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H5

Last edited by gsell

File handling and attributes

1. Open a H5hut file

1.1. Open file with default properties, serial version

C implementation

#include "H5hut.h"

int
main (
	int argc,
	char** argv
	) {
        h5_file_t f = H5OpenFile ("testfile.h5", H5_O_WRONLY, H5_PROP_DEFAULT);

	H5CloseFile (f);
	return 0;
}

Fortran90 implementation

include 'H5hut.f90'

program openclose
  use H5hut
  implicit none
  include 'mpif.h'

  integer*8 :: file_id, status

  file_id = h5_openfile ("testfile.h5", H5_O_WRONLY, H5_PROP_DEFAULT)

  status = h5_closefile (file_id);
end program openclose

1.2. Open file with default properties, parallel version

C implementation

#include "H5hut.h"

int
main (
	int argc,
	char** argv
	) {
	MPI_Init (&argc, &argv);
        h5_file_t f = H5OpenFile ("testfile.h5", H5_O_WRONLY, H5_PROP_DEFAULT);

	H5CloseFile (f);
	MPI_Finalize ();
	return 0;
}

Fortran90 implementation

include 'H5hut.f90'

program openclose
  use H5hut
  implicit none
  include 'mpif.h'

  integer :: ierr
  integer*8 :: file_id, status

  call mpi_init(ierr)
  file_id = h5_openfile ("testfile.h5", H5_O_WRONLY, H5_PROP_DEFAULT)

  status = h5_closefile (file_id);
  call mpi_finalize(ierr)
end program openclose

1.3. Open file to use MPI independent I/O

C implementation

#include "H5hut.h"

int
main (
	int argc,
	char** argv
	) {
	MPI_Init (&argc, &argv);
	MPI_Comm comm = MPI_COMM_WORLD;
        h5_prop_t prop = H5CreateFileProp ();
        H5SetPropFileMPIOIndependent (prop, &comm);
        h5_file_t f = H5OpenFile ("testfile.h5", H5_O_WRONLY, prop);

        H5CloseProp (prop);
	H5CloseFile (f);
	MPI_Finalize ();
	return 0;
}

Fortran90 implementation

include 'H5hut.f90'

program openclose
  use H5hut
  implicit none
  include 'mpif.h'

  integer :: comm, rank, ierr
  integer*8 :: file_id, status
  integer*8 :: props

  comm = MPI_COMM_WORLD
  call mpi_init(ierr)
  call mpi_comm_rank(comm, rank, ierr)

  props = h5_createprop_file ()
  status = h5_setprop_file_mpio_collective (props, comm)
  file_id = h5_openfile ("testfile.h5", H5_O_WRONLY, props)
  status = h5_closeprop (props)
  status = h5_closefile (file_id);

  call mpi_finalize(ierr)
end program openclose

2. File attributes

2.1. Write file attributes

C implementation

#include "H5hut.h"

#define FNAME           "example_file_attribs.h5"

#define ATTR_STRING     "FileAttrString"
#define ATTR_INT32      "FileAttrInt32"
#define ATTR_INT64      "FileAttrInt64"
#define ATTR_FLOAT32    "FileAttrFloat32"
#define ATTR_FLOAT64    "FileAttrFloat64"

#define asize(array)    (sizeof(array)/sizeof(array[0]))

int
main (
	int argc,
	char** argv
	) {
        char* string_value = "This is a string attribute bound to the file.";
        int32_t int32_value[] = {0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144};
        int64_t int64_value[] = {42, 43, 44, 45};
        h5_float32_t float32_value[] = {2.71828};
        h5_float64_t float64_value[] = {3.14159265358979323846264338327950288419716939937510};

	MPI_Init (&argc, &argv);

        H5AbortOnError ();

        // if file properties is set to default, MPI_COMM_WORLD will be used
        h5_file_t f = H5OpenFile (FNAME, H5_O_WRONLY, H5_PROP_DEFAULT);
        H5WriteFileAttribString  (f, ATTR_STRING,  string_value);
        H5WriteFileAttribInt32   (f, ATTR_INT32,   int32_value,   asize(int32_value));
        H5WriteFileAttribInt64   (f, ATTR_INT64,   int64_value,   asize(int64_value));
        H5WriteFileAttribFloat32 (f, ATTR_FLOAT32, float32_value, asize(float32_value));
        H5WriteFileAttribFloat64 (f, ATTR_FLOAT64, float64_value, asize(float32_value));

