Report Typos and Errors    
Semi-Lagrangian Library
Modular library for kinetic and gyrokinetic simulations of plasmas in fusion energy devices.
sll_m_hdf5_io_serial.F90
Go to the documentation of this file.
1 !**************************************************************
2 ! Copyright INRIA
3 !
4 ! This code SeLaLib (for Semi-Lagrangian-Library)
5 ! is a parallel library for simulating the plasma turbulence
6 ! in a tokamak.
7 !
8 ! This software is governed by the CeCILL-B license
9 ! under French law and abiding by the rules of distribution
10 ! of free software. You can use, modify and redistribute
11 ! the software under the terms of the CeCILL-B license as
12 ! circulated by CEA, CNRS and INRIA at the following URL
13 ! "http://www.cecill.info".
14 !**************************************************************
15 
25 module sll_m_hdf5_io_serial
26 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
27 #ifndef NOHDF5
28 
29 #include "sll_assert.h"
30 #include "sll_working_precision.h"
31 
32  use hdf5, only: &
33  h5acreate_f, &
34  h5aclose_f, &
35  h5aopen_f, &
36  h5aread_f, &
37  h5awrite_f, &
38  h5close_f, &
39  h5dclose_f, &
40  h5dcreate_f, &
41  h5dopen_f, &
42  h5dread_f, &
43  h5dwrite_f, &
44  h5f_acc_rdonly_f, &
45  h5f_acc_rdwr_f, &
46  h5f_acc_trunc_f, &
47  h5fclose_f, &
48  h5fcreate_f, &
49  h5fopen_f, &
50  h5gclose_f, &
51  h5gopen_f, &
52  h5o_info_t, &
53  h5oget_info_by_name_f, &
54  h5open_f, &
55  h5s_scalar_f, &
56  h5sclose_f, &
57  h5screate_f, &
58  h5screate_simple_f, &
59  h5t_native_double, &
60  h5t_native_integer, &
61  h5t_native_character, &
62  hid_t, &
63  hsize_t
64 
65  implicit none
66 
67  public :: &
68  sll_t_hdf5_ser_handle, &
69  sll_s_hdf5_ser_file_create, &
70  sll_s_hdf5_ser_file_open, &
71  sll_s_hdf5_ser_file_close, &
72  sll_o_hdf5_ser_write_array, &
73  sll_o_hdf5_ser_read_array, &
74  sll_o_hdf5_ser_write_attribute, &
75  sll_o_hdf5_ser_read_attribute, &
76  sll_s_hdf5_ser_write_file
77 
78  private
79 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
80 
81  ! HDF5 workaround: C enumeration does not seem to be available in Fortran
82  integer, parameter :: h5o_type_group = 0
83  integer, parameter :: h5o_type_dataset = 1
84 
86  type :: sll_t_hdf5_ser_handle
87  integer(hid_t), private :: file_id
88  end type
89 
90  !-----------------------------------------------------------------------------
98  !-----------------------------------------------------------------------------
99  interface sll_o_hdf5_ser_write_array
100  module procedure sll_hdf5_ser_write_dble_array_1d
101  module procedure sll_hdf5_ser_write_dble_array_2d
102  module procedure sll_hdf5_ser_write_dble_array_3d
103  module procedure sll_hdf5_ser_write_int_array_1d
104  module procedure sll_hdf5_ser_write_int_array_2d
105  module procedure sll_hdf5_ser_write_int_array_3d
106  end interface
107 
108  !-----------------------------------------------------------------------------
116  !-----------------------------------------------------------------------------
117  interface sll_o_hdf5_ser_read_array
118  module procedure sll_hdf5_ser_read_dble_array_1d
119  module procedure sll_hdf5_ser_read_dble_array_2d
120  module procedure sll_hdf5_ser_read_dble_array_3d
121  end interface
122 
123  !-----------------------------------------------------------------------------
133  !-----------------------------------------------------------------------------
134  interface sll_o_hdf5_ser_write_attribute
