART_APPEND - open file for writing without truncating
  - \c H5PART_READ - open file read-only

  The typical file extension 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.

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  \return	File handle or \c NULL
 */
H5PartFile*
H5PartOpenFileAlign (
	const char *filename,	/*!< [in] The name of the data file to open. */
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	const char flags,	/*!< [in] The access mode for the file. */
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	h5part_int64_t align	/*!< [in] Alignment size in bytes. */
) {
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	INIT
	SET_FNAME ( "H5PartOpenFileAlign" );
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	MPI_Comm comm = 0;	/* dummy */
	int f_parallel = 0;	/* serial open */

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

/*!
  Checks if a file was successfully opened.

  \return	\c H5PART_SUCCESS or error code
 */
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h5part_int64_t
_H5Part_file_is_valid (
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	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;
}

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/*!
  \ingroup h5part_open

  Closes an open file.

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

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	SET_FNAME ( "H5PartCloseFile" );
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	herr_t r = 0;
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	_h5part_errno = H5PART_SUCCESS;

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

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#ifdef PARALLEL_IO
	if ( f->multiblock && f->close_multiblock ) {
		(*f->close_multiblock) ( f );
		f->multiblock = NULL;
		f->close_multiblock = NULL;
	}
#endif

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	if( f->shape != H5S_ALL ) {
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		r = H5Sclose( f->shape );
		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
		f->shape = 0;
	}
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	if( f->timegroup >= 0 ) {
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		r = H5Gclose( f->timegroup );
		if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
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		f->timegroup = -1;
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	}
	if( f->diskshape != H5S_ALL ) {
		r = H5Sclose( f->diskshape );
		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
		f->diskshape = 0;
	}
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	if( f->memshape != H5S_ALL ) {
		r = H5Sclose( f->memshape );
		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
		f->memshape = 0;
	}
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	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;
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	}
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	if( f->dcreate_prop != H5P_DEFAULT ) {
		r = H5Pclose( f->dcreate_prop );
		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->dcreate_prop" );
		f->dcreate_prop = H5P_DEFAULT;
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	}
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	if ( f->file ) {
		r = H5Fclose( f->file );
		if ( r < 0 ) HANDLE_H5F_CLOSE_ERR;
		f->file = 0;
	}
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	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;
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	}  
	if( f->fcreate_prop != H5P_DEFAULT ) {
		r = H5Pclose( f->fcreate_prop );
		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->fcreate_prop" );
		f->fcreate_prop = H5P_DEFAULT;
	}
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	/* free memory from H5PartFile struct */
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	if( f->pnparticles ) {
		free( f->pnparticles );
	}
	free( f );

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	return _h5part_errno;
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}

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h5part_int64_t
H5PartFileIsValid (
	H5PartFile *f
	) {
	return _H5Part_file_is_valid(f);
}

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/*============== File Writing Functions ==================== */
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h5part_int64_t
_H5Part_get_step_name(
	H5PartFile *f,
	const h5part_int64_t step,
	char *name
	) {

	/* 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_SUCCESS;
}

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h5part_int64_t
H5PartDefineStepName (
	H5PartFile *f,
	const char *name,
	const h5part_int64_t width
	) {
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	CHECK_FILEHANDLE ( f );

	h5part_int64_t len = H5PART_STEPNAME_LEN - width - 2;
	if ( strlen(name) > len ) {
		_H5Part_print_warn (
			"Step name has been truncated to fit within %d chars.",
			H5PART_STEPNAME_LEN );
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	}
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	strncpy ( f->groupname_step, name, len );
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	f->stepno_width = (int)width;
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	_H5Part_print_debug ( "Step name defined as '%s'", f->groupname_step );
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	return H5PART_SUCCESS;
}

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static h5part_int64_t
_set_num_particles (
	H5PartFile *f,				/*!< [in] Handle to open file */
	const h5part_int64_t nparticles,	/*!< [in] Number of particles */
	const h5part_int64_t _stride
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	) {