	H5CloseFile (f);
	MPI_Finalize ();
	return 0;
}

Fortran90 implementation

include 'H5hut.f90'

  program write_file_attribs
    use H5hut
    implicit none
    include 'mpif.h'

    integer*8, parameter :: verbosity_level =             1

    character (len=*), parameter :: FNAME =               "example_file_attribs.h5"
    character (len=*), parameter :: ATTR_STRING =         "FileAttrString"
    character (len=*), parameter :: ATTR_I4 =             "FileAttrInt32"
    character (len=*), parameter :: ATTR_I8 =             "FileAttrInt64"
    character (len=*), parameter :: ATTR_R4 =             "FileAttrFloat32"
    character (len=*), parameter :: ATTR_R8 =             "FileAttrFloat64"

    character (len=*),parameter :: string_value =         "This is a string attribute bound to the file."

    integer*4, parameter, dimension(*) :: i4_value = (/0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144/)
    integer*8, parameter, dimension(*) :: i8_value = (/42, 43, 44, 45/)
    real*4, parameter, dimension(*) ::    r4_value = (/2.71828/)
    real*8, parameter, dimension(*) ::    r8_value = (/3.141592653589793238462643383279502884197169/)

    integer :: ierr
    integer*8 :: file_id, status

    call mpi_init(ierr)

    ! abort program on any H5hut error
    call h5_abort_on_error()

    call h5_set_verbosity_level (verbosity_level)

    !  MPI_COMM_WORLD is used, if file is opened with default properties
    file_id = h5_openfile (FNAME, H5_O_WRONLY, H5_PROP_DEFAULT)

    ! write attributes
    status = h5_writefileattrib_string (file_id, ATTR_STRING, string_value)
    status = h5_writefileattrib_i4     (file_id, ATTR_I4,     i4_value, int8(size(i4_value, 1)))
    status = h5_writefileattrib_i8     (file_id, ATTR_I8,     i8_value, int8(size(i8_value, 1)))
    status = h5_writefileattrib_r4     (file_id, ATTR_R4,     r4_value, int8(size(r4_value, 1)))
    status = h5_writefileattrib_r8     (file_id, ATTR_R8,     r8_value, int8(size(r8_value, 1)))

    ! cleanup
    status = h5_closefile (file_id)
    call mpi_finalize(ierr)

  end program write_file_attribs

2.2. Read file attributes

Read and print the file attributes written by above example.

C implementation

#include "H5hut.h"

#include <stdlib.h>

#define FNAME           "example_file_attribs.h5"
#define VERBOSITY       H5_VERBOSE_ERROR
#define DEBUG_MSK	0

#define ATTR_STRING     "FileAttrString"
#define ATTR_INT32      "FileAttrInt32"
#define ATTR_INT64      "FileAttrInt64"
#define ATTR_FLOAT32    "FileAttrFloat32"
#define ATTR_FLOAT64    "FileAttrFloat64"

int
main (
	int argc,
	char** argv
	) {
	MPI_Init (&argc, &argv);
        H5AbortOnError ();
        H5SetVerbosityLevel (VERBOSITY);
	H5SetDebugMask (DEBUG_MSK);

        // if file properties is set to default, MPI_COMM_WORLD will be used
        h5_file_t f = H5OpenFile (FNAME, H5_O_RDONLY, H5_PROP_DEFAULT);
        h5_size_t len;

        H5GetFileAttribInfoByName (f, ATTR_STRING, NULL, &len);
        char* attr_string = (char*)malloc (len+1);
        H5ReadFileAttribString (f, ATTR_STRING, attr_string);
        printf ("%s: %s\n", ATTR_STRING, attr_string);
        free (attr_string);

        H5GetFileAttribInfoByName (f, ATTR_INT32, NULL, &len);
        int32_t* attr_int32 = (int32_t*)malloc (sizeof(*attr_int32)*len);
        H5ReadFileAttribInt32 (f, ATTR_INT32, attr_int32);
        printf ("%s:", ATTR_INT32);
        for (int i = 0; i < len; i++) {
                printf (" %d", attr_int32[i]);
        }
        printf ("\n");
        free (attr_int32);

        H5GetFileAttribInfoByName (f, ATTR_INT64, NULL, &len);
        int64_t* attr_int64 = (int64_t*)malloc (sizeof(*attr_int64)*len);
        H5ReadFileAttribInt64 (f, ATTR_INT64, attr_int64);
        printf ("%s:", ATTR_INT64);
        for (int i = 0; i < len; i++) {
                printf (" %lld", (long long int)attr_int64[i]);
        }
        printf ("\n");
        free (attr_int64);

        H5GetFileAttribInfoByName (f, ATTR_FLOAT32, NULL, &len);
        h5_float32_t* attr_float32 = (h5_float32_t*)malloc (sizeof(*attr_float32)*len);
        H5ReadFileAttribFloat32 (f, ATTR_FLOAT32, attr_float32);
        printf ("%s:", ATTR_FLOAT32);
        for (int i = 0; i < len; i++) {
                printf (" %f", attr_float32[i]);
        }
        printf ("\n");
        free (attr_float32);

        H5GetFileAttribInfoByName (f, ATTR_FLOAT64, NULL, &len);
        h5_float64_t* attr_float64 = (h5_float64_t*)malloc (sizeof(*attr_float64)*len);
        H5ReadFileAttribFloat64 (f, ATTR_FLOAT64, attr_float64);
        printf ("%s:", ATTR_FLOAT64);
        for (int i = 0; i < len; i++) {
                printf (" %f", attr_float64[i]);
        }
        printf ("\n");
        free (attr_float64);

        // cleanup
	H5CloseFile (f);
	MPI_Finalize ();
	return 0;
}
---

*Fortran implementation*

include 'H5hut.f90'

program read_step_attribs
  use H5hut
  implicit none
  include 'mpif.h'
! the file name we want to read
character (len=*), parameter :: FNAME =               "example_file_attribs.h5"
! verbosity level: set it to a power of 2 minus one or zero
integer*8, parameter :: verbosity_level =             1
! we know the attribute names!
character (len=*), parameter :: ATTR_STRING =         "StepAttrString"
character (len=*), parameter :: ATTR_I4 =             "StepAttrInt32"
character (len=*), parameter :: ATTR_I8 =             "StepAttrInt64"
character (len=*), parameter :: ATTR_R4 =             "StepAttrFloat32"
character (len=*), parameter :: ATTR_R8 =             "StepAttrFloat64"
! for formated output
character (len=128) ::    fmt
! attribute values. Note: allocatable strings aren't supported in Fortran90
character (len=256) ::    string_value
integer*4, allocatable :: i4_value (:)
integer*8, allocatable :: i8_value (:)
real*4, allocatable ::    r4_value (:)
real*8, allocatable ::    r8_value (:)
! used for mpi error return
integer :: ierr
! H5hut file id
integer*8 :: file_id
! H5hut API status return
integer*8 status
! type of attribute
integer*8 type
! len of attribute
integer*8 len
! loop index
integer*8 i
call mpi_init (ierr)
! abort program on any H5hut error
call h5_abort_on_error ()
call h5_set_verbosity_level (verbosity_level)
!  MPI_COMM_WORLD is used, if file is opened with default properties
file_id = h5_openfile (FNAME, H5_O_RDONLY, H5_PROP_DEFAULT)
! open step 1
status = h5_setstep (file_id, int8(1))
! read and output string attribute
status = h5_getstepattribinfo_by_name (file_id, ATTR_STRING, type, len)
status = h5_readstepattrib_string (file_id, ATTR_STRING, string_value)
write (fmt, "(a, i0, a)")  '(a', len, ')'
write (*, "(a, ' = ')", advance='no') ATTR_STRING
write (*, fmt) string_value
! read and output 32bit integer attribute
status = h5_getstepattribinfo_by_name (file_id, ATTR_I4, type, len)
allocate (i4_value(len))
status = h5_readstepattrib_i4 (file_id, ATTR_I4, i4_value)
write (fmt, "(a, i0, a)")  '(', len, 'i4)'
write (*, "(a, ' =')", advance='no') ATTR_I4
write (*, fmt) (i4_value(i), i = 1, len)
! read and output 64bit integer attribute
status = h5_getstepattribinfo_by_name (file_id, ATTR_I8, type, len)
allocate (i8_value(len))
status = h5_readstepattrib_i8 (file_id, ATTR_I8, i8_value)
write (fmt, "(a, i0, a)")  '(', len, 'i4)'
write (*, "(a, ' =')", advance='no') ATTR_I8
write (*, fmt) (i8_value(i), i = 1, len)
! read and output 32bit floating point attribute
status = h5_getstepattribinfo_by_name (file_id, ATTR_R4, type, len)
allocate (r4_value(len))
status = h5_readstepattrib_r4 (file_id, ATTR_R4, r4_value)
write (fmt, "(a, i0, a)")  '(', len, 'f10.5)'
write (*, "(a, ' =')", advance='no') ATTR_R4
write (*, fmt) (r4_value(i), i = 1, len)
! read and output 64bit floating point attribute
status = h5_getstepattribinfo_by_name (file_id, ATTR_R8, type, len)
allocate (r8_value(len))
status = h5_readstepattrib_r8 (file_id, ATTR_R8, r8_value)
write (fmt, "(a, i0, a)")  '(', len, 'f10.5)'
write (*, "(a, ' =')", advance='no') ATTR_R8
write (*, fmt) (r8_value(i), i = 1, len)
! cleanup
status = h5_closefile (file_id)
call mpi_finalize(ierr)
end program read_step_attribs