Context Navigation

rebuild_nemo.F90 @ 7687

Last change on this file since 7687 was 7687, checked in by timgraham, 7 years ago
Reduce chunksize so that ORCA12 restart files can be rebuilt without needing stupid amounts of memory
File size: 58.3 KB

Line
1	PROGRAM rebuild_nemo
2
3	!!=========================================================================
4	!! * rebuild_nemo *
5	!!=========================================================================
6	!!
7	!! A routine to rebuild NEMO files from multiple processors into one file.
8	!! This routine is designed to be much quicker than the old IOIPSL rebuild
9	!! but at the cost of an increased memory usage.
10	!!
11	!! NEMO rebuild has the following features:
12	!! * dynamically works out what variables require rebuilding
13	!! * does not copy subdomain halo regions
14	!! * works for 1,2,3 and 4d arrays or types for all valid NetCDF types
15	!! * utilises OMP shared memory parallelisation where applicable
16	!! * time 'chunking' for lower memory use
17	!! (only for 4D vars with unlimited dimension)
18	!!
19	!! Ed Blockley - August 2011
20	!! (based on original code by Matt Martin)
21	!!
22	!!-------------------------------------------------------------------------
23	!!
24	!! The code reads the filestem and number of subdomains from the namelist file nam_rebuild.
25	!!
26	!! The 1st subdomain file is used to determine the dimensions and variables in all the input files.
27	!! It is also used to find which dimensions (and hence which variables) require rebuilding
28	!! as well as information about the global domain.
29	!!
30	!! It then opens all the input files (unbuffered) and creates an array of netcdf identifiers
31	!! before looping through all the variables and updating the rebuilt output file (either by direct
32	!! copying or looping over the number of domains and rebuilding as appropriate).
33	!!
34	!! The code looks more complicated than it is because it has lots of case statements to deal with all
35	!! the various NetCDF data types and with various data dimensions (up to 4d).
36	!!
37	!! Diagnostic output is written to numout (default 6 - stdout)
38	!! and errors are written to numerr (default 0 - stderr).
39	!!
40	!! If time chunking is specified the code will use less memory but take a little longer.
41	!! It does this by breaking down the 4D input variables over their 4th dimension
42	!! (generally time) by way of a while loop.
43	!!
44	!!-------------------------------------------------------------------------------
45
46	USE netcdf
47
48	!$ USE omp_lib ! Note OpenMP sentinel
49
50	IMPLICIT NONE
51
52	! kind specifications
53	INTEGER,PARAMETER :: i1=SELECTED_INT_KIND(2) ! NF90_BYTE
54	INTEGER,PARAMETER :: i2=SELECTED_INT_KIND(4) ! NF90_SHORT
55	INTEGER,PARAMETER :: i4=SELECTED_INT_KIND(9) ! NF90_INT
56	INTEGER,PARAMETER :: sp=SELECTED_REAL_KIND(6,37) ! NF90_FLOAT
57	INTEGER,PARAMETER :: dp=SELECTED_REAL_KIND(12,307) ! NF90_DOUBLE
58
59	INTEGER,PARAMETER :: numnam = 11
60	INTEGER,PARAMETER :: numout = 6
61	INTEGER,PARAMETER :: numerr = 0
62
63	LOGICAL, PARAMETER :: l_verbose = .true.
64
65	CHARACTER(LEN=nf90_max_name) :: filebase, suffix, attname, dimname, varname, time, date, zone, timestamp
66	CHARACTER(LEN=nf90_max_name), ALLOCATABLE :: filenames(:), indimnames(:)
67	CHARACTER(LEN=nf90_max_name), DIMENSION(2) :: dims
68
69	INTEGER :: ndomain, ifile, ndomain_file, nchunksize, deflate_level
70	INTEGER :: ncid, outid, idim, istop
71	INTEGER :: natts, attid, xtype, varid, rbdims
72	INTEGER :: jv, ndims, nvars, dimlen, dimids(4)
73	INTEGER :: dimid, unlimitedDimId, di, dj, dr
74	INTEGER :: nmax_unlimited, nt, ntchunk
75	INTEGER :: chunksize = 3200000
76	INTEGER :: nthreads = 1
77	INTEGER, ALLOCATABLE :: outdimids(:), outdimlens(:), indimlens(:), inncids(:)
78	INTEGER, ALLOCATABLE :: global_sizes(:), rebuild_dims(:)
79	INTEGER, DIMENSION(2) :: halo_start, halo_end, local_sizes
80	INTEGER, DIMENSION(2) :: idomain, jdomain, rdomain, start_pos
81	INTEGER :: ji, jj, jk, jl, jr
82
83	REAL(sp) :: ValMin, ValMax, InMin, InMax, rmdi
84	REAL(dp), ALLOCATABLE :: mdiVals(:)
85
86	! NF90_BYTE local data arrays
87	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_i1
88	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_i1
89	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_i1
90	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_i1
91
92	! NF90_SHORT local data arrays
93	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_i2
94	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_i2
95	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_i2
96	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_i2
97
98	! NF90_INT local data arrays
99	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_i4
100	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_i4
101	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_i4
102	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_i4
103
104	! NF90_FLOAT local data arrays
105	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_sp
106	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_sp
107	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_sp
108	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_sp
109
110	! NF90_DOUBLE local data arrays
111	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_dp
112	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_dp
113	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_dp
114	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_dp
115
116	! NF90_BYTE global data arrays
117	INTEGER(i1) :: globaldata_0d_i1
118	INTEGER(i1), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_i1
119	INTEGER(i1), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_i1
120	INTEGER(i1), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_i1
121	INTEGER(i1), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_i1
122
123	! NF90_SHORT global data arrays
124	INTEGER(i2) :: globaldata_0d_i2
125	INTEGER(i2), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_i2
126	INTEGER(i2), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_i2
127	INTEGER(i2), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_i2
128	INTEGER(i2), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_i2
129
130	! NF90_INT global data arrays
131	INTEGER(i4) :: globaldata_0d_i4
132	INTEGER(i4), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_i4
133	INTEGER(i4), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_i4
134	INTEGER(i4), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_i4
135	INTEGER(i4), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_i4
136
137	! NF90_FLOAT global data arrays
138	REAL(sp) :: globaldata_0d_sp
139	REAL(sp), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_sp
140	REAL(sp), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_sp
141	REAL(sp), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_sp
142	REAL(sp), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_sp
143
144	! NF90_DOUBLE global data arrays
145	REAL(dp) :: globaldata_0d_dp
146	REAL(dp), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_dp
147	REAL(dp), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_dp
148	REAL(dp), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_dp
149	REAL(dp), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_dp
150
151	LOGICAL :: l_valid = .false.
152	LOGICAL :: l_noRebuild = .false.
153	LOGICAL :: l_findDims = .true.
154	LOGICAL :: l_maskout = .false.
155
156	NAMELIST/nam_rebuild/ filebase, ndomain, dims, nchunksize, l_maskout, deflate_level
157
158	external :: getarg
159	integer, external :: iargc
160	integer :: found_num_args = 0
161	character(256) :: namelist_path
162
163	!End of definitions
164
165	!--------------------------------------------------------------------------------
166	!0. OMP setup
167
168	!$OMP PARALLEL DEFAULT(NONE) SHARED(nthreads)
169	!$OMP MASTER
170	!$ nthreads = omp_get_num_threads()
171	!$ WRITE(numout,*) 'Running OMP with ',nthreads,' thread(s).'