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	int ret;
	h5part_int64_t herr;

	hsize_t count;
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#ifdef HDF5V160
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	hssize_t start;
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#else
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	hsize_t start;
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#endif
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	hsize_t stride;
	hsize_t dmax = H5S_UNLIMITED;
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#ifdef PARALLEL_IO
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	hsize_t total;
	register int i;
#endif

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	if ( nparticles <= 0 )
		return HANDLE_H5PART_INVALID_ERR ( "nparticles", nparticles );

	/* prevent invalid stride value */	
	if (_stride < 1)
	{
		_H5Part_print_warn (
			"Stride < 1 was specified: changing to 1." );
		stride = 1;
	} else {
		stride = (hsize_t) _stride;
	}
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#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
	*/
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	if ( f->nparticles == nparticles && stride == 1 ) {
		_H5Part_print_debug (
			"Serial mode: skipping unnecessary view creation" );
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		return H5PART_SUCCESS;
	}
#endif
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	herr = _reset_view ( f );
	if ( herr < 0 ) return herr;

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	if ( f->shape != H5S_ALL ) {
		herr = H5Sclose ( f->shape );
		if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
		f->shape = H5S_ALL;
	}

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	f->nparticles = (hsize_t) nparticles;

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

	/* we need a hyperslab selection if there is striding
	 * (otherwise, the default H5S_ALL selection is ok)
	 */
	if ( stride > 1 )
	{
		start = 0;
		count = f->nparticles;
		herr = H5Sselect_hyperslab (
			f->memshape,
			H5S_SELECT_SET,
			&start,
			&stride,
			&count, NULL );
		if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
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	}
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#ifndef PARALLEL_IO
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	count = f->nparticles;
	f->shape = H5Screate_simple ( 1, &count, NULL );
	if ( f->shape < 0 ) HANDLE_H5S_CREATE_SIMPLE_ERR ( count );
	f->viewstart = 0;
	f->viewend   = nparticles - 1; // view range is *inclusive*
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#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
	*/
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	ret = MPI_Allgather (
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		&nparticles, 1, MPI_LONG_LONG,
		f->pnparticles, 1, MPI_LONG_LONG,
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		f->comm );
	if ( ret != MPI_SUCCESS) return HANDLE_MPI_ALLGATHER_ERR;

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	if ( f->myproc == 0 ) {
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		for ( i=0; i<f->nprocs; i++ ) 
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			_H5Part_print_debug_detail (
				"[%d] np=%lld",
				i, (long long) f->pnparticles[i] );
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	}

	/* compute start offsets */
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	start = 0;
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	for (i=0; i<f->myproc; i++) {
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		start += f->pnparticles[i];
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	}
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	f->viewstart = start;
	f->viewend   = start + f->nparticles - 1; // view range is *inclusive*
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	/* compute total nparticles */
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	total = 0;
	for (i=0; i < f->nprocs; i++) {
		total += f->pnparticles[i];
	}

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	/* declare overall datasize */
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	count = total;
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	f->shape = H5Screate_simple (1, &count, NULL);
	if ( f->shape < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( count );
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	/* declare overall data size  but then will select a subset */
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	f->diskshape = H5Screate_simple (1, &count, NULL);
	if ( f->diskshape < 0 ) return HANDLE_H5S_CREATE_SIMPLE_ERR ( count );
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	count = nparticles;
	stride = 1;
	herr = H5Sselect_hyperslab (
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		f->diskshape,
		H5S_SELECT_SET,
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		&start,
		&stride,
		&count, NULL );
	if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
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#endif
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	return H5PART_SUCCESS;
}

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/*!
  \ingroup h5part_model

  Set the number of particles for the current time-step.
  After you call this subroutine, all subsequent 
  operations will assume this number of particles will be written.

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  For the parallel library, the \c nparticles value is the number of
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  particles that the \e individual task will write. You can use
  a different value on different tasks.
  This function uses an \c MPI_Allgather
  call to aggregate each tasks number of particles and determine
  the appropiate offsets. Because of the use of this MPI collective,
  it is advisable to call this function as
  few times as possible when running at large concurrency.

  This function assumes that your particles' data fields are in stored in
  contiguous 1D arrays.
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  For instance, the fields \e x and \e y for your particles are stored
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  in separate arrays \c x[] and \c y[].
  