135  module procedure s_hdf5_ser_write_attribute_dble
136  module procedure s_hdf5_ser_write_attribute_int
137  end interface
138 
139  !-----------------------------------------------------------------------------
149  !-----------------------------------------------------------------------------
150  interface sll_o_hdf5_ser_read_attribute
151  module procedure s_hdf5_ser_read_attribute_dble
152  module procedure s_hdf5_ser_read_attribute_int
153  end interface
154 
155 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
156 contains
157 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
158 
159  !-----------------------------------------------------------------------------
167  !-----------------------------------------------------------------------------
168  subroutine sll_s_hdf5_ser_file_create(filename, handle, error)
169  character(len=*), intent(in) :: filename
170  type(sll_t_hdf5_ser_handle), intent(out) :: handle
171  integer, intent(out) :: error
172 
173  call h5open_f(error)
174  sll_assert_always(error == 0)
175  call h5fcreate_f(filename, h5f_acc_trunc_f, handle%file_id, error)
176  sll_assert_always(error == 0)
177  end subroutine sll_s_hdf5_ser_file_create
178 
179  !-----------------------------------------------------------------------------
185  !-----------------------------------------------------------------------------
186  subroutine sll_s_hdf5_ser_file_open(filename, handle, error)
187  character(len=*), intent(in) :: filename
188  type(sll_t_hdf5_ser_handle), intent(out) :: handle
189  integer, intent(out) :: error
190 
191  call h5open_f(error)
192  sll_assert_always(error == 0)
193  call h5fopen_f(filename, h5f_acc_rdwr_f, handle%file_id, error)
194  sll_assert_always(error == 0)
195  end subroutine sll_s_hdf5_ser_file_open
196 
197  !-----------------------------------------------------------------------------
202  !-----------------------------------------------------------------------------
203  subroutine sll_s_hdf5_ser_file_close(handle, error)
204  type(sll_t_hdf5_ser_handle), intent(in) :: handle
205  integer, intent(out) :: error
206 
207  call h5fclose_f(handle%file_id, error) ! Close property list and file
208  sll_assert_always(error == 0)
209  call h5close_f(error) ! Close FORTRAN interface
210  sll_assert_always(error == 0)
211  end subroutine sll_s_hdf5_ser_file_close
212 
213  !-----------------------------------------------------------------------------
215  !-----------------------------------------------------------------------------
216  subroutine sll_hdf5_ser_write_int_array_1d(handle, array, dsetname, error)
217  integer, parameter :: rank = 1
218  type(sll_t_hdf5_ser_handle), intent(in) :: handle
219  integer(i32), intent(in) :: array(:)
220  character(len=*), intent(in) :: dsetname
221  integer, intent(out) :: error
222 
223 #define DATATYPE H5T_NATIVE_INTEGER
224 #include "sll_k_hdf5_ser_write_array.F90"
225 #undef DATATYPE
226 
227  end subroutine sll_hdf5_ser_write_int_array_1d
228 
229  !-----------------------------------------------------------------------------
231  !-----------------------------------------------------------------------------
232  subroutine sll_hdf5_ser_write_int_array_2d(handle, array, dsetname, error)
233  integer, parameter :: rank = 2
234  type(sll_t_hdf5_ser_handle), intent(in) :: handle
235  integer(i32), intent(in) :: array(:, :)
236  character(len=*), intent(in) :: dsetname
237  integer, intent(out) :: error
238 
239 #define DATATYPE H5T_NATIVE_INTEGER
240 #include "sll_k_hdf5_ser_write_array.F90"
241 #undef DATATYPE
242 
243  end subroutine sll_hdf5_ser_write_int_array_2d
244 
245  !-----------------------------------------------------------------------------
247  !-----------------------------------------------------------------------------
248  subroutine sll_hdf5_ser_write_int_array_3d(handle, array, dsetname, error)
249  integer, parameter :: rank = 3
250  type(sll_t_hdf5_ser_handle), intent(in) :: handle
251  integer(i32), intent(in) :: array(:, :, :)
252  character(len=*), intent(in) :: dsetname
253  integer, intent(out) :: error
254 
255 #define DATATYPE H5T_NATIVE_INTEGER
256 #include "sll_k_hdf5_ser_write_array.F90"
257 #undef DATATYPE
258 
259  end subroutine sll_hdf5_ser_write_int_array_3d
260 
261  !-----------------------------------------------------------------------------
263  !-----------------------------------------------------------------------------
264  subroutine sll_hdf5_ser_write_dble_array_1d(handle, array, dsetname, error)
265  integer, parameter :: rank = 1
266  type(sll_t_hdf5_ser_handle), intent(in) :: handle
267  real(f64), intent(in) :: array(:)
268  character(len=*), intent(in) :: dsetname
269  integer, intent(out) :: error
270 
271 #define DATATYPE H5T_NATIVE_DOUBLE
272 #include "sll_k_hdf5_ser_write_array.F90"
273 #undef DATATYPE
274 
275  end subroutine sll_hdf5_ser_write_dble_array_1d
276 
277  !-----------------------------------------------------------------------------
279  !-----------------------------------------------------------------------------
280  subroutine sll_hdf5_ser_write_dble_array_2d(handle, array, dsetname, error)
281  integer, parameter :: rank = 2
282  type(sll_t_hdf5_ser_handle), intent(in) :: handle
283  real(f64), intent(in) :: array(:, :)
284  character(len=*), intent(in) :: dsetname
285  integer, intent(out) :: error
286 
287 #define DATATYPE H5T_NATIVE_DOUBLE
288 #include "sll_k_hdf5_ser_write_array.F90"
289 #undef DATATYPE
290 
291  end subroutine sll_hdf5_ser_write_dble_array_2d
292 
293  !-----------------------------------------------------------------------------
295  !-----------------------------------------------------------------------------
296  subroutine sll_hdf5_ser_write_dble_array_3d(handle, array, dsetname, error)
297  integer, parameter :: rank = 3
298  type(sll_t_hdf5_ser_handle), intent(in) :: handle
299  real(f64), intent(in) :: array(:, :, :)
300  character(len=*), intent(in) :: dsetname
301  integer, intent(out) :: error
302 
303 #define DATATYPE H5T_NATIVE_DOUBLE
304 #include "sll_k_hdf5_ser_write_array.F90"
305 #undef DATATYPE
306 
307  end subroutine sll_hdf5_ser_write_dble_array_3d
308 
309  !-----------------------------------------------------------------------------
311  !-----------------------------------------------------------------------------
312  subroutine sll_hdf5_ser_read_dble_array_1d(handle, array, dsetname, error)
313  integer, parameter :: rank = 1
314  type(sll_t_hdf5_ser_handle), intent(in) :: handle
315  real(f64), intent(out) :: array(:)
316  character(len=*), intent(in) :: dsetname
317  integer, intent(out) :: error
318 
319 #define DATATYPE H5T_NATIVE_DOUBLE
320 #include "sll_k_hdf5_ser_read_array.F90"
321 #undef DATATYPE
322 
323  end subroutine sll_hdf5_ser_read_dble_array_1d
324 
325  !-----------------------------------------------------------------------------
327  !-----------------------------------------------------------------------------
328  subroutine sll_hdf5_ser_read_dble_array_2d(handle, array, dsetname, error)
329  integer, parameter :: rank = 2
330  type(sll_t_hdf5_ser_handle), intent(in) :: handle
331  real(f64), intent(out) :: array(:, :)
332  character(len=*), intent(in) :: dsetname
333  integer, intent(out) :: error
334 
335 #define DATATYPE H5T_NATIVE_DOUBLE
336 #include "sll_k_hdf5_ser_read_array.F90"
337 #undef DATATYPE
338 
339  end subroutine sll_hdf5_ser_read_dble_array_2d
340 
341  !-----------------------------------------------------------------------------
343  !-----------------------------------------------------------------------------
344  subroutine sll_hdf5_ser_read_dble_array_3d(handle, array, dsetname, error)
345  integer, parameter :: rank = 3
346  type(sll_t_hdf5_ser_handle), intent(in) :: handle
347  real(f64), intent(out) :: array(:, :, :)
348  character(len=*), intent(in) :: dsetname
349  integer, intent(out) :: error
350 
351 #define DATATYPE H5T_NATIVE_DOUBLE
352 #include "sll_k_hdf5_ser_read_array.F90"
353 #undef DATATYPE
354 
355  end subroutine sll_hdf5_ser_read_dble_array_3d
356 
357  !-----------------------------------------------------------------------------
364  !-----------------------------------------------------------------------------
365  subroutine sll_hdf5_ser_write_char_array(handle, string, dsetname, error)
366  type(sll_t_hdf5_ser_handle), intent(in) :: handle
367  character(len=*), intent(in) :: string
368  character(len=*), intent(in) :: dsetname
369  integer, intent(out) :: error
370 
371  integer(hsize_t) :: array_dim(1)
372  integer(hid_t) :: dataset_id
373  integer(hid_t) :: dataspace_id
374 
375  array_dim = int(len(string), hsize_t)
376 
377  ! Create dataspace
378  call h5screate_simple_f(1, array_dim, dataspace_id, error)
379  sll_assert_always(error == 0)
380 
381  ! Create dataset
382  call h5dcreate_f(handle%file_id, dsetname, h5t_native_character, &
383  dataspace_id, dataset_id, error)
384  sll_assert_always(error == 0)
385 
386  ! Write dataset
387  call h5dwrite_f(dataset_id, h5t_native_character, string, array_dim, error)
388  sll_assert_always(error == 0)
389 
390  ! Close dataspace
391  call h5sclose_f(dataspace_id, error)
392  sll_assert_always(error == 0)
393 
394  ! Close dataset
395  call h5dclose_f(dataset_id, error)
396  sll_assert_always(error == 0)
397 
398  end subroutine sll_hdf5_ser_write_char_array
399 
400  !-----------------------------------------------------------------------------
407  !-----------------------------------------------------------------------------
408  subroutine sll_s_hdf5_ser_write_file(handle, filename, dsetname, error)
409  type(sll_t_hdf5_ser_handle), intent(in) :: handle
410  character(len=*), intent(in) :: filename
411  character(len=*), intent(in) :: dsetname
412  integer, intent(out) :: error
413 
414  integer :: fileid, filesize
415  character(len=:), allocatable :: content
416 
417  open (newunit=fileid, file=filename, &
418  form='UNFORMATTED', access='STREAM', iostat=error)
419 
420  !get size of file
421  inquire (file=filename, size=filesize)
422  if (filesize > 0) then
423 
424  ! Allocate memory
425  allocate (character(len=filesize) :: content)
426 
427  ! Read the whole file into one string
428  read (fileid, pos=1, iostat=error) content
429 
430  if (error == 0) then
431  !try to read more in case not everything was read
432  read (fileid, pos=filesize + 1, iostat=error) content
433  if (.not. is_iostat_end(error)) then
434  write (*, *) "ERROR: file ", filename, "was not completely read."
435  end if
436  else
437  write (*, *) 'ERROR reading file: ', filename
438  end if
439 
440  else
441  write (*, *) 'Error getting size of file: ', filename
442  end if
443 
444  close (fileid)
445  call sll_hdf5_ser_write_char_array(handle, content, dsetname, error)
446 
447  end subroutine sll_s_hdf5_ser_write_file
448 
449  !-----------------------------------------------------------------------------
451  !-----------------------------------------------------------------------------
452  subroutine s_hdf5_ser_write_attribute_dble(handle, objpath, attrname, attrvalue, error)
453  type(sll_t_hdf5_ser_handle), intent(in) :: handle
454  character(len=*), intent(in) :: objpath
455  character(len=*), intent(in) :: attrname
456  real(f64), intent(in) :: attrvalue
457  integer, intent(out) :: error
458 
459 #define DATATYPE H5T_NATIVE_DOUBLE
460 #include "sll_k_hdf5_ser_write_attribute.F90"
461 #undef DATATYPE
462 
463  end subroutine s_hdf5_ser_write_attribute_dble
464 
465  !-----------------------------------------------------------------------------
467  !-----------------------------------------------------------------------------
468  subroutine s_hdf5_ser_write_attribute_int(handle, objpath, attrname, attrvalue, error)
469  type(sll_t_hdf5_ser_handle), intent(in) :: handle
470  character(len=*), intent(in) :: objpath
471  character(len=*), intent(in) :: attrname
472  integer, intent(in) :: attrvalue
473  integer, intent(out) :: error
474 
475 #define DATATYPE H5T_NATIVE_INTEGER
476 #include "sll_k_hdf5_ser_write_attribute.F90"
477 #undef DATATYPE
478 
479  end subroutine s_hdf5_ser_write_attribute_int
480 
481  !-----------------------------------------------------------------------------
483  !-----------------------------------------------------------------------------
484  subroutine s_hdf5_ser_read_attribute_dble(handle, objpath, attrname, attrvalue, error)
485  type(sll_t_hdf5_ser_handle), intent(in) :: handle
486  character(len=*), intent(in) :: objpath
487  character(len=*), intent(in) :: attrname
488  real(f64), intent(out) :: attrvalue
489  integer, intent(out) :: error
490 
491 #define DATATYPE H5T_NATIVE_DOUBLE
492 #include "sll_k_hdf5_ser_read_attribute.F90"
493 #undef DATATYPE
494 
495  end subroutine s_hdf5_ser_read_attribute_dble
496 
497  !-----------------------------------------------------------------------------
499  !-----------------------------------------------------------------------------
500  subroutine s_hdf5_ser_read_attribute_int(handle, objpath, attrname, attrvalue, error)
501  type(sll_t_hdf5_ser_handle), intent(in) :: handle
502  character(len=*), intent(in) :: objpath
503  character(len=*), intent(in) :: attrname
504  integer, intent(out) :: attrvalue
505  integer, intent(out) :: error
506 
507 #define DATATYPE H5T_NATIVE_INTEGER
508 #include "sll_k_hdf5_ser_read_attribute.F90"
509 #undef DATATYPE
510 
511  end subroutine s_hdf5_ser_read_attribute_int
512 
513  !-----------------------------------------------------------------------------
514 #endif
515 
516 end module sll_m_hdf5_io_serial
sll_m_hdf5_io_serial::sll_o_hdf5_ser_read_array
Read nD array of double precision floats or integers from HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:117
sll_m_hdf5_io_serial::sll_o_hdf5_ser_read_attribute
Read pre-existing named scalar attribute (double precision float or integer) from HDF5 object (group ...
Definition: sll_m_hdf5_io_serial.F90:150
sll_m_hdf5_io_serial::sll_o_hdf5_ser_write_array
Write nD array of double precision floats or integers into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:99
sll_m_hdf5_io_serial::sll_o_hdf5_ser_write_attribute
Attach new named scalar attribute (double precision float or integer) to HDF5 object (group or datase...
Definition: sll_m_hdf5_io_serial.F90:134
sll_m_hdf5_io_serial
Implements the functions to write hdf5 file to store heavy data.
Definition: sll_m_hdf5_io_serial.F90:25
sll_m_hdf5_io_serial::sll_hdf5_ser_write_dble_array_2d
subroutine sll_hdf5_ser_write_dble_array_2d(handle, array, dsetname, error)
Write 2D array of float64 into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:281
sll_m_hdf5_io_serial::s_hdf5_ser_write_attribute_dble
subroutine s_hdf5_ser_write_attribute_dble(handle, objpath, attrname, attrvalue, error)
Attach named float64 attribute to existing group or dataset.
Definition: sll_m_hdf5_io_serial.F90:453
sll_m_hdf5_io_serial::sll_hdf5_ser_write_char_array
subroutine sll_hdf5_ser_write_char_array(handle, string, dsetname, error)
Write Fortran string to HDF5 file as 1D array of characters.
Definition: sll_m_hdf5_io_serial.F90:366
sll_m_hdf5_io_serial::h5o_type_group
integer, parameter h5o_type_group
Definition: sll_m_hdf5_io_serial.F90:82
sll_m_hdf5_io_serial::sll_hdf5_ser_read_dble_array_1d
subroutine sll_hdf5_ser_read_dble_array_1d(handle, array, dsetname, error)
Read 1D array of float64 from HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:313
sll_m_hdf5_io_serial::s_hdf5_ser_read_attribute_int
subroutine s_hdf5_ser_read_attribute_int(handle, objpath, attrname, attrvalue, error)
Read named integer attribute from existing group or dataset.
Definition: sll_m_hdf5_io_serial.F90:501
sll_m_hdf5_io_serial::s_hdf5_ser_read_attribute_dble
subroutine s_hdf5_ser_read_attribute_dble(handle, objpath, attrname, attrvalue, error)
Read named float64 attribute from existing group or dataset.
Definition: sll_m_hdf5_io_serial.F90:485
sll_m_hdf5_io_serial::sll_hdf5_ser_write_int_array_1d
subroutine sll_hdf5_ser_write_int_array_1d(handle, array, dsetname, error)
Write 1D array of int32 into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:217
sll_m_hdf5_io_serial::sll_s_hdf5_ser_file_create
subroutine, public sll_s_hdf5_ser_file_create(filename, handle, error)
Create new HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:169
sll_m_hdf5_io_serial::sll_hdf5_ser_write_dble_array_1d
subroutine sll_hdf5_ser_write_dble_array_1d(handle, array, dsetname, error)
Write 1D array of float64 into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:265
sll_m_hdf5_io_serial::sll_hdf5_ser_write_int_array_3d
subroutine sll_hdf5_ser_write_int_array_3d(handle, array, dsetname, error)
Write 3D array of int32 into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:249
sll_m_hdf5_io_serial::sll_hdf5_ser_write_int_array_2d
subroutine sll_hdf5_ser_write_int_array_2d(handle, array, dsetname, error)
Write 2D array of int32 into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:233
sll_m_hdf5_io_serial::sll_hdf5_ser_read_dble_array_2d
subroutine sll_hdf5_ser_read_dble_array_2d(handle, array, dsetname, error)
Read 2D array of float64 from HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:329
sll_m_hdf5_io_serial::sll_hdf5_ser_read_dble_array_3d
subroutine sll_hdf5_ser_read_dble_array_3d(handle, array, dsetname, error)
Read 3D array of float64 from HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:345
sll_m_hdf5_io_serial::s_hdf5_ser_write_attribute_int
subroutine s_hdf5_ser_write_attribute_int(handle, objpath, attrname, attrvalue, error)
Attach named integer attribute to existing group or dataset.
Definition: sll_m_hdf5_io_serial.F90:469
sll_m_hdf5_io_serial::h5o_type_dataset
integer, parameter h5o_type_dataset
Definition: sll_m_hdf5_io_serial.F90:83
sll_m_hdf5_io_serial::sll_s_hdf5_ser_file_close
subroutine, public sll_s_hdf5_ser_file_close(handle, error)
Close existing HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:204
sll_m_hdf5_io_serial::sll_s_hdf5_ser_file_open
subroutine, public sll_s_hdf5_ser_file_open(filename, handle, error)
Open existing HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:187
sll_m_hdf5_io_serial::sll_s_hdf5_ser_write_file
subroutine, public sll_s_hdf5_ser_write_file(handle, filename, dsetname, error)
Read complete file to string and store it into HDF5 data structure.
Definition: sll_m_hdf5_io_serial.F90:409
sll_m_hdf5_io_serial::sll_hdf5_ser_write_dble_array_3d
subroutine sll_hdf5_ser_write_dble_array_3d(handle, array, dsetname, error)
Write 3D array of float64 into HDF5 file.
Definition: sll_m_hdf5_io_serial.F90:297
sll_m_hdf5_io_serial::sll_t_hdf5_ser_handle
Opaque object around HDF5 file id.
Definition: sll_m_hdf5_io_serial.F90:86
    Report Typos and Errors
Generated on Mon Oct 23 2023 19:15:40 for Semi-Lagrangian Library by   doxygen 1.9.1