172	!$OMP END MASTER
173	!$OMP END PARALLEL
174
175	!--------------------------------------------------------------------------------
176	!1.1 Get the namelist path
177	!Determine the number of arguments on the command line
178	found_num_args=iargc()
179	!Check that the required argument is present, if it is not then set it to the default value: nam_rebuild
180	IF (found_num_args <= 0) THEN
181	WRITE(numout,*) 'Namelist path not supplied as command line argument. Using default, nam_rebuild.'
182	namelist_path='nam_rebuild'
183	ELSE IF (found_num_args == 1) THEN
184	CALL getarg(1, namelist_path)
185	ELSE
186	WRITE(numerr,*) 'ERROR! : Incorrect number of command line arguments. Please supply only'
187	WRITE(numerr,*) ' the path to the namelist file, or no arguments to use default value'
188	STOP 1
189	END IF
190
191	!1.2 Read in the namelist
192
193	dims(:) = ""
194	nchunksize = 0
195	deflate_level = 0
196	OPEN( UNIT=numnam, FILE=TRIM(namelist_path), FORM='FORMATTED', STATUS='OLD' )
197	READ( numnam, nam_rebuild )
198	CLOSE( numnam )
199	IF( .NOT. ALL(dims(:) == "") ) l_findDims = .false.
200
201	!1.1 Set up the filenames and fileids
202
203	ALLOCATE(filenames(ndomain))
204	IF (l_verbose) WRITE(numout,*) 'Rebuilding the following files:'
205	DO ifile = 1, ndomain
206	WRITE(suffix,'(i4.4)') ifile-1
207	filenames(ifile) = TRIM(filebase)//'_'//TRIM(suffix)//'.nc'
208	IF (l_verbose) WRITE(numout,*) TRIM(filenames(ifile))
209	END DO
210	ALLOCATE(inncids(ndomain))
211
212	!---------------------------------------------------------------------------
213	!2. Read in the global dimensions from the first input file and set up the output file
214
215	CALL check_nf90( nf90_open( TRIM(filenames(1)), nf90_share, ncid ) )
216	CALL check_nf90( nf90_inquire( ncid, ndims, nvars, natts ) )
217
218	!2.0 Read in the total number of processors the file is expecting and check it's correct
219
220	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_number_total', ndomain_file ) )
221	IF( ndomain /= ndomain_file ) THEN
222	WRITE(numerr,*) 'ERROR! : number of files to rebuild in file does not agree with namelist'
223	WRITE(numerr,*) 'Attribute DOMAIN_number_total is : ', ndomain_file
224	WRITE(numerr,*) 'Number of files specified in namelist is: ', ndomain
225	STOP 2
226	ENDIF
227
228	!2.1 Set up the output file
229	!#if defined key_netcdf4
230	CALL check_nf90( nf90_create( TRIM(filebase)//'.nc', nf90_netcdf4, outid, chunksize=chunksize ) )
231	!#else
232	! CALL check_nf90( nf90_create( TRIM(filebase)//'.nc', nf90_64bit_offset, outid, chunksize=chunksize ) )
233	!#endif
234
235	!2.2 Set up dimensions in output file
236
237	!2.2.0 Find out how many dimensions are required to be rebuilt and which ones they are
238	CALL check_nf90( nf90_inquire_attribute( ncid, nf90_global, 'DOMAIN_dimensions_ids', xtype, rbdims, attid ) )
239
240	ALLOCATE(rebuild_dims(rbdims))
241	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_dimensions_ids', rebuild_dims ) )
242
243	ALLOCATE(global_sizes(rbdims))
244	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_size_global', global_sizes ) )
245	IF (l_verbose) WRITE(numout,*) 'Size of global arrays: ', global_sizes
246
247
248	!2.2.1 Copy the dimensions into the output file apart from rebuild_dims() which are dimensioned globally
249	ALLOCATE(indimlens(ndims), indimnames(ndims), outdimlens(ndims))
250	CALL check_nf90( nf90_inquire( ncid, unlimitedDimId = unlimitedDimId ) )
251	istop = 0
252	DO idim = 1, ndims
253	CALL check_nf90( nf90_inquire_dimension( ncid, idim, dimname, dimlen ) )
254	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_size_local', local_sizes ) )
255	indimlens(idim) = dimlen
256	indimnames(idim) = dimname
257	IF (l_findDims) THEN
258	IF( idim == rebuild_dims(1) ) THEN
259	IF( dimlen == local_sizes(1) ) THEN
260	dimlen = global_sizes(1)
261	dims(1) = trim(dimname)
262	ELSE
263	istop = 1
264	ENDIF
265	ENDIF
266	IF( rbdims > 1 .AND. idim == rebuild_dims(2) ) THEN
267	IF( dimlen == local_sizes(2) ) THEN
268	dimlen = global_sizes(2)
269	dims(2) = trim(dimname)
270	ELSE
271	istop = 1
272	ENDIF
273	ENDIF
274	ELSE ! l_findDims = false
275	IF( TRIM(dimname) == TRIM(dims(1))) THEN
276	dimlen = global_sizes(1)
277	rebuild_dims(1) = idim
278	ENDIF
279	IF( rbdims > 1 .AND. TRIM(dimname) == TRIM(dims(2))) THEN
280	dimlen = global_sizes(2)
281	rebuild_dims(2) = idim
282	ENDIF
283	ENDIF
284
285	IF( idim == unlimitedDimId ) THEN
286	CALL check_nf90( nf90_def_dim( outid, dimname, nf90_unlimited, dimid) )
287	nmax_unlimited = dimlen
288	ELSE
289	CALL check_nf90( nf90_def_dim( outid, dimname, dimlen, dimid) )
290	ENDIF
291	outdimlens(idim) = dimlen
292	END DO
293	! nmax_unlimited is only used for time-chunking so we set it to be at least 1 to
294	! account for files with no record dimension or zero length record dimension(!)
295	nmax_unlimited = max(nmax_unlimited,1)
296
297	IF( istop == 1 ) THEN
298	WRITE(numerr,*) 'ERROR! : DOMAIN_local_sizes attribute does not match rebuild dimension lengths in the first file'
299	WRITE(numerr,*) 'Attribute DOMAIN_local_sizes is : ', local_sizes
300	WRITE(numerr,*) 'Dimensions to be rebuilt are of size : ', outdimlens(rebuild_dims(1)), outdimlens(rebuild_dims(2))
301	STOP 3
302	ENDIF
303
304	IF (l_findDims) THEN
305	IF (l_verbose) WRITE(numout,*) 'Finding rebuild dimensions from the first file...'
306	ELSE
307	IF (l_verbose) WRITE(numout,*) 'Using rebuild dimensions given in namelist...'
308	ENDIF
309
310	IF( rbdims > 1 ) THEN
311	IF (l_verbose) WRITE(numout,*) 'Rebuilding across dimensions '//TRIM(indimnames(rebuild_dims(1)))// &
312	& ' and '//TRIM(indimnames(rebuild_dims(2)))
313	ELSE
314	IF (l_verbose) WRITE(numout,*) 'Rebuilding across dimension '//TRIM(indimnames(rebuild_dims(1)))
315	ENDIF
316
317	!2.2.2 Copy the global attributes into the output file, apart from those beginning with DOMAIN_
318	! Also need to change the file_name attribute and the TimeStamp attribute.
