Neko 0.9.1
A portable framework for high-order spectral element flow simulations
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hdf5_file.F90
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34module hdf5_file
35 use num_types, only : rp
36 use generic_file, only : generic_file_t
37 use checkpoint, only : chkp_t
38 use utils, only : neko_error, filename_suffix_pos
39 use mesh, only : mesh_t
40 use field, only : field_t, field_ptr_t
41 use field_list, only : field_list_t
42 use field_series, only : field_series_t, field_series_ptr_t
43 use dofmap, only : dofmap_t
44 use logger
45 use comm
46 use mpi_f08
47#ifdef HAVE_HDF5
48 use hdf5
49#endif
50 implicit none
51 private
52
54 type, public, extends(generic_file_t) :: hdf5_file_t
55 contains
56 procedure :: read => hdf5_file_read
57 procedure :: write => hdf5_file_write
58 end type hdf5_file_t
59
60contains
61
62#ifdef HAVE_HDF5
63
65 subroutine hdf5_file_write(this, data, t)
66 class(hdf5_file_t), intent(inout) :: this
67 class(*), target, intent(in) :: data
68 real(kind=rp), intent(in), optional :: t
69 type(mesh_t), pointer :: msh
70 type(dofmap_t), pointer :: dof
71 type(field_ptr_t), allocatable :: fp(:)
72 type(field_series_ptr_t), allocatable :: fsp(:)
73 real(kind=rp), pointer :: dtlag(:)
74 real(kind=rp), pointer :: tlag(:)
75 integer :: ierr, info, drank, i, j
76 integer(hid_t) :: plist_id, file_id, dset_id, grp_id, attr_id
77 integer(hid_t) :: filespace, memspace
78 integer(hsize_t), dimension(1) :: ddim, dcount, doffset
79 integer :: suffix_pos
80 character(len=5) :: id_str
81 character(len=1024) :: fname
82
83 call hdf5_file_determine_data(data, msh, dof, fp, fsp, dtlag, tlag)
84
85 suffix_pos = filename_suffix_pos(this%fname)
86 write(id_str, '(i5.5)') this%counter
87 fname = trim(this%fname(1:suffix_pos-1))//id_str//'.h5'
88
89 call h5open_f(ierr)
90 call h5pcreate_f(h5p_file_access_f, plist_id, ierr)
91 info = mpi_info_null%mpi_val
92 call h5pset_fapl_mpio_f(plist_id, neko_comm%mpi_val, info, ierr)
93
94 call h5fcreate_f(fname, h5f_acc_trunc_f, &
95 file_id, ierr, access_prp = plist_id)
96
97 call h5pcreate_f(h5p_dataset_xfer_f, plist_id, ierr)
98 call h5pset_dxpl_mpio_f(plist_id, h5fd_mpio_collective_f, ierr)
99
100 call h5screate_f(h5s_scalar_f, filespace, ierr)
101 ddim = 1
102
103 if (present(t)) then
104 call h5acreate_f(file_id, "Time", h5t_native_double, filespace, attr_id, &
105 ierr, h5p_default_f, h5p_default_f)
106 call h5awrite_f(attr_id, h5t_native_double, t, ddim, ierr)
107 call h5aclose_f(attr_id, ierr)
108 end if
109
110 if (associated(dof)) then
111 call h5acreate_f(file_id, "Lx", h5t_native_integer, filespace, attr_id, &
112 ierr, h5p_default_f, h5p_default_f)
113 call h5awrite_f(attr_id, h5t_native_integer, dof%Xh%lx, ddim, ierr)
114 call h5aclose_f(attr_id, ierr)
115 end if
116
117 if (associated(msh)) then
118 call h5gcreate_f(file_id, "Mesh", grp_id, ierr, lcpl_id=h5p_default_f, &
119 gcpl_id=h5p_default_f, gapl_id=h5p_default_f)
120
121 call h5acreate_f(grp_id, "Elements", h5t_native_integer, filespace, attr_id, &
122 ierr, h5p_default_f, h5p_default_f)
123 call h5awrite_f(attr_id, h5t_native_integer, msh%glb_nelv, ddim, ierr)
124 call h5aclose_f(attr_id, ierr)
125
126 call h5acreate_f(grp_id, "Dimension", h5t_native_integer, filespace, attr_id, &
127 ierr, h5p_default_f, h5p_default_f)
128 call h5awrite_f(attr_id, h5t_native_integer, msh%gdim, ddim, ierr)
129 call h5aclose_f(attr_id, ierr)
130
131 call h5gclose_f(grp_id, ierr)
132 end if
133
134
135 call h5sclose_f(filespace, ierr)
136
137 !