  If instead you store your particles as tuples, so that the values
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  are arranged \f$ x_1,y_1,x_2,y_2\f$... than you need to setup striding
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  (in this case with value 2) using \ref H5PartSetNumParticlesStrided.

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

	SET_FNAME ( "H5PartSetNumParticles" );
	CHECK_FILEHANDLE( f );

	h5part_int64_t herr;
	h5part_int64_t stride = 1;

	herr = _set_num_particles ( f, nparticles, stride );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

/*!
  \ingroup h5part_model

  Set the number of particles for the current time-step.
  After you call this subroutine, all subsequent 
  operations will assume this number of particles will be written.

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  For the parallel library, the \c nparticles value is the number of
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  particles that the \e individual task will write. You can use
  a different value on different tasks.
  This function uses an \c MPI_Allgather
  call to aggregate each tasks number of particles and determine
  the appropiate offsets. Because of the use of this MPI collective,
  it is advisable to call this function as
  few times as possible when running at large concurrency.

  This function assumes that your particles' data fields are
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  stored tuples. For instance, the fields \e x and \e y of your
  particles are arranged \f$x_1,y_1,x_2,y_2\f$... in a single data
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  array. In this example, the stride value would be 2.
  
  If you instead have a separate array for each fields,
  such as \c x[] and \c y[],
  use \ref H5PartSetNumParticles.

  \return	\c H5PART_SUCCESS or error code
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*/
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h5part_int64_t
H5PartSetNumParticlesStrided (
	H5PartFile *f,				/*!< [in] Handle to open file */
	const h5part_int64_t nparticles,	/*!< [in] Number of particles */
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	const h5part_int64_t stride		/*!< [in] Stride value (e.g. number of fields in the particle array) */
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	) {

	SET_FNAME ( "H5PartSetNumParticlesStrided" );
	CHECK_FILEHANDLE( f );

	h5part_int64_t herr;

	herr = _set_num_particles ( f, nparticles, stride );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

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/*!
  \ingroup h5part_model

  Define the chunk \c size and enables chunking in the underlying
  HDF5 layer. When combined with the \c align value in the
  \ref H5PartOpenFileAlign or \ref H5PartOpenFileParallelAlign
  function, this causes each group of \c size particles to be
  padded on disk out to the nearest multiple of \c align bytes.

  Note that this policy wastes disk space, but can improve write
  bandwidth on parallel filesystems that are sensitive to alignment
  to stripe boundaries (e.g. lustre).

  \return	\c H5PART_SUCCESS or error code
*/
h5part_int64_t
H5PartSetChunkSize (
	H5PartFile *f,
	const h5part_int64_t size
	) {

	SET_FNAME ( "H5PartSetChunkSize" );
	CHECK_FILEHANDLE( f );

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	_H5Part_print_info (
		"Setting chunk size to %lld elements",
		(long long)size );
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	if ( f->dcreate_prop == H5P_DEFAULT ) {
		f->dcreate_prop = H5Pcreate (H5P_DATASET_CREATE);
		if ( f->dcreate_prop < 0 ) return HANDLE_H5P_CREATE_ERR;
	}

	hsize_t hsize = (hsize_t)size;

	herr_t herr = H5Pset_chunk ( f->dcreate_prop, 1, &hsize );
	if ( herr < 0 ) return HANDLE_H5P_SET_CHUNK_ERR;

	return H5PART_SUCCESS;
}

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static void
_normalize_dataset_name (
	const char *name,
	char *name2
	) {

	if ( strlen(name) > H5PART_DATANAME_LEN ) {
		strncpy ( name2, name, H5PART_DATANAME_LEN - 1 );
		name2[H5PART_DATANAME_LEN-1] = '\0';
		_H5Part_print_warn (
			"Dataset name '%s' is longer than maximum %d chars. "
			"Truncated to: '%s'",
			name, H5PART_DATANAME_LEN, name2 );
	} else {
		strcpy ( name2, name );
	}
}

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static h5part_int64_t
_write_data (
	H5PartFile *f,		/*!< IN: Handle to open file */
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	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 */
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	) {
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	herr_t herr;
	hid_t dataset_id;