319	DO attid = 1, natts
320	CALL check_nf90( nf90_inq_attname( ncid, nf90_global, attid, attname ) )
321	IF( INDEX( attname, "DOMAIN_" ) == 1 ) CYCLE
322	IF( INDEX( attname, "file_name") == 1 ) CYCLE
323	IF( INDEX( attname, "associate_file") == 1 ) CYCLE
324	IF (l_verbose) WRITE(numout,*) 'Copying attribute '//TRIM(attname)//' into destination file...'
325	CALL check_nf90( nf90_copy_att( ncid, nf90_global, attname, outid, nf90_global ) )
326	END DO
327	CALL check_nf90( nf90_put_att( outid, nf90_global, "file_name", TRIM(filebase)//'.nc') )
328	IF (l_verbose) WRITE(numout,*) 'Writing new file_name attribute'
329	CALL DATE_AND_TIME ( date=date, time=time, zone=zone )
330	timestamp = date(7:8) // "/" // date(5:6) // "/" // date(1:4) // " " // &
331	time(1:2) // ":" // time(3:4) // ":" // time(5:6) // " " // &
332	zone
333	CALL check_nf90( nf90_put_att( outid, nf90_global, "TimeStamp", timestamp ) )
334	IF (l_verbose) WRITE(numout,*) 'Writing new TimeStamp attribute'
335
336	!2.2.3 Copy the variable definitions and attributes into the output file.
337	ALLOCATE(mdiVals(nvars))
338	mdiVals(:)=0
339	DO jv = 1, nvars
340	CALL check_nf90( nf90_inquire_variable( ncid, jv, varname, xtype, ndims, dimids, natts ) )
341	ALLOCATE(outdimids(ndims))
342	DO idim = 1, ndims
343	outdimids(idim) = dimids(idim)
344	END DO
345	#if defined key_netcdf4
346	CALL check_nf90( nf90_def_var( outid, varname, xtype, outdimids, varid, &
347	deflate_level=deflate_level ) )
348	#else
349	CALL check_nf90( nf90_def_var( outid, varname, xtype, outdimids, varid ) )
350	#endif
351	DEALLOCATE(outdimids)
352	IF (l_verbose) WRITE(numout,*) 'Defining variable '//TRIM(varname)//'...'
353	IF( natts > 0 ) THEN
354	DO attid = 1, natts
355	CALL check_nf90( nf90_inq_attname( ncid, varid, attid, attname ) )
356	IF ( attname == "_FillValue" ) THEN
357	CALL check_nf90( nf90_get_att( ncid, varid, attname, rmdi ) )
358	mdiVals(jv)=rmdi
359	ENDIF
360	CALL check_nf90( nf90_copy_att( ncid, varid, attname, outid, varid ) )
361	END DO
362	ENDIF
363	END DO
364
365	!2.3 End definitions in output file and copy 1st file ncid to the inncids array
366
367	CALL check_nf90( nf90_enddef( outid ) )
368	inncids(1) = ncid
369	IF (l_verbose) WRITE(numout,*) 'Finished defining output file.'
370
371	!---------------------------------------------------------------------------
372	!3. Read in data from each file for each variable
373
374	!3.1 Open each file and store the ncid in inncids array
375
376	IF (l_verbose) WRITE(numout,*) 'Opening input files...'
377	DO ifile = 2, ndomain
378	CALL check_nf90( nf90_open( TRIM(filenames(ifile)), nf90_share, ncid, chunksize=chunksize ) )
379	inncids(ifile) = ncid
380	END DO
381	IF (l_verbose) WRITE(numout,*) 'All input files open.'
382
383	DO jv = 1, nvars
384
385	ValMin = 1.e10
386	ValMax = -1.e10
387	l_valid = .false.
388	istop = nf90_noerr
389	nt = 1
390	ntchunk = nmax_unlimited
391	IF( nchunksize == 0 ) nchunksize = nmax_unlimited
392
393	!3.2 Inquire variable to find out name and how many dimensions it has
394	! and importantly whether it contains the dimensions in rebuild_dims()
395
396	ncid = inncids(1)
397	CALL check_nf90( nf90_inquire_variable( ncid, jv, varname, xtype, ndims, dimids, natts ) )
398
399	l_noRebuild = .true.
400	IF( ANY( dimids(1:ndims) == rebuild_dims(1) )) l_noRebuild = .false.
401	IF( rbdims > 1 ) THEN
402	IF( ANY( dimids(1:ndims) == rebuild_dims(2) )) l_noRebuild = .false.
403	ENDIF
404
405	!3.2.0 start while loop for time chunking
406
407	DO WHILE( nt <= nmax_unlimited )
408
409	IF( ndims > 3 ) THEN
410	ntchunk = MIN( nchunksize, nmax_unlimited + 1 - nt )
411	ENDIF
412
413	IF (l_noRebuild) THEN
414
415	IF( nchunksize == nmax_unlimited .OR. ndims <= 3 ) THEN
416	IF (l_verbose) WRITE(numout,*) 'Copying data from variable '//TRIM(varname)//'...'
417	ELSE
418	IF (l_verbose) WRITE(numout,'(A,I3,A,I3,A)') ' Copying data from variable ' &
419	& //TRIM(varname)//' for chunks ',nt,' to ',nt+ntchunk-1,' ...'
420	ENDIF
421
422	!3.2.1 If rebuilding not required then just need to read in variable
423	! for copying direct into output file after the OMP (files) loop.