138 ! Write restart group (tlag, dtlag)
139 !
140 if (associated(tlag) .and. associated(dtlag)) then
141 call h5gcreate_f(file_id, "Restart", grp_id, ierr, lcpl_id=h5p_default_f, &
142 gcpl_id=h5p_default_f, gapl_id=h5p_default_f)
143
144 drank = 1
145 ddim = size(tlag)
146 doffset(1) = 0
147 if (pe_rank .eq. 0) then
148 dcount = size(tlag)
149 else
150 dcount = 0
151 end if
152
153 call h5screate_simple_f(drank, ddim, filespace, ierr)
154
155 call h5dcreate_f(grp_id,'tlag', h5t_native_double, &
156 filespace, dset_id, ierr)
157 call h5dget_space_f(dset_id, filespace, ierr)
158 call h5sselect_hyperslab_f (filespace, h5s_select_set_f, &
159 doffset, dcount, ierr)
160 call h5dwrite_f(dset_id, h5t_native_double, tlag, &
161 ddim, ierr, xfer_prp = plist_id)
162 call h5dclose_f(dset_id, ierr)
163
164 call h5dcreate_f(grp_id,'dtlag', h5t_native_double, &
165 filespace, dset_id, ierr)
166 call h5dget_space_f(dset_id, filespace, ierr)
167 call h5sselect_hyperslab_f (filespace, h5s_select_set_f, &
168 doffset, dcount, ierr)
169 call h5dwrite_f(dset_id, h5t_native_double, dtlag, &
170 ddim, ierr, xfer_prp = plist_id)
171 call h5dclose_f(dset_id, ierr)
172
173 call h5sclose_f(filespace, ierr)
174 call h5gclose_f(grp_id, ierr)
175
176 end if
177
178
179 !
180 ! Write fields group
181 !
182 if (allocated(fp) .or. allocated(fsp)) then
183 call h5gcreate_f(file_id, "Fields", grp_id, ierr, lcpl_id=h5p_default_f, &
184 gcpl_id=h5p_default_f, gapl_id=h5p_default_f)
185
186 dcount(1) = int(dof%size(), 8)
187 doffset(1) = int(msh%offset_el, 8) * int((dof%Xh%lx**3),8)
188 ddim = int(dof%size(), 8)
189 drank = 1
190 call mpi_allreduce(mpi_in_place, ddim(1), 1, &
191 mpi_integer8, mpi_sum, neko_comm, ierr)
192
193 call h5screate_simple_f(drank, ddim, filespace, ierr)
194 call h5screate_simple_f(drank, dcount, memspace, ierr)
195
196
197 if (allocated(fp)) then
198 do i = 1, size(fp)
199 call h5dcreate_f(grp_id, fp(i)%ptr%name, h5t_native_double, &
200 filespace, dset_id, ierr)
201 call h5dget_space_f(dset_id, filespace, ierr)
202 call h5sselect_hyperslab_f(filespace, h5s_select_set_f, &
203 doffset, dcount, ierr)
204 call h5dwrite_f(dset_id, h5t_native_double, &
205 fp(i)%ptr%x(1,1,1,1), &
206 ddim, ierr, file_space_id = filespace, &
207 mem_space_id = memspace, xfer_prp = plist_id)
208 call h5dclose_f(dset_id, ierr)
209 end do
210 deallocate(fp)
211 end if
212
213 if (allocated(fsp)) then
214 do i = 1, size(fsp)
215 do j = 1, fsp(i)%ptr%size()
216 call h5dcreate_f(grp_id, fsp(i)%ptr%lf(j)%name, &
217 h5t_native_double, filespace, dset_id, ierr)
218 call h5dget_space_f(dset_id, filespace, ierr)
219 call h5sselect_hyperslab_f(filespace, h5s_select_set_f, &
220 doffset, dcount, ierr)
221 call h5dwrite_f(dset_id, h5t_native_double, &
