H5Part.c File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <hdf5.h>
#include "H5Part.h"

Classes
struct	H5IO_getname_t
Typedefs
typedef H5IO_getname_t	H5IO_getname_t
Functions
herr_t	H5PartIOcounter (hid_t group_id, const char *member_name, void *operator_data)
H5PartFile *	H5PartOpenFileParallel (const char *filename, unsigned flags)
H5PartFile *	H5PartOpenFile (const char *filename, unsigned flags)
int	H5PartFileIsValid (H5PartFile *f)
void	H5PartCloseFile (H5PartFile *f)
void	H5PartSetNumParticles (H5PartFile *f, long long nparticles)
int	H5PartWriteDataFloat64 (H5PartFile *f, char *name, double *array)
int	H5PartWriteDataInt64 (H5PartFile *f, char *name, long long *array)
int	H5PartWriteFileAttribString (H5PartFile *f, char *name, char *attrib)
int	H5PartWriteStepAttribString (H5PartFile *f, char *name, char *attrib)
int	H5PartWriteStepAttrib (H5PartFile *f, char *name, hid_t type, void *value, int nelem)
int	H5PartWriteAttrib (H5PartFile *f, char *name, hid_t type, void *value, int nelem)
int	H5PartWriteFileAttrib (H5PartFile *f, char *name, hid_t type, void *value, int nelem)
herr_t	H5PartAttribcounter (hid_t group_id, const char *member_name, void *operator_data)
int	H5PartGetNumStepAttribs (H5PartFile *f)
int	H5PartGetNumFileAttribs (H5PartFile *f)
hid_t	H5PartNormType (hid_t type)
void	H5PartGetStepAttribInfo (H5PartFile *f, int idx, char *name, size_t maxname, hid_t *type, int *nelem)
void	H5PartGetFileAttribInfo (H5PartFile *f, int idx, char *name, size_t maxname, hid_t *type, int *nelem)
int	H5PartReadStepAttrib (H5PartFile *f, char *name, void *data)
void	H5PartReadAttrib (H5PartFile *f, char *name, void *data)
int	H5PartReadFileAttrib (H5PartFile *f, char *name, void *data)
void	H5PartSetStep (H5PartFile *f, int step)
herr_t	H5PartDScounter (hid_t group_id, const char *member_name, void *operator_data)
herr_t	H5IOgetname (hid_t group_id, const char *member_name, void *operator_data)
int	H5PartGetNumSteps (H5PartFile *f)
int	H5PartGetNumDatasets (H5PartFile *f)
int	H5PartGetDatasetName (H5PartFile *f, int _index, char *name, int maxlen)
hid_t	H5PartGetDiskShape (H5PartFile *f, hid_t dataset)
hid_t	H5PartGetMemShape (H5PartFile *f, hid_t dataset)
herr_t	H5PartGetFirstDS (hid_t group_id, const char *member_name, void *operator_data)
long long	H5PartGetNumParticles (H5PartFile *f)
void	H5PartSetView (H5PartFile *f, long long start, long long end)
int	H5PartGetView (H5PartFile *f, long long *start, long long *end)
void	H5PartSetCanonicalView (H5PartFile *f)
int	H5PartReadDataFloat64 (H5PartFile *f, char *name, double *array)
int	H5PartReadDataInt64 (H5PartFile *f, char *name, long long *array)
int	H5PartReadParticleStep (H5PartFile *f, int step, double *x, double *y, double *z, double *px, double *py, double *pz, long long *id)
herr_t	H5NameExists (hid_t group_id, const char *member_name, void *v)
int	H5PartFileHasName (H5PartFile *f, char *dir, char *name)
int	H5PartStashFile (H5PartFile *f, char *filename)
int	H5PartUnstashFile (H5PartFile *f, char *filename, char *outputpath)
int	H5PartGetNumStashFiles (H5PartFile *f)
int	H5PartFileGetStashFileName (H5PartFile *f, int nameindex, char *filename, int maxnamelen)

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Typedef Documentation

typedef struct H5IO_getname_t H5IO_getname_t

H5IO_getname_t: Private

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Function Documentation

herr_t H5IOgetname (  hid_t  group_id, const char *  member_name, void *  operator_data )