424	IF( ndims == 0 ) THEN
425
426	SELECT CASE( xtype )
427	CASE( NF90_BYTE )
428	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_i1 ) )
429	CASE( NF90_SHORT )
430	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_i2 ) )
431	CASE( NF90_INT )
432	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_i4 ) )
433	CASE( NF90_FLOAT )
434	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_sp ) )
435	CASE( NF90_DOUBLE )
436	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_dp ) )
437	CASE DEFAULT
438	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
439	STOP 4
440	END SELECT
441
442	ELSEIF( ndims == 1 ) THEN
443
444	SELECT CASE( xtype )
445	CASE( NF90_BYTE )
446	ALLOCATE(globaldata_1d_i1(indimlens(dimids(1))))
447	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_i1 ) )
448	CASE( NF90_SHORT )
449	ALLOCATE(globaldata_1d_i2(indimlens(dimids(1))))
450	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_i2 ) )
451	CASE( NF90_INT )
452	ALLOCATE(globaldata_1d_i4(indimlens(dimids(1))))
453	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_i4 ) )
454	CASE( NF90_FLOAT )
455	ALLOCATE(globaldata_1d_sp(indimlens(dimids(1))))
456	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_sp ) )
457	CASE( NF90_DOUBLE )
458	ALLOCATE(globaldata_1d_dp(indimlens(dimids(1))))
459	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_dp ) )
460	CASE DEFAULT
461	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
462	STOP 4
463	END SELECT
464
465	ELSEIF( ndims == 2 ) THEN
466
467	SELECT CASE( xtype )
468	CASE( NF90_BYTE )
469	ALLOCATE(globaldata_2d_i1(indimlens(dimids(1)),indimlens(dimids(2))))
470	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_i1 ) )
471	CASE( NF90_SHORT )
472	ALLOCATE(globaldata_2d_i2(indimlens(dimids(1)),indimlens(dimids(2))))
473	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_i2 ) )
474	CASE( NF90_INT )
475	ALLOCATE(globaldata_2d_i4(indimlens(dimids(1)),indimlens(dimids(2))))
476	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_i4 ) )
477	CASE( NF90_FLOAT )
478	ALLOCATE(globaldata_2d_sp(indimlens(dimids(1)),indimlens(dimids(2))))
479	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_sp ) )
480	CASE( NF90_DOUBLE )
481	ALLOCATE(globaldata_2d_dp(indimlens(dimids(1)),indimlens(dimids(2))))
482	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_dp ) )
483	CASE DEFAULT
484	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
485	STOP 4
486	END SELECT
487
488	ELSEIF( ndims == 3 ) THEN
489
490	SELECT CASE( xtype )
491	CASE( NF90_BYTE )
492	ALLOCATE(globaldata_3d_i1(indimlens(dimids(1)),indimlens(dimids(2)), &
493	& indimlens(dimids(3))))
494	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_i1 ) )
495	CASE( NF90_SHORT )
496	ALLOCATE(globaldata_3d_i2(indimlens(dimids(1)),indimlens(dimids(2)), &
497	& indimlens(dimids(3))))
498	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_i2 ) )
499	CASE( NF90_INT )
500	ALLOCATE(globaldata_3d_i4(indimlens(dimids(1)),indimlens(dimids(2)), &
501	& indimlens(dimids(3))))
502	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_i4 ) )
503	CASE( NF90_FLOAT )
504	ALLOCATE(globaldata_3d_sp(indimlens(dimids(1)),indimlens(dimids(2)), &
505	& indimlens(dimids(3))))
506	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_sp ) )
507	CASE( NF90_DOUBLE )
508	ALLOCATE(globaldata_3d_dp(indimlens(dimids(1)),indimlens(dimids(2)), &
509	& indimlens(dimids(3))))
510	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_dp ) )
511	CASE DEFAULT
512	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
513	STOP 4
514	END SELECT
515
516	ELSEIF( ndims == 4 ) THEN
517
518	SELECT CASE( xtype )
519	CASE( NF90_BYTE )
520	ALLOCATE(globaldata_4d_i1(indimlens(dimids(1)),indimlens(dimids(2)), &
521	& indimlens(dimids(3)),ntchunk))
522	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i1, start=(/1,1,1,nt/) ) )
523	CASE( NF90_SHORT )
524	ALLOCATE(globaldata_4d_i2(indimlens(dimids(1)),indimlens(dimids(2)), &
525	& indimlens(dimids(3)),ntchunk))
526	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i2, start=(/1,1,1,nt/) ) )
527	CASE( NF90_INT )
528	ALLOCATE(globaldata_4d_i4(indimlens(dimids(1)),indimlens(dimids(2)), &
529	& indimlens(dimids(3)),ntchunk))
530	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i4, start=(/1,1,1,nt/) ) )
531	CASE( NF90_FLOAT )
532	ALLOCATE(globaldata_4d_sp(indimlens(dimids(1)),indimlens(dimids(2)), &
533	& indimlens(dimids(3)),ntchunk))
534	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_sp, start=(/1,1,1,nt/) ) )
535	CASE( NF90_DOUBLE )
536	ALLOCATE(globaldata_4d_dp(indimlens(dimids(1)),indimlens(dimids(2)), &
537	& indimlens(dimids(3)),ntchunk))
538	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_dp, start=(/1,1,1,nt/) ) )
539	CASE DEFAULT
540	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
541	STOP 4
542	END SELECT
543
544	ENDIF
545
546	ELSE ! l_noRebuild = .false.
547
548	!3.2.2 For variables that require rebuilding we need to read in from all ndomain files
549	! Here we allocate global variables ahead of looping over files
550	IF( nchunksize == nmax_unlimited .OR. ndims <= 3 ) THEN
551	IF (l_verbose) WRITE(numout,*) 'Rebuilding data from variable '//TRIM(varname)//'...'
552	ELSE
553	IF (l_verbose) WRITE(numout,'(A,I3,A,I3,A)') ' Rebuilding data from variable ' &
554	& //TRIM(varname)//' for chunks ',nt,' to ',nt+ntchunk-1,' ...'
555	ENDIF
556	IF( ndims == 1 ) THEN
557
558	SELECT CASE( xtype )
559	CASE( NF90_BYTE )
560	ALLOCATE(globaldata_1d_i1(outdimlens(dimids(1))))
561	IF (l_maskout) globaldata_1d_i1(:)=mdiVals(jv)
562	CASE( NF90_SHORT )
563	ALLOCATE(globaldata_1d_i2(outdimlens(dimids(1))))
564	IF (l_maskout) globaldata_1d_i2(:)=mdiVals(jv)
565	CASE( NF90_INT )
566	ALLOCATE(globaldata_1d_i4(outdimlens(dimids(1))))
567	IF (l_maskout) globaldata_1d_i4(:)=mdiVals(jv)
568	CASE( NF90_FLOAT )
569	ALLOCATE(globaldata_1d_sp(outdimlens(dimids(1))))
570	IF (l_maskout) globaldata_1d_sp(:)=mdiVals(jv)
571	CASE( NF90_DOUBLE )
572	ALLOCATE(globaldata_1d_dp(outdimlens(dimids(1))))
573	IF (l_maskout) globaldata_1d_dp(:)=mdiVals(jv)
574	CASE DEFAULT
575	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
576	STOP 4
577	END SELECT
578
579	ELSEIF( ndims == 2 ) THEN