222 fsp(i)%ptr%lf(j)%x(1,1,1,1), &
223 ddim, ierr, file_space_id = filespace, &
224 mem_space_id = memspace, xfer_prp = plist_id)
225 call h5dclose_f(dset_id, ierr)
226 end do
227 end do
228 deallocate(fsp)
229 end if
230
231 call h5gclose_f(grp_id, ierr)
232 call h5sclose_f(filespace, ierr)
233 call h5sclose_f(memspace, ierr)
234 end if
235
236 call h5pclose_f(plist_id, ierr)
237 call h5fclose_f(file_id, ierr)
238
239 call h5close_f(ierr)
240
241 this%counter = this%counter + 1
242
243 end subroutine hdf5_file_write
244
246 subroutine hdf5_file_read(this, data)
247 class(hdf5_file_t) :: this
248 class(*), target, intent(inout) :: data
249 integer(hid_t) :: plist_id, file_id, dset_id, grp_id, attr_id
250 integer(hid_t) :: filespace, memspace
251 integer(hsize_t), dimension(1) :: ddim, dcount, doffset
252 integer :: i,j, ierr, info, glb_nelv, gdim, lx, drank
253 type(mesh_t), pointer :: msh
254 type(dofmap_t), pointer :: dof
255 type(field_ptr_t), allocatable :: fp(:)
256 type(field_series_ptr_t), allocatable :: fsp(:)
257 real(kind=rp), pointer :: dtlag(:)
258 real(kind=rp), pointer :: tlag(:)
259 real(kind=rp) :: t
260
261 call hdf5_file_determine_data(data, msh, dof, fp, fsp, dtlag, tlag)
262
263 call h5open_f(ierr)
264 call h5pcreate_f(h5p_file_access_f, plist_id, ierr)
265 info = mpi_info_null%mpi_val
266 call h5pset_fapl_mpio_f(plist_id, neko_comm%mpi_val, info, ierr)
267
268 call h5fopen_f(trim(this%fname), h5f_acc_rdonly_f, &
269 file_id, ierr, access_prp = plist_id)
270
271 call h5pcreate_f(h5p_dataset_xfer_f, plist_id, ierr)
272 call h5pset_dxpl_mpio_f(plist_id, h5fd_mpio_collective_f, ierr)
273
274 ddim = 1
275 call h5aopen_name_f(file_id, 'Time', attr_id, ierr)
276 call h5aread_f(attr_id, h5t_native_double, t, ddim, ierr)
277 call h5aclose_f(attr_id, ierr)
278
279 select type(data)
280 type is(chkp_t)
281 data%t = t
282 end select
283
284 call h5aopen_name_f(file_id, 'Lx', attr_id, ierr)
285 call h5aread_f(attr_id, h5t_native_integer, lx, ddim, ierr)
286 call h5aclose_f(attr_id, ierr)
287
288 call h5gopen_f(file_id, 'Mesh', grp_id, ierr, gapl_id=h5p_default_f)
289
290 call h5aopen_name_f(grp_id, 'Elements', attr_id, ierr)
291 call h5aread_f(attr_id, h5t_native_integer, glb_nelv, ddim, ierr)
292 call h5aclose_f(attr_id, ierr)
293
294 call h5aopen_name_f(grp_id, 'Dimension', attr_id, ierr)
295 call h5aread_f(attr_id, h5t_native_integer, gdim, ddim, ierr)
296 call h5aclose_f(attr_id, ierr)
297 call h5gclose_f(grp_id, ierr)
298
299
300 if (associated(tlag) .and. associated(dtlag)) then
301 drank = 1
302 ddim = size(tlag)
303 doffset(1) = 0
304 if (pe_rank .eq. 0) then
305 dcount = size(tlag)
306 else
307 dcount = 0
308 end if
309
310 call h5gopen_f(file_id, 'Restart', grp_id, ierr, gapl_id=h5p_default_f)