H5IOgetname: Private

herr_t H5NameExists (  hid_t  group_id, const char *  member_name, void *  v )

H5NameExists: Private

herr_t H5PartAttribcounter (  hid_t  group_id, const char *  member_name, void *  operator_data )

void H5PartCloseFile (  H5PartFile *  f  )

H5PartCloseFile: closes an open file. Parameters: f  filehandle of the file to close Returns: void

herr_t H5PartDScounter (  hid_t  group_id, const char *  member_name, void *  operator_data )

H5PartDScounter: Private

int H5PartFileGetStashFileName (  H5PartFile *  f, int  nameindex, char *  filename, int  maxnamelen )

int H5PartFileHasName (  H5PartFile *  f, char *  dir, char *  name )

H5PartFileHasName: Private

int H5PartFileIsValid (  H5PartFile *  f  )

H5PartFileIsValid: checks if a file was successfully opened. Parameters: f  filehandle of the file to check validity Returns: 1 if success 0 if failure

int H5PartGetDatasetName (  H5PartFile *  f, int  _index, char *  name, int  maxlen )

H5PartGetDatasetName: This reads the name of a datasetes specified by it's index. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). _index  integer specifying the index of the dataset. If the number of datasets is nds, the range of index is 0 to nds-1. name  A null-terminated string for the name of the dataset. maxlen  An integer specifying the maximum length of the name array. Returns: 1 on success, 0 on failure.

hid_t H5PartGetDiskShape (  H5PartFile *  f, hid_t  dataset )

H5PartGetDiskShape: Private

void H5PartGetFileAttribInfo (  H5PartFile *  f, int  idx, char *  name, size_t  maxname, hid_t *  type, int *  nelem )

H5PartGetFileAttribInfo: gets the name, type and number of elements of a file attribute . Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). idx  Index of the attribute name  A null-terminated string with the name of the attribute. maxname  The length of the attribute name. type  One of the following ones: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR. nelem  Number of elements of type "type". Returns: void.

herr_t H5PartGetFirstDS (  hid_t  group_id, const char *  member_name, void *  operator_data )

H5PartGetFirstDS: Private

hid_t H5PartGetMemShape (  H5PartFile *  f, hid_t  dataset )

int H5PartGetNumDatasets (  H5PartFile *  f  )

H5PartGetNumDatasets: This reads the number of datasetes that are stored at a particular time step. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: number of datasets.

int H5PartGetNumFileAttribs (  H5PartFile *  f  )

H5PartGetNumFileAttribs: gets the number of attributes bound to the file. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: number of attributes of the File.

long long H5PartGetNumParticles (  H5PartFile *  f  )

H5PartGetNumParticles: This gets the number of particles that are stored in the current timestep. It will arbitrarily select a timestep if you haven't already set the timestep with H5PartSetStep(). Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: number of particles in current timestep.

int H5PartGetNumStashFiles (  H5PartFile *  f  )

H5PartGetNumStashFiles: returns the number of stashed files. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: Number of stashed files.

int H5PartGetNumStepAttribs (  H5PartFile *  f  )

H5PartGetNumStepAttribs: gets the number of attributes bound to the current step. The step has to be set with H5PartSetStep(). Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: number of attributes of the current step.

int H5PartGetNumSteps (  H5PartFile *  f  )

H5PartGetNumSteps: This reads the number of datasteps that are currently stored in the datafile. (simple return of an int). It works for both reading and writing of files, but is probably only typically used when you are reading. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: number of timesteps currently stored in the file.

void H5PartGetStepAttribInfo (  H5PartFile *  f, int  idx, char *  name, size_t  maxname, hid_t *  type, int *  nelem )

H5PartGetStepAttribInfo: gets the name, type and number of elements of a step attribute . Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). idx  Index of the attribute name  A null-terminated string with the name of the attribute. maxname  the length of the name of the attribute. type  One of the following ones: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR. nelem  Number of elements of type "type". Returns: void.

int H5PartGetView (  H5PartFile *  f, long long *  start, long long *  end )

H5PartGetView: Allows you to query the current view. Start and End will be -1 if there is no current view established. Use H5PartHasView to see if the view is smaller than the total dataset. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). start  start particle end  end particle Returns: the number of elements in the view

herr_t H5PartIOcounter (  hid_t  group_id, const char *  member_name, void *  operator_data )