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	char name2[H5PART_DATANAME_LEN];
	_normalize_dataset_name ( name, name2 );

	_H5Part_print_debug (
			"Create a dataset[%s] mounted on "
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			"timestep %lld",
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			name2, (long long)f->timestep );
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	if ( f->shape == H5S_ALL ) {
		_H5Part_print_warn (
			"The view is unset or invalid: please "
			"set the view or specify a number of particles." );
		return HANDLE_H5PART_BAD_VIEW_ERR ( f->viewstart, f->viewend );
	}

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	H5E_BEGIN_TRY
	dataset_id = H5Dopen ( f->timegroup, name2
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#ifndef H5_USE_16_API
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		, H5P_DEFAULT
#endif
		);
	H5E_END_TRY
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	if ( dataset_id > 0 ) {
		_H5Part_print_warn (
			"Dataset[%s] at timestep %lld "
			"already exists", name2, (long long)f->timestep );
	} else {
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		dataset_id = H5Dcreate ( 
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			f->timegroup,
			name2,
			type,
			f->shape,
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#ifndef H5_USE_16_API
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			H5P_DEFAULT,
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			f->dcreate_prop,
			H5P_DEFAULT
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#else
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			f->dcreate_prop
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#endif
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                );
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		if ( dataset_id < 0 )
			return HANDLE_H5D_CREATE_ERR ( name2, f->timestep );
	}
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#ifdef PARALLEL_IO
	herr = _H5Part_start_throttle ( f );
	if ( herr < 0 ) return herr;
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#endif
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	herr = H5Dwrite (
		dataset_id,
		type,
		f->memshape,
		f->diskshape,
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		f->xfer_prop,
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		array );

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#ifdef PARALLEL_IO
	herr = _H5Part_end_throttle ( f );
	if ( herr < 0 ) return herr;
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#endif
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	if ( herr < 0 ) return HANDLE_H5D_WRITE_ERR ( name2, f->timestep );
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	herr = H5Dclose ( dataset_id );
	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;

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	f->empty = 0;

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	return H5PART_SUCCESS;
}

/*!
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  \ingroup h5part_data
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  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 */
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	const char *name,	/*!< [in] Name to associate array with */
	const h5part_float64_t *array	/*!< [in] Array to commit to disk */
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	) {

	SET_FNAME ( "H5PartWriteDataFloat64" );
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	h5part_int64_t herr;
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	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;
}

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/*!
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  \ingroup h5part_data
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  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;
}

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/*!
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  \ingroup h5part_data
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  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 */
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	const char *name,	/*!< [in] Name to associate array with */
	const h5part_int64_t *array	/*!< [in] Array to commit to disk */
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	) {

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	SET_FNAME ( "H5PartWriteDataInt64" );
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	h5part_int64_t herr;
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	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;
}

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/*!
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  \ingroup h5part_data
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  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;
}

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/********************** reading and writing attribute ************************/

/********************** private functions to handle attributes ***************/
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/*!
  \ingroup h5partkernel
  @{
*/

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h5part_int64_t
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_H5Part_make_string_type(
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	hid_t *stype,
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	int size
	) {
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	*stype = H5Tcopy ( H5T_C_S1 );
	if ( *stype < 0 ) return HANDLE_H5T_STRING_ERR;
	herr_t herr = H5Tset_size ( *stype, size );
	if ( herr < 0 ) return HANDLE_H5T_STRING_ERR;
	return H5PART_SUCCESS;
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}

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/*!
   Normalize HDF5 type
*/
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h5part_int64_t
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_H5Part_normalize_h5_type (
	hid_t type
	) {
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	H5T_class_t tclass = H5Tget_class ( type );
	int size = H5Tget_size ( type );

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	switch ( tclass ) {
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	case H5T_INTEGER:
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		if ( size==8 ) {
			return H5PART_INT64;
		}
	  	else if ( size==1 ) {
			return H5PART_CHAR;
		}
		break;
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	case H5T_FLOAT:
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		if ( size==8 ) {
			return H5PART_FLOAT64;
		}
		else if ( size==4 ) {
			return H5PART_FLOAT32;
		}
		break;
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	case H5T_STRING:
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		return H5PART_STRING;
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	default:
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		;/* NOP */
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	}
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	return HANDLE_H5PART_TYPE_ERR;
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}

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

	herr_t herr;
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	h5part_int64_t h5err;
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	hid_t attrib_id;
	hid_t space_id;
	hid_t type_id;

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#ifdef H5PART_HAVE_HDF5_18
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	if (! H5Aexists ( id, attrib_name )) {
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		_H5Part_print_warn ( "Attribute '%s' does not exist!", attrib_name );
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	}
	attrib_id = H5Aopen ( id, attrib_name, H5P_DEFAULT );
#else
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	attrib_id = H5Aopen_name ( id, attrib_name );
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#endif
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	if ( attrib_id <= 0 ) return HANDLE_H5A_OPEN_NAME_ERR( attrib_name );

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	type_id = H5Aget_type ( attrib_id );
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	if ( type_id < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
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	space_id = H5Aget_space ( attrib_id );
	if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;

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

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

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	herr = H5Tclose ( type_id );
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	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
	) {

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	h5part_int64_t herr;
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	hid_t space_id;
	hid_t attrib_id;
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	hid_t type = attrib_type;

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	if ( attrib_type == H5PART_STRING )
	{
		herr = _H5Part_make_string_type ( &type, attrib_nelem );
		if ( herr < 0 ) return herr;

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		space_id = H5Screate (H5S_SCALAR);
		if ( space_id < 0 )
			return HANDLE_H5S_CREATE_SCALAR_ERR;
	}
	else {
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		space_id = H5Screate_simple ( 1, &attrib_nelem, NULL );
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		if ( space_id < 0 )
			return HANDLE_H5S_CREATE_SIMPLE_ERR ( attrib_nelem );
	}
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	attrib_id = H5Acreate(
		id,
		attrib_name,
		type,
		space_id,
		H5P_DEFAULT
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#ifndef H5_USE_16_API
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		, H5P_DEFAULT
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#endif
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		);
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	if ( attrib_id < 0 ) return HANDLE_H5A_CREATE_ERR ( attrib_name );

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	herr = H5Awrite ( attrib_id, type, attrib_value);
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	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;

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	if ( attrib_type == H5PART_STRING ) {
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		herr = H5Tclose ( type );
		if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
	}

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	return H5PART_SUCCESS;
}

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h5part_int64_t
_H5Part_write_file_attrib (
	H5PartFile *f,
	const char *name,
	const hid_t type,
	const void *value,
	const hsize_t nelem
	) {

	hid_t group_id = H5Gopen ( f->file, "/"
#ifndef H5_USE_16_API
				  , H5P_DEFAULT
#endif
				  );

	if ( group_id < 0 ) return HANDLE_H5G_OPEN_ERR( "/" );

	h5part_int64_t herr = _H5Part_write_attrib (
		group_id,
		name,
		type,
		value,
		nelem );
	if ( herr < 0 ) return herr;

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

	return H5PART_SUCCESS;
}

h5part_int64_t
_H5Part_write_step_attrib (
	H5PartFile *f,
	const char *name,
	const hid_t type,
	const void *value,
	const hsize_t nelem
	) {

	CHECK_TIMEGROUP( f );

	h5part_int64_t herr = _H5Part_write_attrib (
		f->timegroup,
		name,
		type,
		value,
		nelem );
	if ( herr < 0 ) return herr;

	return H5PART_SUCCESS;
}

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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;

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	attrib_id = H5Aopen_idx ( id, (unsigned int)attrib_idx );
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	if ( attrib_id < 0 ) return HANDLE_H5A_OPEN_IDX_ERR ( attrib_idx );

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

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		*attrib_nelem = H5Sget_simple_extent_npoints ( space_id );
		if ( *attrib_nelem < 0 )
			return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR;
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		herr = H5Sclose ( space_id );
		if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
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	}
	if ( attrib_name ) {
		herr = H5Aget_name (
			attrib_id,
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			(size_t)len_attrib_name,
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