311 call h5dopen_f(grp_id, 'tlag', dset_id, ierr)
312 call h5dget_space_f(dset_id, filespace, ierr)
313 call h5sselect_hyperslab_f (filespace, h5s_select_set_f, &
314 doffset, dcount, ierr)
315 call h5dread_f(dset_id, h5t_native_double, tlag, ddim, ierr, xfer_prp=plist_id)
316 call h5dclose_f(dset_id, ierr)
317 call h5sclose_f(filespace, ierr)
318
319 call h5dopen_f(grp_id, 'dtlag', dset_id, ierr)
320 call h5dget_space_f(dset_id, filespace, ierr)
321 call h5sselect_hyperslab_f (filespace, h5s_select_set_f, &
322 doffset, dcount, ierr)
323 call h5dread_f(dset_id, h5t_native_double, dtlag, ddim, ierr, xfer_prp=plist_id)
324 call h5dclose_f(dset_id, ierr)
325 call h5sclose_f(filespace, ierr)
326
327 call h5gclose_f(grp_id, ierr)
328 end if
329
330 if (allocated(fp) .or. allocated(fsp)) then
331 call h5gopen_f(file_id, 'Fields', grp_id, ierr, gapl_id=h5p_default_f)
332
333 dcount(1) = int(dof%size(), 8)
334 doffset(1) = int(msh%offset_el, 8) * int((dof%Xh%lx**3),8)
335 ddim = int(dof%size(), 8)
336 drank = 1
337
338 dcount(1) = int(dof%size(), 8)
339 doffset(1) = int(msh%offset_el, 8) * int((dof%Xh%lx**3),8)
340 ddim = int(dof%size(), 8)
341 drank = 1
342 call mpi_allreduce(mpi_in_place, ddim(1), 1, &
343 mpi_integer8, mpi_sum, neko_comm, ierr)
344
345 call h5screate_simple_f(drank, dcount, memspace, ierr)
346
347 if (allocated(fp)) then
348 do i = 1, size(fp)
349 call h5dopen_f(grp_id, fp(i)%ptr%name, dset_id, ierr)
350 call h5dget_space_f(dset_id, filespace, ierr)
351 call h5sselect_hyperslab_f (filespace, h5s_select_set_f, &
352 doffset, dcount, ierr)
353 call h5dread_f(dset_id, h5t_native_double, &
354 fp(i)%ptr%x(1,1,1,1), &
355 ddim, ierr, file_space_id = filespace, &
356 mem_space_id = memspace, xfer_prp=plist_id)
357 call h5dclose_f(dset_id, ierr)
358 call h5sclose_f(filespace, ierr)
359 end do
360 end if
361
362 if (allocated(fsp)) then
363 do i = 1, size(fsp)
364 do j = 1, fsp(i)%ptr%size()
365 call h5dopen_f(grp_id, fsp(i)%ptr%lf(j)%name, dset_id, ierr)
366 call h5dget_space_f(dset_id, filespace, ierr)
367 call h5sselect_hyperslab_f (filespace, h5s_select_set_f, &
368 doffset, dcount, ierr)
369 call h5dread_f(dset_id, h5t_native_double, &
370 fsp(i)%ptr%lf(j)%x(1,1,1,1), &
371 ddim, ierr, file_space_id = filespace, &
372 mem_space_id = memspace, xfer_prp=plist_id)
373 call h5dclose_f(dset_id, ierr)
374 call h5sclose_f(filespace, ierr)
375 end do
376 end do
377 end if
378 call h5sclose_f(memspace, ierr)
379 call h5gclose_f(grp_id, ierr)
380 end if
381
382 call h5pclose_f(plist_id, ierr)
383 call h5fclose_f(file_id, ierr)
384
385 call h5close_f(ierr)
386
387 end subroutine hdf5_file_read
388
389
390 subroutine hdf5_file_determine_data(data, msh, dof, fp, fsp, dtlag, tlag)
391 class(*), target, intent(in) :: data