H5PartIOcounter: This is an entirely internal callback function which is used in conjunction with HDF5 iterators. The HDF5 Group iterator will call this repeatedly in order to count how many timesteps of data have been stored in a particular file. This is used by H5PartGetNumSteps().

hid_t H5PartNormType (  hid_t  type  )

H5PartNormType: Private

H5PartFile* H5PartOpenFile (  const char *  filename, unsigned  flags )

H5PartOpenFile: Opens file with specified filename. If you open with flag H5PART_WRITE, it will truncate any file with the specified filename and start writing to it. If you open with H5PART_READ, then it will open the file readonly. 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. Parameters: filename  The name of the IEEEIO data file to open. The typical extension for these files is .h5 flags  The accessmode for the file. This is one of 2 different access modes: H5PART_READ, H5PART_WRITE. Returns: A new filehandle with an open file or NULL if error.

H5PartFile* H5PartOpenFileParallel (  const char *  filename, unsigned  flags )

H5PartOpenFileParallel: Opens file with specified filename. If you open with flag H5PART_WRITE, it will truncate any file with the specified filename and start writing to it. If you open with H5PART_READ, then it will open the file readonly. 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. Parameters: filename  The name of the IEEEIO data file to open. The typical extension for these files is .h5 flags  The accessmode for the file. This is one of 2 different access modes: H5PART_READ, H5PART_WRITE. comm  This argument is only available if the program has been compiled with the PARALLEL_IO Returns: A new filehandle with an open file or NULL if error.

void H5PartReadAttrib (  H5PartFile *  f, char *  name, void *  data )

H5PartReadAttrib: reads a step attribute NOTE: it has been superseeded by H5PartReadStepAttrib. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string with the name of the attribute. data  of the attribute. Returns: 1 on success, -1 on failure.

int H5PartReadDataFloat64 (  H5PartFile *  f, char *  name, double *  array )

H5PartReadDataFloat64: This reads in an individual array from a particlar timestep. If you haven't selected a particular timestep, it will pick the current one. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the array. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. array  A buffer to read array of particle data. The datatype for elements in the buffer is implicit in the name of the subroutine call. Returns: 1 on success, 0 on failure.

int H5PartReadDataInt64 (  H5PartFile *  f, char *  name, long long *  array )

H5PartReadDataInt64: This reads in an individual array from a particlar timestep. If you haven't selected a particular timestep, it will pick the current one. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the array. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. array  A buffer to read array of particle data. The datatype for elements in the buffer is implicit in the name of the subroutine call. Returns: 1 on success, 0 on failure.

int H5PartReadFileAttrib (  H5PartFile *  f, char *  name, void *  data )

H5PartReadFileAttrib: reads a file attribute Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string with the name of the attribute. data  Value of the attribute. Returns: 1 on success, -1 on failure.

int H5PartReadParticleStep (  H5PartFile *  f, int  step, double *  x, double *  y, double *  z, double *  px, double *  py, double *  pz, long long *  id )

H5PartReadParticleStep: This is the mongo read function that pulls in all of the data for a given timestep in one shot. It also takes the timestep as an argument and will call H5PartSetStep() internally so that you don't have to make that call separately. See also: H5PartReadArray() if you want to just read in one of the many arrays.

int H5PartReadStepAttrib (  H5PartFile *  f, char *  name, void *  data )

H5PartReadStepAttrib: reads a step attribute Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string with the name of the attribute. data  of the attribute. Returns: 1 on success, -1 on failure.

void H5PartSetCanonicalView (  H5PartFile *  f  )

H5SetCanonicalView: If it is too tedious to manually set the start and end coordinates for a view, the H5SetCanonicalView() will automatically select an appropriate domain decomposition of the data arrays for the degree of parallelism and set the "view" accordingly. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). Returns: void

void H5PartSetNumParticles (  H5PartFile *  f, long long  nparticles )

H5PartSetNumParticles: This function's sole purpose is to prevent needless creation of new HDF5 DataSpace handles if the number of particles is invariant throughout the sim. That's its only reason for existence. After you call this subroutine, all subsequent operations will assume this number of particles will be written. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). nparticles  A long long integer specifying the number of particles Returns: void

void H5PartSetStep (  H5PartFile *  f, int  step )