580
581	SELECT CASE( xtype )
582	CASE( NF90_BYTE )
583	ALLOCATE(globaldata_2d_i1(outdimlens(dimids(1)),outdimlens(dimids(2))))
584	IF (l_maskout) globaldata_2d_i1(:,:)=mdiVals(jv)
585	CASE( NF90_SHORT )
586	ALLOCATE(globaldata_2d_i2(outdimlens(dimids(1)),outdimlens(dimids(2))))
587	IF (l_maskout) globaldata_2d_i2(:,:)=mdiVals(jv)
588	CASE( NF90_INT )
589	ALLOCATE(globaldata_2d_i4(outdimlens(dimids(1)),outdimlens(dimids(2))))
590	IF (l_maskout) globaldata_2d_i4(:,:)=mdiVals(jv)
591	CASE( NF90_FLOAT )
592	ALLOCATE(globaldata_2d_sp(outdimlens(dimids(1)),outdimlens(dimids(2))))
593	IF (l_maskout) globaldata_2d_sp(:,:)=mdiVals(jv)
594	CASE( NF90_DOUBLE )
595	ALLOCATE(globaldata_2d_dp(outdimlens(dimids(1)),outdimlens(dimids(2))))
596	IF (l_maskout) globaldata_2d_dp(:,:)=mdiVals(jv)
597	CASE DEFAULT
598	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
599	STOP 4
600	END SELECT
601
602	ELSEIF( ndims == 3 ) THEN
603
604	SELECT CASE( xtype )
605	CASE( NF90_BYTE )
606	ALLOCATE(globaldata_3d_i1(outdimlens(dimids(1)),outdimlens(dimids(2)), &
607	& outdimlens(dimids(3))))
608	IF (l_maskout) globaldata_3d_i1(:,:,:)=mdiVals(jv)
609	CASE( NF90_SHORT )
610	ALLOCATE(globaldata_3d_i2(outdimlens(dimids(1)),outdimlens(dimids(2)), &
611	& outdimlens(dimids(3))))
612	IF (l_maskout) globaldata_3d_i2(:,:,:)=mdiVals(jv)
613	CASE( NF90_INT )
614	ALLOCATE(globaldata_3d_i4(outdimlens(dimids(1)),outdimlens(dimids(2)), &
615	& outdimlens(dimids(3))))
616	IF (l_maskout) globaldata_3d_i4(:,:,:)=mdiVals(jv)
617	CASE( NF90_FLOAT )
618	ALLOCATE(globaldata_3d_sp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
619	& outdimlens(dimids(3))))
620	IF (l_maskout) globaldata_3d_sp(:,:,:)=mdiVals(jv)
621	CASE( NF90_DOUBLE )
622	ALLOCATE(globaldata_3d_dp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
623	& outdimlens(dimids(3))))
624	IF (l_maskout) globaldata_3d_dp(:,:,:)=mdiVals(jv)
625	CASE DEFAULT
626	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
627	STOP 4
628	END SELECT
629
630	ELSEIF( ndims == 4 ) THEN
631
632	SELECT CASE( xtype )
633	CASE( NF90_BYTE )
634	ALLOCATE(globaldata_4d_i1(outdimlens(dimids(1)),outdimlens(dimids(2)), &
635	& outdimlens(dimids(3)),ntchunk))
636	IF (l_maskout) globaldata_4d_i1(:,:,:,:)=mdiVals(jv)
637	CASE( NF90_SHORT )
638	ALLOCATE(globaldata_4d_i2(outdimlens(dimids(1)),outdimlens(dimids(2)), &
639	& outdimlens(dimids(3)),ntchunk))
640	IF (l_maskout) globaldata_4d_i2(:,:,:,:)=mdiVals(jv)
641	CASE( NF90_INT )
642	ALLOCATE(globaldata_4d_i4(outdimlens(dimids(1)),outdimlens(dimids(2)), &
643	& outdimlens(dimids(3)),ntchunk))
644	IF (l_maskout) globaldata_4d_i4(:,:,:,:)=mdiVals(jv)
645	CASE( NF90_FLOAT )
646	ALLOCATE(globaldata_4d_sp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
647	& outdimlens(dimids(3)),ntchunk))
648	IF (l_maskout) globaldata_4d_sp(:,:,:,:)=mdiVals(jv)
649	CASE( NF90_DOUBLE )
650	ALLOCATE(globaldata_4d_dp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
651	& outdimlens(dimids(3)),ntchunk))
652	IF (l_maskout) globaldata_4d_dp(:,:,:,:)=mdiVals(jv)
653	CASE DEFAULT
654	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
655	STOP 4
656	END SELECT
657	ELSE
658	WRITE(numerr,*) 'ERROR! : A netcdf variable has more than 4 dimensions which is not taken into account'
659	STOP 4
660	ENDIF
661
662	!$OMP PARALLEL DO DEFAULT(NONE) &
663	!$OMP& PRIVATE(ifile,ncid,xtype,start_pos,local_sizes,InMin,InMax,natts, &
664	!$OMP& ndims,attid,attname,dimids,idim,dimname,dimlen,unlimitedDimId, &
665	!$OMP& halo_start,halo_end,idomain,jdomain,rdomain,di,dj,dr, &
666	!$OMP& localdata_1d_i2,localdata_1d_i4,localdata_1d_sp,localdata_1d_dp, &
667	!$OMP& localdata_2d_i2,localdata_2d_i4,localdata_2d_sp,localdata_2d_dp, &
668	!$OMP& localdata_3d_i2,localdata_3d_i4,localdata_3d_sp,localdata_3d_dp, &
669	!$OMP& localdata_4d_i2,localdata_4d_i4,localdata_4d_sp,localdata_4d_dp, &
670	!$OMP& localdata_1d_i1,localdata_2d_i1,localdata_3d_i1,localdata_4d_i1) &
671	!$OMP& SHARED(jv,nvars,varname,filenames,ValMin,ValMax,indimlens,outdimlens,rbdims, &
672	!$OMP& ndomain,outid,chunksize,istop,l_valid,nthreads,inncids,rebuild_dims, &
673	!$OMP& globaldata_1d_i2,globaldata_1d_i4,globaldata_1d_sp,globaldata_1d_dp, &
674	!$OMP& globaldata_2d_i2,globaldata_2d_i4,globaldata_2d_sp,globaldata_2d_dp, &
675	!$OMP& globaldata_3d_i2,globaldata_3d_i4,globaldata_3d_sp,globaldata_3d_dp, &
676	!$OMP& globaldata_4d_i2,globaldata_4d_i4,globaldata_4d_sp,globaldata_4d_dp, &
677	!$OMP& globaldata_1d_i1,globaldata_2d_i1,globaldata_3d_i1,globaldata_4d_i1, &
678	!$OMP& ntchunk,nt,nmax_unlimited,indimnames,dims)
679
680	DO ifile = 1, ndomain
681
682	ncid = inncids(ifile)
683	!$OMP CRITICAL
684	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_size_local', local_sizes ), istop )
685	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_position_first', start_pos ), istop )
686	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_halo_size_start', halo_start ), istop )
687	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_halo_size_end', halo_end ), istop )
688	CALL check_nf90( nf90_inquire_variable( ncid, jv, varname, xtype, ndims, dimids, natts ), istop )
689	CALL check_nf90( nf90_inquire( ncid, unlimitedDimId = unlimitedDimId ), istop )
690	!$OMP END CRITICAL
691
692	! set defaults for rebuilding so that i is 1st, j 2nd
693	di=1
694	dj=2
695
696	IF( rbdims == 1 ) THEN
697	! override defaults above and set other variables
698	start_pos(2) = 1
699	local_sizes(2) = outdimlens(3-dimids(2))
700	halo_end(2) = 0
701	halo_start(2) = 0
702	di=rebuild_dims(1)
703	dj=3-di
704	ENDIF
705
706	!3.3.1 Generate local domain interior sizes from local_sizes and halo sizes
707	! idomain defines the 1st and last interior points in the i direction and
708	! jdomain defines the 1st and last interior points in the j direction
709
710	idomain(1) = 1 + halo_start(di)
711	idomain(2) = local_sizes(di) - halo_end(di)
712	jdomain(1) = 1 + halo_start(dj)
713	jdomain(2) = local_sizes(dj) - halo_end(dj)
714
715	!3.3.2 For rbdims or more dimensions put the data array from this input file into the correct
716	! part of the output data array. Assume the first dimensions are those to be rebuilt.