392 type(mesh_t), pointer, intent(inout) :: msh
393 type(dofmap_t), pointer, intent(inout) :: dof
394 type(field_ptr_t), allocatable, intent(inout) :: fp(:)
395 type(field_series_ptr_t), allocatable, intent(inout) :: fsp(:)
396 real(kind=rp), pointer, intent(inout) :: dtlag(:)
397 real(kind=rp), pointer, intent(inout) :: tlag(:)
398 integer :: i, j, fp_size, fp_cur, fsp_size, fsp_cur
399
400 select type(data)
401 type is (field_t)
402 dof => data%dof
403 msh => data%msh
404 fp_size = 1
405 allocate(fp(fp_size))
406 fp(1)%ptr => data
407
408 nullify(dtlag)
409 nullify(tlag)
410
411 type is (field_list_t)
412
413 if (data%size() .gt. 0) then
414 allocate(fp(data%size()))
415
416 dof => data%dof(1)
417 msh => data%msh(1)
418
419 do i = 1, data%size()
420 fp(i)%ptr => data%items(i)%ptr
421 end do
422 else
423 call neko_error('Empty field list')
424 end if
425
426 nullify(dtlag)
427 nullify(tlag)
428
429 type is(chkp_t)
430
431 if ( .not. associated(data%u) .or. &
432 .not. associated(data%v) .or. &
433 .not. associated(data%w) .or. &
434 .not. associated(data%p) ) then
435 call neko_error('Checkpoint not initialized')
436 end if
437
438 fp_size = 4
439
440 if (associated(data%s)) then
441 fp_size = fp_size + 1
442 end if
443
444 if (associated(data%abx1)) then
445 fp_size = fp_size + 6
446 end if
447
448 if (associated(data%abs1)) then
449 fp_size = fp_size + 2
450 end if
451
452 allocate(fp(fp_size))
453
454 fsp_size = 0
455 if (associated(data%ulag)) then
456 fsp_size = fsp_size + 3
457 end if
458
459 if (associated(data%slag)) then
460 fsp_size = fsp_size + 1
461 end if
462
463 if (fsp_size .gt. 0) then
464 allocate(fsp(fsp_size))
465 fsp_cur = 1
466 end if
467
468 dof => data%u%dof
469 msh => data%u%msh
470
471 fp(1)%ptr => data%u
472 fp(2)%ptr => data%v
473 fp(3)%ptr => data%w
474 fp(4)%ptr => data%p
475
476 fp_cur = 5
477 if (associated(data%s)) then
478 fp(fp_cur)%ptr => data%s
479 fp_cur = fp_cur + 1
480 end if
481
482 if (associated(data%abx1)) then
483 fp(fp_cur)%ptr => data%abx1
484 fp(fp_cur+1)%ptr => data%abx2
485 fp(fp_cur+2)%ptr => data%aby1
486 fp(fp_cur+3)%ptr => data%aby2
487 fp(fp_cur+4)%ptr => data%abz1
488 fp(fp_cur+5)%ptr => data%abz2
489 fp_cur = fp_cur + 6
490 end if
491
492 if (associated(data%abs1)) then
493 fp(fp_cur)%ptr => data%abs1
494 fp(fp_cur+1)%ptr => data%abs2
495 fp_cur = fp_cur + 2
496 end if
497
498 if (associated(data%ulag)) then
499 fsp(fsp_cur)%ptr => data%ulag
500 fsp(fsp_cur+1)%ptr => data%vlag
501 fsp(fsp_cur+2)%ptr => data%wlag
502 fsp_cur = fsp_cur + 3
503 end if
504
505 if (associated(data%slag)) then
506 fsp(fsp_cur)%ptr => data%slag
507 fsp_cur = fsp_cur + 1
508 end if
509
510 if (associated(data%tlag)) then
511 tlag => data%tlag
512 dtlag => data%dtlag
513 end if
514