H5PartSetStep: When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). step  the time step to set. Returns: void

void H5PartSetView (  H5PartFile *  f, long long  start, long long  end )

H5SetView: For parallel I/O or for subsetting operations on the datafile, the H5SetView subroutine allows you to define a subset of the total particle dataset to read. The concept of "view" works for both serial and for parallel I/O. The "view" will remain in effect until a new view is set, or the number of particles in a dataset changes, or the view is "unset" by calling H5SetView(file,-1,-1); Before you set a view, the H5PartGetNumParticles will return the total number of particles in a file (even for the parallel reads). However, after you set a view, it will return the number of particles contained in the view. The range is inclusive (the start and the end index). Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). start  start particle end  end particle Returns: void

int H5PartStashFile (  H5PartFile *  f, char *  filename )

NOTE: it's missing the read! H5PartStashFile: stash a file in the hdf5 file. If it does not exists a UserData and a Files group will be created. /param f A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). /param filename A null-terminated string for the name of the filename. /return 1 on succes, 0 on failure.

int H5PartUnstashFile (  H5PartFile *  f, char *  filename, char *  outputpath )

H5PartUnstashFile: unstash a file in the hdf5 file. /param f A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). /param filename A null-terminated string for the name of the filename. /param The path to the directory to create the file. /return 1 on succes, 0 on failure.

int H5PartWriteAttrib (  H5PartFile *  f, char *  name, hid_t  type, void *  value, int  nelem )

H5PartWriteAttr: writes a step attribute. Note: this call has been superseeded by H5PartWriteStepAttr. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the attribute. type  One of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64, H5T_NATIVE_CHAR. value  Value of the attribute. nelem  Number of elements of type "type". Returns: 1 on success, 0 on failure.

int H5PartWriteDataFloat64 (  H5PartFile *  f, char *  name, double *  array )

H5PartWriteDataFloat64: After setting the number of particles with H5PartSetNumParticles() and the current timestep using 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 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. The data is committed to disk before the routine returns. 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. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the array. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. array  A buffer containing an array of particle data to commit to disk. The datatype for elements in the buffer is implicit in the name of the subroutine call. Returns: 1 on success, 0 on failure.

int H5PartWriteDataInt64 (  H5PartFile *  f, char *  name, long long *  array )

H5PartWriteDataInt64: After setting the number of particles with H5PartSetNumParticles() and the current timestep using 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 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. The data is committed to disk before the routine returns. 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. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the array. When retrieving datasets from disk, you ask for them by name. There are no restrictions on naming of arrays, but it is useful to arrive at some common naming convention when sharing data with other groups. array  A buffer containing an array of particle data to commit to disk. The datatype for elements in the buffer is implicit in the name of the subroutine call. Returns: 1 on success, 0 on failure.

int H5PartWriteFileAttrib (  H5PartFile *  f, char *  name, hid_t  type, void *  value, int  nelem )

H5PartWriteStepAttr: writes a string attribute bound to a step. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the attribute. type  One of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64, H5T_NATIVE_CHAR. value  Value of the attribute. nelem  Number of elements of type "type". Returns: 1 on success, 0 on failure.

int H5PartWriteFileAttribString (  H5PartFile *  f, char *  name, char *  attrib )

H5PartWriteFileAttribString: writes a string attribute bound to a file. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the attribute. attrib  A null-terminated string for the attribute. Returns: 1 on success, 0 on failure.

int H5PartWriteStepAttrib (  H5PartFile *  f, char *  name, hid_t  type, void *  value, int  nelem )

H5PartWriteStepAttrib: writes a step attribute. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the attribute. type  One of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64, H5T_NATIVE_CHAR. value  Value of the attribute. nelem  Number of elements of type "type". Returns: 1 on success, 0 on failure.

int H5PartWriteStepAttribString (  H5PartFile *  f, char *  name, char *  attrib )

H5PartWriteStepAttrString: writes a string attribute bound to the current step. Parameters: f  A FileHandle opened by H5PartOpenFile() or H5PartOpenFileParallel(). name  A null-terminated string for the name of the attribute. attrib  A null-terminated string for the attribute. Returns: 1 on success, 0 on failure.

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