717
718	IF( ndims == 1 ) THEN
719
720	IF( rebuild_dims(1) == 1 ) THEN
721	dr = di
722	rdomain = idomain
723	ELSE
724	dr = dj
725	rdomain = jdomain
726	ENDIF
727
728	SELECT CASE( xtype )
729	CASE( NF90_BYTE )
730	ALLOCATE(localdata_1d_i1(local_sizes(dr)))
731	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_i1 ), istop )
732	DO jr = rdomain(1), rdomain(2)
733	globaldata_1d_i1(start_pos(dr) + jr - 1) = localdata_1d_i1(jr)
734	END DO
735	DEALLOCATE(localdata_1d_i1)
736	CASE( NF90_SHORT )
737	ALLOCATE(localdata_1d_i2(local_sizes(dr)))
738	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_i2 ), istop )
739	DO jr = rdomain(1), rdomain(2)
740	globaldata_1d_i2(start_pos(dr) + jr - 1) = localdata_1d_i2(jr)
741	END DO
742	DEALLOCATE(localdata_1d_i2)
743	CASE( NF90_INT )
744	ALLOCATE(localdata_1d_i4(local_sizes(dr)))
745	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_i4 ), istop )
746	DO jr = rdomain(1), rdomain(2)
747	globaldata_1d_i4(start_pos(dr) + jr - 1) = localdata_1d_i4(jr)
748	END DO
749	DEALLOCATE(localdata_1d_i4)
750	CASE( NF90_FLOAT )
751	ALLOCATE(localdata_1d_sp(local_sizes(dr)))
752	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_sp ), istop )
753	DO jr = rdomain(1), rdomain(2)
754	globaldata_1d_sp(start_pos(dr) + jr - 1) = localdata_1d_sp(jr)
755	END DO
756	DEALLOCATE(localdata_1d_sp)
757	CASE( NF90_DOUBLE )
758	ALLOCATE(localdata_1d_dp(local_sizes(dr)))
759	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_dp ), istop )
760	DO jr = rdomain(1), rdomain(2)
761	globaldata_1d_dp(start_pos(dr) + jr - 1) = localdata_1d_dp(jr)
762	END DO
763	DEALLOCATE(localdata_1d_dp)
764	CASE DEFAULT
765	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
766	istop = istop + 1
767	END SELECT
768
769	ELSEIF( ndims == 2 ) THEN
770
771	SELECT CASE( xtype )
772	CASE( NF90_BYTE )
773	ALLOCATE(localdata_2d_i1(local_sizes(di),local_sizes(dj)))
774	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_i1 ), istop )
775	DO jj = jdomain(1), jdomain(2)
776	DO ji = idomain(1), idomain(2)
777	globaldata_2d_i1(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_i1(ji,jj)
778	END DO
779	END DO
780	DEALLOCATE(localdata_2d_i1)
781	CASE( NF90_SHORT )
782	ALLOCATE(localdata_2d_i2(local_sizes(di),local_sizes(dj)))
783	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_i2 ), istop )
784	DO jj = jdomain(1), jdomain(2)
785	DO ji = idomain(1), idomain(2)
786	globaldata_2d_i2(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_i2(ji,jj)
787	END DO
788	END DO
789	DEALLOCATE(localdata_2d_i2)
790	CASE( NF90_INT )
791	ALLOCATE(localdata_2d_i4(local_sizes(di),local_sizes(dj)))
792	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_i4 ), istop )
793	DO jj = jdomain(1), jdomain(2)
794	DO ji = idomain(1), idomain(2)
795	globaldata_2d_i4(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_i4(ji,jj)
796	END DO
797	END DO
798	DEALLOCATE(localdata_2d_i4)
799	CASE( NF90_FLOAT )
800	ALLOCATE(localdata_2d_sp(local_sizes(di),local_sizes(dj)))
801	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_sp ), istop )
802	DO jj = jdomain(1), jdomain(2)
803	DO ji = idomain(1), idomain(2)
804	globaldata_2d_sp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_sp(ji,jj)
805	END DO
806	END DO
807	DEALLOCATE(localdata_2d_sp)
808	CASE( NF90_DOUBLE )
809	ALLOCATE(localdata_2d_dp(local_sizes(di),local_sizes(dj)))
810	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_dp ), istop )
811	DO jj = jdomain(1), jdomain(2)
812	DO ji = idomain(1), idomain(2)
813	globaldata_2d_dp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_dp(ji,jj)
814	END DO
815	END DO
816	DEALLOCATE(localdata_2d_dp)
817	CASE DEFAULT
818	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
819	istop = istop + 1
820	END SELECT
821
822	ELSEIF( ndims == 3 ) THEN
823
824	SELECT CASE( xtype )
825	CASE( NF90_BYTE )
826	ALLOCATE(localdata_3d_i1(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
827	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_i1 ), istop )
828	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
829	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_i1,localdata_3d_i1,di,dj)
830	DO jk = 1, indimlens(dimids(3))
831	DO jj = jdomain(1), jdomain(2)
832	DO ji = idomain(1), idomain(2)
833	globaldata_3d_i1(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_i1(ji,jj,jk)
834	END DO
835	END DO
836	END DO
837	!$OMP END PARALLEL DO
838	DEALLOCATE(localdata_3d_i1)
839	CASE( NF90_SHORT )
840	ALLOCATE(localdata_3d_i2(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
841	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_i2 ), istop )
842	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
843	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_i2,localdata_3d_i2,di,dj)
844	DO jk = 1, indimlens(dimids(3))
845	DO jj = jdomain(1), jdomain(2)
846	DO ji = idomain(1), idomain(2)
847	globaldata_3d_i2(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_i2(ji,jj,jk)
848	END DO
849	END DO
850	END DO
851	!$OMP END PARALLEL DO
852	DEALLOCATE(localdata_3d_i2)
853	CASE( NF90_INT )
854	ALLOCATE(localdata_3d_i4(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
855	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_i4 ), istop )
856	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
857	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_i4,localdata_3d_i4,di,dj)
858	DO jk = 1, indimlens(dimids(3))
859	DO jj = jdomain(1), jdomain(2)
860	DO ji = idomain(1), idomain(2)
861	globaldata_3d_i4(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_i4(ji,jj,jk)
862	END DO
863	END DO
864	END DO
865	!$OMP END PARALLEL DO
866	DEALLOCATE(localdata_3d_i4)
867	CASE( NF90_FLOAT )
868	! TG: This if statement is added to check if the 1st dimension is the corners (for lon_bounds) variables
869	! TG: Had to add the unsatisfactory check for 'lon' as it failed for diaptr files
870	! TG: Would like to find a better assumption for this.