515 class default
516 call neko_log%error('Invalid data')
517 end select
518
519 end subroutine hdf5_file_determine_data
520
521#else
522
524 subroutine hdf5_file_write(this, data, t)
525 class(hdf5_file_t), intent(inout) :: this
526 class(*), target, intent(in) :: data
527 real(kind=rp), intent(in), optional :: t
528 call neko_error('Neko needs to be built with HDF5 support')
529 end subroutine hdf5_file_write
530
532 subroutine hdf5_file_read(this, data)
533 class(hdf5_file_t) :: this
534 class(*), target, intent(inout) :: data
535 call neko_error('Neko needs to be built with HDF5 support')
536 end subroutine hdf5_file_read
537
538
539#endif
540
541end module hdf5_file
utils::neko_error
Definition utils.f90:42
checkpoint
Defines a checkpoint.
Definition checkpoint.f90:34
comm
Definition comm.F90:1
comm::pe_rank
integer pe_rank
MPI rank.
Definition comm.F90:28
comm::neko_comm
type(mpi_comm) neko_comm
MPI communicator.
Definition comm.F90:16
dofmap
Defines a mapping of the degrees of freedom.
Definition dofmap.f90:35
field_list
Definition field_list.f90:1
field_series
Stores a series fields.
Definition field_series.f90:34
field
Defines a field.
Definition field.f90:34
generic_file
Definition generic_file.f90:33
hdf5_file
HDF5 file format.
Definition hdf5_file.F90:34
hdf5_file::hdf5_file_read
subroutine hdf5_file_read(this, data)
Read data in HDF5 format.
Definition hdf5_file.F90:533
hdf5_file::hdf5_file_write
subroutine hdf5_file_write(this, data, t)
Write data in HDF5 format.
Definition hdf5_file.F90:525
logger
Logging routines.
Definition log.f90:34
logger::neko_log
type(log_t), public neko_log
Global log stream.
Definition log.f90:65
mesh
Defines a mesh.
Definition mesh.f90:34
num_types
Definition num_types.f90:1
num_types::rp
integer, parameter, public rp
Global precision used in computations.
Definition num_types.f90:12
utils
Utilities.
Definition utils.f90:35
utils::filename_suffix_pos
pure integer function, public filename_suffix_pos(fname)
Find position (in the string) of a filename's suffix.
Definition utils.f90:56
checkpoint::chkp_t
Definition checkpoint.f90:46
dofmap::dofmap_t
Definition dofmap.f90:53
field::field_ptr_t
field_ptr_t, To easily obtain a pointer to a field
Definition field.f90:80
field::field_t
Definition field.f90:46
field_list::field_list_t
field_list_t, To be able to group fields together
Definition field_list.f90:13
field_series::field_series_ptr_t
field_series_ptr_t, To easily obtain a pointer to a field series
Definition field_series.f90:53
field_series::field_series_t
Definition field_series.f90:40
generic_file::generic_file_t
A generic file handler.
Definition generic_file.f90:38
hdf5_file::hdf5_file_t
Interface for HDF5 files.
Definition hdf5_file.F90:54
mesh::mesh_t
Definition mesh.f90:64