871	IF ( trim(indimnames(dimids(1))) /= dims(1) .AND. indimnames(dimids(1)) .NE. 'lon' ) THEN
872	ALLOCATE(localdata_3d_sp(indimlens(dimids(1)),local_sizes(di),local_sizes(dj)))
873	WRITE(,) 'test', ifile, jv, indimlens(dimids(1)),local_sizes(di),local_sizes(dj)
874	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_sp ), istop )
875	WRITE(,) 'test2'
876	DO jj = jdomain(1), jdomain(2)
877	DO ji = idomain(1), idomain(2)
878	DO jk = 1, indimlens(dimids(1))
879	globaldata_3d_sp(jk, start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_3d_sp(jk,ji,jj)
880	END DO
881	END DO
882	END DO
883	ELSE
884	ALLOCATE(localdata_3d_sp(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
885	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_sp ), istop )
886	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
887	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_sp,localdata_3d_sp,di,dj)
888	DO jk = 1, indimlens(dimids(3))
889	DO jj = jdomain(1), jdomain(2)
890	DO ji = idomain(1), idomain(2)
891	globaldata_3d_sp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_sp(ji,jj,jk)
892	END DO
893	END DO
894	END DO
895	!$OMP END PARALLEL DO
896	ENDIF
897	DEALLOCATE(localdata_3d_sp)
898	CASE( NF90_DOUBLE )
899	IF ( trim(indimnames(dimids(1))) /= dims(1) ) THEN
900	ALLOCATE(localdata_3d_dp(indimlens(dimids(1)),local_sizes(di),local_sizes(dj)))
901	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_dp ), istop )
902	DO jj = jdomain(1), jdomain(2)
903	DO ji = idomain(1), idomain(2)
904	DO jk = 1, indimlens(dimids(1))
905	globaldata_3d_dp(jk, start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_3d_dp(jk,ji,jj)
906	END DO
907	END DO
908	END DO
909	ELSE
910	ALLOCATE(localdata_3d_dp(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
911	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_dp ), istop )
912	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
913	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_dp,localdata_3d_dp,di,dj)
914	DO jk = 1, indimlens(dimids(3))
915	DO jj = jdomain(1), jdomain(2)
916	DO ji = idomain(1), idomain(2)
917	globaldata_3d_dp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_dp(ji,jj,jk)
918	END DO
919	END DO
920	END DO
921	!$OMP END PARALLEL DO
922	ENDIF
923	DEALLOCATE(localdata_3d_dp)
924	CASE DEFAULT
925	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
926	istop = istop + 1
927	END SELECT
928
929	ELSEIF (ndims == 4) THEN
930
931	SELECT CASE( xtype )
932	CASE( NF90_BYTE )
933	ALLOCATE(localdata_4d_i1(local_sizes(di),local_sizes(dj), &
934	& indimlens(dimids(3)),ntchunk))
935	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i1, start=(/1,1,1,nt/) ), istop )
936	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
937	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i1,localdata_4d_i1,di,dj,nt,ntchunk)
938	DO jl = 1, ntchunk
939	!$OMP DO
940	DO jk = 1, indimlens(dimids(3))
941	DO jj = jdomain(1), jdomain(2)
942	DO ji = idomain(1), idomain(2)
943	globaldata_4d_i1(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_i1(ji,jj,jk,jl)
944	END DO
945	END DO
946	END DO
947	!$OMP END DO nowait
948	END DO
949	!$OMP END PARALLEL
950	DEALLOCATE(localdata_4d_i1)
951	CASE( NF90_SHORT )
952	ALLOCATE(localdata_4d_i2(local_sizes(di),local_sizes(dj), &
953	& indimlens(dimids(3)),ntchunk))
954	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i2, start=(/1,1,1,nt/) ), istop )
955	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
956	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i2,localdata_4d_i2,di,dj,nt,ntchunk)
957	DO jl = 1, ntchunk
958	!$OMP DO
959	DO jk = 1, indimlens(dimids(3))
960	DO jj = jdomain(1), jdomain(2)
961	DO ji = idomain(1), idomain(2)
962	globaldata_4d_i2(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_i2(ji,jj,jk,jl)
963	END DO
964	END DO
965	END DO
966	!$OMP END DO nowait
967	END DO
968	!$OMP END PARALLEL
969	DEALLOCATE(localdata_4d_i2)
970	CASE( NF90_INT )
971	ALLOCATE(localdata_4d_i4(local_sizes(di),local_sizes(dj), &
972	& indimlens(dimids(3)),ntchunk))
973	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i4, start=(/1,1,1,nt/) ), istop )
974	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
975	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i4,localdata_4d_i4,di,dj,nt,ntchunk)
976	DO jl = 1, ntchunk
977	!$OMP DO
978	DO jk = 1, indimlens(dimids(3))
979	DO jj = jdomain(1), jdomain(2)
980	DO ji = idomain(1), idomain(2)
981	globaldata_4d_i4(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_i4(ji,jj,jk,jl)
982	END DO
983	END DO
984	END DO
985	!$OMP END DO nowait
986	END DO
987	!$OMP END PARALLEL
988	DEALLOCATE(localdata_4d_i4)
989	CASE( NF90_FLOAT )
990	ALLOCATE(localdata_4d_sp(local_sizes(di),local_sizes(dj), &
991	& indimlens(dimids(3)),ntchunk))
992	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_sp, start=(/1,1,1,nt/) ), istop )
993	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
994	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_sp,localdata_4d_sp,di,dj,nt,ntchunk)
995	DO jl = 1, ntchunk
996	!$OMP DO
997	DO jk = 1, indimlens(dimids(3))
998	DO jj = jdomain(1), jdomain(2)
999	DO ji = idomain(1), idomain(2)
1000	globaldata_4d_sp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_sp(ji,jj,jk,jl)
1001	END DO
1002	END DO
1003	END DO
1004	!$OMP END DO nowait
1005	END DO
1006	!$OMP END PARALLEL
1007	DEALLOCATE(localdata_4d_sp)
1008	CASE( NF90_DOUBLE )
1009	ALLOCATE(localdata_4d_dp(local_sizes(di),local_sizes(dj), &
1010	& indimlens(dimids(3)),ntchunk))
1011	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_dp, start=(/1,1,1,nt/) ), istop )
1012	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
1013	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_dp,localdata_4d_dp,di,dj,nt,ntchunk)
1014	DO jl = 1, ntchunk
1015	!$OMP DO
1016	DO jk = 1, indimlens(dimids(3))
1017	DO jj = jdomain(1), jdomain(2)
1018	DO ji = idomain(1), idomain(2)
1019	globaldata_4d_dp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_dp(ji,jj,jk,jl)
1020	END DO
1021	END DO
1022	END DO
1023	!$OMP END DO nowait
1024	END DO
1025	!$OMP END PARALLEL
1026	DEALLOCATE(localdata_4d_dp)
1027	CASE DEFAULT
1028	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1029	istop = istop + 1
1030	END SELECT
1031
1032	ENDIF ! l_noRebuild false
1033
1034	!3.4 Work out if the valid_min and valid_max attributes exist for this variable.
1035	! If they do then calculate the extrema over all input files.
1036
1037	DO attid = 1, natts
1038	CALL check_nf90( nf90_inq_attname( ncid, jv, attid, attname ), istop )
1039	IF( INDEX( attname, "valid_min" ) == 1 ) THEN
1040	CALL check_nf90( nf90_get_att( ncid, jv, attname, InMin), istop )
1041	l_valid = .true.
1042	ENDIF
1043	IF( INDEX( attname, "valid_max" ) == 1 ) THEN
1044	CALL check_nf90( nf90_get_att( ncid, jv, attname, InMax ), istop )
1045	l_valid = .true.
1046	ENDIF
1047	END DO
1048
1049	IF (l_valid) THEN
1050	!$OMP CRITICAL
1051	IF( InMin < ValMin ) ValMin = InMin
1052	IF( InMax > ValMax ) ValMax = InMax
1053	!$OMP END CRITICAL
1054	ENDIF
1055
1056	!3.5 Abort if failure and only 1 thread
1057
1058	IF( nthreads == 1 .AND. istop /= nf90_noerr ) THEN
1059	WRITE(numerr,) ' NEMO rebuild failed! *'
1060	STOP 5
1061	ENDIF
1062
1063	END DO ! loop over files
1064	!$OMP END PARALLEL DO
1065
1066	!3.6 Abort if any of the OMP threads failed
1067	IF( istop /= nf90_noerr ) THEN
1068	WRITE(numerr,) ' NEMO rebuild failed! *'
1069	STOP 5
1070	ENDIF
1071
1072	ENDIF ! ndims > 2
1073
1074	!---------------------------------------------------------------------------
1075	!4. Write data to output file
1076
1077	IF (l_verbose) WRITE(numout,*) 'Writing variable '//TRIM(varname)//'...'
1078
1079	!4.1 If the valid min and max attributes exist then update them in the file
1080
1081	IF( l_valid ) THEN
1082	CALL check_nf90( nf90_put_att( outid, jv, "valid_min", ValMin ) )
1083	CALL check_nf90( nf90_put_att( outid, jv, "valid_max", ValMax ) )
1084	ENDIF
1085
1086	!4.2 Write the data to the output file depending on how many dimensions it has
1087
1088	IF( ndims == 0 ) THEN
1089
1090	SELECT CASE( xtype )
1091	CASE( NF90_BYTE )
1092	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_i1 ) )
1093	CASE( NF90_SHORT )
1094	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_i2 ) )
1095	CASE( NF90_INT )
1096	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_i4 ) )
1097	CASE( NF90_FLOAT )
1098	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_sp ) )
1099	CASE( NF90_DOUBLE )
1100	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_dp ) )
1101	END SELECT
1102
1103	ELSEIF( ndims == 1 ) THEN
1104
1105	SELECT CASE( xtype )
1106	CASE( NF90_BYTE )
1107	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_i1 ) )
1108	DEALLOCATE(globaldata_1d_i1)
1109	CASE( NF90_SHORT )
1110	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_i2 ) )
1111	DEALLOCATE(globaldata_1d_i2)
1112	CASE( NF90_INT )
1113	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_i4 ) )
1114	DEALLOCATE(globaldata_1d_i4)
1115	CASE( NF90_FLOAT )
1116	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_sp ) )
1117	DEALLOCATE(globaldata_1d_sp)
1118	CASE( NF90_DOUBLE )
1119	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_dp ) )
1120	DEALLOCATE(globaldata_1d_dp)
1121	END SELECT
1122
1123	ELSEIF( ndims == 2 ) THEN
1124
1125	SELECT CASE( xtype )
1126	CASE( NF90_BYTE )
1127	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_i1 ) )
1128	DEALLOCATE(globaldata_2d_i1)
1129	CASE( NF90_SHORT )
1130	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_i2 ) )
1131	DEALLOCATE(globaldata_2d_i2)
1132	CASE( NF90_INT )
1133	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_i4 ) )
1134	DEALLOCATE(globaldata_2d_i4)
1135	CASE( NF90_FLOAT )
1136	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_sp ) )
1137	DEALLOCATE(globaldata_2d_sp)
1138	CASE( NF90_DOUBLE )
1139	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_dp ) )
1140	DEALLOCATE(globaldata_2d_dp)
1141	CASE DEFAULT
1142	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1143	STOP 4
1144	END SELECT
1145
1146	ELSEIF( ndims == 3 ) THEN
1147
1148	SELECT CASE( xtype )
1149	CASE( NF90_BYTE )
1150	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_i1 ) )
1151	DEALLOCATE(globaldata_3d_i1)
1152	CASE( NF90_SHORT )
1153	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_i2 ) )
1154	DEALLOCATE(globaldata_3d_i2)
1155	CASE( NF90_INT )
1156	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_i4 ) )
1157	DEALLOCATE(globaldata_3d_i4)
1158	CASE( NF90_FLOAT )
1159	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_sp ) )
1160	DEALLOCATE(globaldata_3d_sp)
1161	CASE( NF90_DOUBLE )
1162	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_dp ) )
1163	DEALLOCATE(globaldata_3d_dp)
1164	CASE DEFAULT
1165	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1166	STOP 4
1167	END SELECT
1168
1169	ELSEIF( ndims == 4 ) THEN
1170
1171	SELECT CASE( xtype )
1172	CASE( NF90_BYTE )
1173	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i1, start=(/1,1,1,nt/) ) )
1174	DEALLOCATE(globaldata_4d_i1)
1175	CASE( NF90_SHORT )
1176	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i2, start=(/1,1,1,nt/) ) )
1177	DEALLOCATE(globaldata_4d_i2)
1178	CASE( NF90_INT )
1179	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i4, start=(/1,1,1,nt/) ) )
1180	DEALLOCATE(globaldata_4d_i4)
1181	CASE( NF90_FLOAT )
1182	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_sp, start=(/1,1,1,nt/) ) )
1183	DEALLOCATE(globaldata_4d_sp)
1184	CASE( NF90_DOUBLE )
1185	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_dp, start=(/1,1,1,nt/) ) )
1186	DEALLOCATE(globaldata_4d_dp)
1187	CASE DEFAULT
1188	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1189	STOP 4
1190	END SELECT
1191
1192	ENDIF
1193
1194	nt = nt + ntchunk
1195
1196	END DO ! WHILE loop
1197
1198	END DO ! loop over variables
1199
1200	!---------------------------------------------------------------------------
1201	!5. Close files
1202
1203	!5.1 Close input files
1204
1205	IF (l_verbose) WRITE(numout,*) 'Closing input files...'
1206	DO ifile = 1, ndomain
1207	ncid = inncids(ifile)
1208	CALL check_nf90( nf90_close( ncid ) )
1209	END DO
1210
1211	!5.2 Close output file
1212
1213	IF (l_verbose) WRITE(numout,*) 'Closing output file...'
1214	CALL check_nf90( nf90_close( outid ) )
1215
1216	IF (l_verbose) WRITE(numout,*) 'NEMO rebuild completed successfully'
1217	IF (l_verbose) WRITE(numout,*)
1218
1219	CONTAINS
1220
1221
1222	SUBROUTINE check_nf90(status, errorFlag)
1223	!---------------------------------------------------------------------
1224	! Checks return code from nf90 library calls and warns if needed
1225	! If errorFlag is present then it just increments this flag (OMP use)
1226	!
1227	!---------------------------------------------------------------------
1228	INTEGER, INTENT(IN ) :: status
1229	INTEGER, INTENT(INOUT), OPTIONAL :: errorFlag
1230	!---------------------------------------------------------------------
1231
1232	IF( status /= nf90_noerr ) THEN
1233	WRITE(numerr,*) 'ERROR! : '//TRIM(nf90_strerror(status))
1234	IF( PRESENT( errorFlag ) ) THEN
1235	errorFlag = errorFlag + status
1236	ELSE
1237	WRITE(numerr,) " NEMO rebuild failed *"
1238	WRITE(numerr,*)
1239	STOP 4
1240	ENDIF
1241	ENDIF
1242
1243	END SUBROUTINE check_nf90
1244
1245
1246	END PROGRAM rebuild_nemo

Note: See TracBrowser for help on using the repository browser.

New URL for NEMO forge! http://forge.nemo-ocean.eu

Context Navigation

source: branches/UKMO/dev_r7681_rebuild_nemo/NEMOGCM/TOOLS/REBUILD_NEMO/src/rebuild_nemo.F90 @ 7687

Download in other formats: