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rebuild_nemo.f90 in branches/UKMO/icebergs_restart_single_file/NEMOGCM/TOOLS/REBUILD_NEMO/src – NEMO

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source: branches/UKMO/icebergs_restart_single_file/NEMOGCM/TOOLS/REBUILD_NEMO/src/rebuild_nemo.f90 @ 6019

Last change on this file since 6019 was 6019, checked in by timgraham, 8 years ago
Reinstated svn keywords before upgrading to head of trunk
Property svn:keywords set to `Id`
File size: 53.3 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
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 = 32000000
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
84
85	! NF90_BYTE local data arrays
86	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_i1
87	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_i1
88	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_i1
89	INTEGER(i1), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_i1
90
91	! NF90_SHORT local data arrays
92	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_i2
93	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_i2
94	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_i2
95	INTEGER(i2), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_i2
96
97	! NF90_INT local data arrays
98	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_i4
99	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_i4
100	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_i4
101	INTEGER(i4), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_i4
102
103	! NF90_FLOAT local data arrays
104	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_sp
105	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_sp
106	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_sp
107	REAL(sp), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_sp
108
109	! NF90_DOUBLE local data arrays
110	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:) :: localdata_1d_dp
111	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:,:) :: localdata_2d_dp
112	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: localdata_3d_dp
113	REAL(dp), ALLOCATABLE, SAVE, DIMENSION(:,:,:,:) :: localdata_4d_dp
114
115	! NF90_BYTE global data arrays
116	INTEGER(i1) :: globaldata_0d_i1
117	INTEGER(i1), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_i1
118	INTEGER(i1), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_i1
119	INTEGER(i1), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_i1
120	INTEGER(i1), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_i1
121
122	! NF90_SHORT global data arrays
123	INTEGER(i2) :: globaldata_0d_i2
124	INTEGER(i2), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_i2
125	INTEGER(i2), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_i2
126	INTEGER(i2), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_i2
127	INTEGER(i2), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_i2
128
129	! NF90_INT global data arrays
130	INTEGER(i4) :: globaldata_0d_i4
131	INTEGER(i4), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_i4
132	INTEGER(i4), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_i4
133	INTEGER(i4), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_i4
134	INTEGER(i4), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_i4
135
136	! NF90_FLOAT global data arrays
137	REAL(sp) :: globaldata_0d_sp
138	REAL(sp), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_sp
139	REAL(sp), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_sp
140	REAL(sp), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_sp
141	REAL(sp), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_sp
142
143	! NF90_DOUBLE global data arrays
144	REAL(dp) :: globaldata_0d_dp
145	REAL(dp), ALLOCATABLE, DIMENSION(:) :: globaldata_1d_dp
146	REAL(dp), ALLOCATABLE, DIMENSION(:,:) :: globaldata_2d_dp
147	REAL(dp), ALLOCATABLE, DIMENSION(:,:,:) :: globaldata_3d_dp
148	REAL(dp), ALLOCATABLE, DIMENSION(:,:,:,:) :: globaldata_4d_dp
149
150	LOGICAL :: l_valid = .false.
151	LOGICAL :: l_noRebuild = .false.
152	LOGICAL :: l_findDims = .true.
153
154	NAMELIST/nam_rebuild/ filebase, ndomain, dims, nchunksize
155
156	!End of definitions
157
158	!--------------------------------------------------------------------------------
159	!0. OMP setup
160
161	!$OMP PARALLEL DEFAULT(NONE) SHARED(nthreads)
162	!$OMP MASTER
163	!$ nthreads = omp_get_num_threads()
164	!$ WRITE(numout,*) 'Running OMP with ',nthreads,' thread(s).'
165	!$OMP END MASTER
166	!$OMP END PARALLEL
167
168	!--------------------------------------------------------------------------------
169	!1. Read in the namelist
170
171	dims(:) = ""
172	nchunksize = 0
173	OPEN( UNIT=numnam, FILE='nam_rebuild', FORM='FORMATTED', STATUS='OLD' )
174	READ( numnam, nam_rebuild )
175	CLOSE( numnam )
176	IF( .NOT. ALL(dims(:) == "") ) l_findDims = .false.
177
178	!1.1 Set up the filenames and fileids
179
180	ALLOCATE(filenames(ndomain))
181	IF (l_verbose) WRITE(numout,*) 'Rebuilding the following files:'
182	DO ifile = 1, ndomain
183	WRITE(suffix,'(i4.4)') ifile-1
184	filenames(ifile) = TRIM(filebase)//'_'//TRIM(suffix)//'.nc'
185	IF (l_verbose) WRITE(numout,*) TRIM(filenames(ifile))
186	END DO
187	ALLOCATE(inncids(ndomain))
188
189	!---------------------------------------------------------------------------
190	!2. Read in the global dimensions from the first input file and set up the output file
191
192	CALL check_nf90( nf90_open( TRIM(filenames(1)), nf90_share, ncid ) )
193	CALL check_nf90( nf90_inquire( ncid, ndims, nvars, natts ) )
194
195	!2.0 Read in the total number of processors the file is expecting and check its correct
196
197	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_number_total', ndomain_file ) )
198	IF( ndomain /= ndomain_file ) THEN
199	WRITE(numerr,*) 'ERROR! : number of files to rebuild in file does not agree with namelist'
200	WRITE(numerr,*) 'Attribute DOMAIN_number_total is : ', ndomain_file
201	WRITE(numerr,*) 'Number of files specified in namelist is: ', ndomain
202	STOP
203	ENDIF
204
205	!2.1 Set up the output file
206
207	CALL check_nf90( nf90_create( TRIM(filebase)//'.nc', nf90_64bit_offset, outid, chunksize=chunksize ) )
208
209	!2.2 Set up dimensions in output file
210
211	!2.2.0 Find out how many dimensions are required to be rebuilt and which ones they are
212	CALL check_nf90( nf90_inquire_attribute( ncid, nf90_global, 'DOMAIN_dimensions_ids', xtype, rbdims, attid ) )
213
214	ALLOCATE(rebuild_dims(rbdims))
215	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_dimensions_ids', rebuild_dims ) )
216
217	ALLOCATE(global_sizes(rbdims))
218	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_size_global', global_sizes ) )
219	IF (l_verbose) WRITE(numout,*) 'Size of global arrays: ', global_sizes
220
221
222	!2.2.1 Copy the dimensions into the output file apart from rebuild_dims() which are dimensioned globally
223	ALLOCATE(indimlens(ndims), indimnames(ndims), outdimlens(ndims))
224	CALL check_nf90( nf90_inquire( ncid, unlimitedDimId = unlimitedDimId ) )
225	istop = 0
226	DO idim = 1, ndims
227	CALL check_nf90( nf90_inquire_dimension( ncid, idim, dimname, dimlen ) )
228	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_size_local', local_sizes ) )
229	indimlens(idim) = dimlen
230	indimnames(idim) = dimname
231	IF (l_findDims) THEN
232	IF( idim == rebuild_dims(1) ) THEN
233	IF( dimlen == local_sizes(1) ) THEN
234	dimlen = global_sizes(1)
235	ELSE
236	istop = 1
237	ENDIF
238	ENDIF
239	IF( rbdims > 1 .AND. idim == rebuild_dims(2) ) THEN
240	IF( dimlen == local_sizes(2) ) THEN
241	dimlen = global_sizes(2)
242	ELSE
243	istop = 1
244	ENDIF
245	ENDIF
246	ELSE ! l_findDims = false
247	IF( TRIM(dimname) == TRIM(dims(1))) THEN
248	dimlen = global_sizes(1)
249	rebuild_dims(1) = idim
250	ENDIF
251	IF( rbdims > 1 .AND. TRIM(dimname) == TRIM(dims(2))) THEN
252	dimlen = global_sizes(2)
253	rebuild_dims(2) = idim
254	ENDIF
255	ENDIF
256
257	IF( idim == unlimitedDimId ) THEN
258	CALL check_nf90( nf90_def_dim( outid, dimname, nf90_unlimited, dimid) )
259	nmax_unlimited = dimlen
260	ELSE
261	CALL check_nf90( nf90_def_dim( outid, dimname, dimlen, dimid) )
262	ENDIF
263	outdimlens(idim) = dimlen
264	END DO
265
266	IF( istop == 1 ) THEN
267	WRITE(numerr,*) 'ERROR! : DOMAIN_local_sizes attribute does not match rebuild dimension lengths in the first file'
268	WRITE(numerr,*) 'Attribute DOMAIN_local_sizes is : ', local_sizes
269	WRITE(numerr,*) 'Dimensions to be rebuilt are of size : ', outdimlens(rebuild_dims(1)), outdimlens(rebuild_dims(2))
270	STOP
271	ENDIF
272
273	IF (l_findDims) THEN
274	IF (l_verbose) WRITE(numout,*) 'Finding rebuild dimensions from the first file...'
275	ELSE
276	IF (l_verbose) WRITE(numout,*) 'Using rebuild dimensions given in namelist...'
277	ENDIF
278
279	IF( rbdims > 1 ) THEN
280	IF (l_verbose) WRITE(numout,*) 'Rebuilding across dimensions '//TRIM(indimnames(rebuild_dims(1)))// &
281	& ' and '//TRIM(indimnames(rebuild_dims(2)))
282	ELSE
283	IF (l_verbose) WRITE(numout,*) 'Rebuilding across dimension '//TRIM(indimnames(rebuild_dims(1)))
284	ENDIF
285
286	!2.2.2 Copy the global attributes into the output file, apart from those beginning with DOMAIN_
287	! Also need to change the file_name attribute and the TimeStamp attribute.
288	DO attid = 1, natts
289	CALL check_nf90( nf90_inq_attname( ncid, nf90_global, attid, attname ) )
290	IF( INDEX( attname, "DOMAIN_" ) == 1 ) CYCLE
291	IF( INDEX( attname, "file_name") == 1 ) CYCLE
292	IF( INDEX( attname, "associate_file") == 1 ) CYCLE
293	IF (l_verbose) WRITE(numout,*) 'Copying attribute '//TRIM(attname)//' into destination file...'
294	CALL check_nf90( nf90_copy_att( ncid, nf90_global, attname, outid, nf90_global ) )
295	END DO
296	CALL check_nf90( nf90_put_att( outid, nf90_global, "file_name", TRIM(filebase)//'.nc') )
297	IF (l_verbose) WRITE(numout,*) 'Writing new file_name attribute'
298	CALL DATE_AND_TIME ( date=date, time=time, zone=zone )
299	timestamp = date(7:8) // "/" // date(5:6) // "/" // date(1:4) // " " // &
300	time(1:2) // ":" // time(3:4) // ":" // time(5:6) // " " // &
301	zone
302	CALL check_nf90( nf90_put_att( outid, nf90_global, "TimeStamp", timestamp ) )
303	IF (l_verbose) WRITE(numout,*) 'Writing new TimeStamp attribute'
304
305	!2.2.3 Copy the variable definitions and attributes into the output file.
306	DO jv = 1, nvars
307	CALL check_nf90( nf90_inquire_variable( ncid, jv, varname, xtype, ndims, dimids, natts ) )
308	ALLOCATE(outdimids(ndims))
309	DO idim = 1, ndims
310	outdimids(idim) = dimids(idim)
311	END DO
312	CALL check_nf90( nf90_def_var( outid, varname, xtype, outdimids, varid ) )
313	DEALLOCATE(outdimids)
314	IF (l_verbose) WRITE(numout,*) 'Defining variable '//TRIM(varname)//'...'
315	IF( natts > 0 ) THEN
316	DO attid = 1, natts
317	CALL check_nf90( nf90_inq_attname( ncid, varid, attid, attname ) )
318	CALL check_nf90( nf90_copy_att( ncid, varid, attname, outid, varid ) )
319	END DO
320	ENDIF
321	END DO
322
323	!2.3 End definitions in output file and copy 1st file ncid to the inncids array
324
325	CALL check_nf90( nf90_enddef( outid ) )
326	inncids(1) = ncid
327	IF (l_verbose) WRITE(numout,*) 'Finished defining output file.'
328
329	!---------------------------------------------------------------------------
330	!3. Read in data from each file for each variable
331
332	!3.1 Open each file and store the ncid in inncids array
333
334	IF (l_verbose) WRITE(numout,*) 'Opening input files...'
335	DO ifile = 2, ndomain
336	CALL check_nf90( nf90_open( TRIM(filenames(ifile)), nf90_share, ncid, chunksize=chunksize ) )
337	inncids(ifile) = ncid
338	END DO
339	IF (l_verbose) WRITE(numout,*) 'All input files open.'
340
341	DO jv = 1, nvars
342
343	ValMin = 1.e10
344	ValMax = -1.e10
345	l_valid = .false.
346	istop = nf90_noerr
347	nt = 1
348	ntchunk = nmax_unlimited
349	IF( nchunksize == 0 ) nchunksize = nmax_unlimited
350
351	!3.2 Inquire variable to find out name and how many dimensions it has
352	! and importantly whether it contains the dimensions in rebuild_dims()
353
354	ncid = inncids(1)
355	CALL check_nf90( nf90_inquire_variable( ncid, jv, varname, xtype, ndims, dimids, natts ) )
356
357	l_noRebuild = .true.
358	IF( ANY( dimids(1:ndims) == rebuild_dims(1) )) l_noRebuild = .false.
359	IF( rbdims > 1 ) THEN
360	IF( ANY( dimids(1:ndims) == rebuild_dims(2) )) l_noRebuild = .false.
361	ENDIF
362
363	!3.2.0 start while loop for time chunking
364
365	DO WHILE( nt <= nmax_unlimited )
366
367	IF( ndims > 3 ) THEN
368	ntchunk = MIN( nchunksize, nmax_unlimited + 1 - nt )
369	ENDIF
370
371	IF (l_noRebuild) THEN
372
373	IF( nchunksize == nmax_unlimited .OR. ndims <= 3 ) THEN
374	IF (l_verbose) WRITE(numout,*) 'Copying data from variable '//TRIM(varname)//'...'
375	ELSE
376	IF (l_verbose) WRITE(numout,'(A,I3,A,I3,A)') ' Copying data from variable ' &
377	& //TRIM(varname)//' for chunks ',nt,' to ',nt+ntchunk-1,' ...'
378	ENDIF
379
380	!3.2.1 If rebuilding not required then just need to read in variable
381	! for copying direct into output file after the OMP (files) loop.
382	IF( ndims == 0 ) THEN
383
384	SELECT CASE( xtype )
385	CASE( NF90_BYTE )
386	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_i1 ) )
387	CASE( NF90_SHORT )
388	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_i2 ) )
389	CASE( NF90_INT )
390	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_i4 ) )
391	CASE( NF90_FLOAT )
392	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_sp ) )
393	CASE( NF90_DOUBLE )
394	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_0d_dp ) )
395	CASE DEFAULT
396	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
397	STOP
398	END SELECT
399
400	ELSEIF( ndims == 1 ) THEN
401
402	SELECT CASE( xtype )
403	CASE( NF90_BYTE )
404	ALLOCATE(globaldata_1d_i1(indimlens(dimids(1))))
405	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_i1 ) )
406	CASE( NF90_SHORT )
407	ALLOCATE(globaldata_1d_i2(indimlens(dimids(1))))
408	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_i2 ) )
409	CASE( NF90_INT )
410	ALLOCATE(globaldata_1d_i4(indimlens(dimids(1))))
411	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_i4 ) )
412	CASE( NF90_FLOAT )
413	ALLOCATE(globaldata_1d_sp(indimlens(dimids(1))))
414	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_sp ) )
415	CASE( NF90_DOUBLE )
416	ALLOCATE(globaldata_1d_dp(indimlens(dimids(1))))
417	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_1d_dp ) )
418	CASE DEFAULT
419	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
420	STOP
421	END SELECT
422
423	ELSEIF( ndims == 2 ) THEN
424
425	SELECT CASE( xtype )
426	CASE( NF90_BYTE )
427	ALLOCATE(globaldata_2d_i1(indimlens(dimids(1)),indimlens(dimids(2))))
428	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_i1 ) )
429	CASE( NF90_SHORT )
430	ALLOCATE(globaldata_2d_i2(indimlens(dimids(1)),indimlens(dimids(2))))
431	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_i2 ) )
432	CASE( NF90_INT )
433	ALLOCATE(globaldata_2d_i4(indimlens(dimids(1)),indimlens(dimids(2))))
434	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_i4 ) )
435	CASE( NF90_FLOAT )
436	ALLOCATE(globaldata_2d_sp(indimlens(dimids(1)),indimlens(dimids(2))))
437	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_sp ) )
438	CASE( NF90_DOUBLE )
439	ALLOCATE(globaldata_2d_dp(indimlens(dimids(1)),indimlens(dimids(2))))
440	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_2d_dp ) )
441	CASE DEFAULT
442	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
443	STOP
444	END SELECT
445
446	ELSEIF( ndims == 3 ) THEN
447
448	SELECT CASE( xtype )
449	CASE( NF90_BYTE )
450	ALLOCATE(globaldata_3d_i1(indimlens(dimids(1)),indimlens(dimids(2)), &
451	& indimlens(dimids(3))))
452	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_i1 ) )
453	CASE( NF90_SHORT )
454	ALLOCATE(globaldata_3d_i2(indimlens(dimids(1)),indimlens(dimids(2)), &
455	& indimlens(dimids(3))))
456	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_i2 ) )
457	CASE( NF90_INT )
458	ALLOCATE(globaldata_3d_i4(indimlens(dimids(1)),indimlens(dimids(2)), &
459	& indimlens(dimids(3))))
460	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_i4 ) )
461	CASE( NF90_FLOAT )
462	ALLOCATE(globaldata_3d_sp(indimlens(dimids(1)),indimlens(dimids(2)), &
463	& indimlens(dimids(3))))
464	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_sp ) )
465	CASE( NF90_DOUBLE )
466	ALLOCATE(globaldata_3d_dp(indimlens(dimids(1)),indimlens(dimids(2)), &
467	& indimlens(dimids(3))))
468	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_3d_dp ) )
469	CASE DEFAULT
470	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
471	STOP
472	END SELECT
473
474	ELSEIF( ndims == 4 ) THEN
475
476	SELECT CASE( xtype )
477	CASE( NF90_BYTE )
478	ALLOCATE(globaldata_4d_i1(indimlens(dimids(1)),indimlens(dimids(2)), &
479	& indimlens(dimids(3)),ntchunk))
480	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i1, start=(/1,1,1,nt/) ) )
481	CASE( NF90_SHORT )
482	ALLOCATE(globaldata_4d_i2(indimlens(dimids(1)),indimlens(dimids(2)), &
483	& indimlens(dimids(3)),ntchunk))
484	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i2, start=(/1,1,1,nt/) ) )
485	CASE( NF90_INT )
486	ALLOCATE(globaldata_4d_i4(indimlens(dimids(1)),indimlens(dimids(2)), &
487	& indimlens(dimids(3)),ntchunk))
488	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i4, start=(/1,1,1,nt/) ) )
489	CASE( NF90_FLOAT )
490	ALLOCATE(globaldata_4d_sp(indimlens(dimids(1)),indimlens(dimids(2)), &
491	& indimlens(dimids(3)),ntchunk))
492	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_sp, start=(/1,1,1,nt/) ) )
493	CASE( NF90_DOUBLE )
494	ALLOCATE(globaldata_4d_dp(indimlens(dimids(1)),indimlens(dimids(2)), &
495	& indimlens(dimids(3)),ntchunk))
496	CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_dp, start=(/1,1,1,nt/) ) )
497	CASE DEFAULT
498	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
499	STOP
500	END SELECT
501
502	ENDIF
503
504	ELSE ! l_noRebuild = .false.
505
506	!3.2.2 For variables that require rebuilding we need to read in from all ndomain files
507	! Here we allocate global variables ahead of looping over files
508	IF( nchunksize == nmax_unlimited .OR. ndims <= 3 ) THEN
509	IF (l_verbose) WRITE(numout,*) 'Rebuilding data from variable '//TRIM(varname)//'...'
510	ELSE
511	IF (l_verbose) WRITE(numout,'(A,I3,A,I3,A)') ' Rebuilding data from variable ' &
512	& //TRIM(varname)//' for chunks ',nt,' to ',nt+ntchunk-1,' ...'
513	ENDIF
514	IF( ndims == 1 ) THEN
515
516	SELECT CASE( xtype )
517	CASE( NF90_BYTE )
518	ALLOCATE(globaldata_1d_i1(outdimlens(dimids(1))))
519	CASE( NF90_SHORT )
520	ALLOCATE(globaldata_1d_i2(outdimlens(dimids(1))))
521	CASE( NF90_INT )
522	ALLOCATE(globaldata_1d_i4(outdimlens(dimids(1))))
523	CASE( NF90_FLOAT )
524	ALLOCATE(globaldata_1d_sp(outdimlens(dimids(1))))
525	CASE( NF90_DOUBLE )
526	ALLOCATE(globaldata_1d_dp(outdimlens(dimids(1))))
527	CASE DEFAULT
528	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
529	STOP
530	END SELECT
531
532	ELSEIF( ndims == 2 ) THEN
533
534	SELECT CASE( xtype )
535	CASE( NF90_BYTE )
536	ALLOCATE(globaldata_2d_i1(outdimlens(dimids(1)),outdimlens(dimids(2))))
537	CASE( NF90_SHORT )
538	ALLOCATE(globaldata_2d_i2(outdimlens(dimids(1)),outdimlens(dimids(2))))
539	CASE( NF90_INT )
540	ALLOCATE(globaldata_2d_i4(outdimlens(dimids(1)),outdimlens(dimids(2))))
541	CASE( NF90_FLOAT )
542	ALLOCATE(globaldata_2d_sp(outdimlens(dimids(1)),outdimlens(dimids(2))))
543	CASE( NF90_DOUBLE )
544	ALLOCATE(globaldata_2d_dp(outdimlens(dimids(1)),outdimlens(dimids(2))))
545	CASE DEFAULT
546	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
547	STOP
548	END SELECT
549
550	ELSEIF( ndims == 3 ) THEN
551
552	SELECT CASE( xtype )
553	CASE( NF90_BYTE )
554	ALLOCATE(globaldata_3d_i1(outdimlens(dimids(1)),outdimlens(dimids(2)), &
555	& outdimlens(dimids(3))))
556	CASE( NF90_SHORT )
557	ALLOCATE(globaldata_3d_i2(outdimlens(dimids(1)),outdimlens(dimids(2)), &
558	& outdimlens(dimids(3))))
559	CASE( NF90_INT )
560	ALLOCATE(globaldata_3d_i4(outdimlens(dimids(1)),outdimlens(dimids(2)), &
561	& outdimlens(dimids(3))))
562	CASE( NF90_FLOAT )
563	ALLOCATE(globaldata_3d_sp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
564	& outdimlens(dimids(3))))
565	CASE( NF90_DOUBLE )
566	ALLOCATE(globaldata_3d_dp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
567	& outdimlens(dimids(3))))
568	CASE DEFAULT
569	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
570	STOP
571	END SELECT
572
573	ELSEIF( ndims == 4 ) THEN
574
575	SELECT CASE( xtype )
576	CASE( NF90_BYTE )
577	ALLOCATE(globaldata_4d_i1(outdimlens(dimids(1)),outdimlens(dimids(2)), &
578	& outdimlens(dimids(3)),ntchunk))
579	CASE( NF90_SHORT )
580	ALLOCATE(globaldata_4d_i2(outdimlens(dimids(1)),outdimlens(dimids(2)), &
581	& outdimlens(dimids(3)),ntchunk))
582	CASE( NF90_INT )
583	ALLOCATE(globaldata_4d_i4(outdimlens(dimids(1)),outdimlens(dimids(2)), &
584	& outdimlens(dimids(3)),ntchunk))
585	CASE( NF90_FLOAT )
586	ALLOCATE(globaldata_4d_sp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
587	& outdimlens(dimids(3)),ntchunk))
588	CASE( NF90_DOUBLE )
589	ALLOCATE(globaldata_4d_dp(outdimlens(dimids(1)),outdimlens(dimids(2)), &
590	& outdimlens(dimids(3)),ntchunk))
591	CASE DEFAULT
592	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
593	STOP
594	END SELECT
595	ELSE
596	WRITE(numerr,*) 'ERROR! : A netcdf variable has more than 4 dimensions which is not taken into account'
597	STOP
598	ENDIF
599
600	!$OMP PARALLEL DO DEFAULT(NONE) &
601	!$OMP& PRIVATE(ifile,ncid,xtype,start_pos,local_sizes,InMin,InMax,natts, &
602	!$OMP& ndims,attid,attname,dimids,idim,dimname,dimlen,unlimitedDimId, &
603	!$OMP& halo_start,halo_end,idomain,jdomain,rdomain,di,dj,dr, &
604	!$OMP& localdata_1d_i2,localdata_1d_i4,localdata_1d_sp,localdata_1d_dp, &
605	!$OMP& localdata_2d_i2,localdata_2d_i4,localdata_2d_sp,localdata_2d_dp, &
606	!$OMP& localdata_3d_i2,localdata_3d_i4,localdata_3d_sp,localdata_3d_dp, &
607	!$OMP& localdata_4d_i2,localdata_4d_i4,localdata_4d_sp,localdata_4d_dp, &
608	!$OMP& localdata_1d_i1,localdata_2d_i1,localdata_3d_i1,localdata_4d_i1) &
609	!$OMP& SHARED(jv,nvars,varname,filenames,ValMin,ValMax,indimlens,outdimlens,rbdims, &
610	!$OMP& ndomain,outid,chunksize,istop,l_valid,nthreads,inncids,rebuild_dims, &
611	!$OMP& globaldata_1d_i2,globaldata_1d_i4,globaldata_1d_sp,globaldata_1d_dp, &
612	!$OMP& globaldata_2d_i2,globaldata_2d_i4,globaldata_2d_sp,globaldata_2d_dp, &
613	!$OMP& globaldata_3d_i2,globaldata_3d_i4,globaldata_3d_sp,globaldata_3d_dp, &
614	!$OMP& globaldata_4d_i2,globaldata_4d_i4,globaldata_4d_sp,globaldata_4d_dp, &
615	!$OMP& globaldata_1d_i1,globaldata_2d_i1,globaldata_3d_i1,globaldata_4d_i1, &
616	!$OMP& ntchunk,nt,nmax_unlimited)
617
618	DO ifile = 1, ndomain
619
620	ncid = inncids(ifile)
621	!$OMP CRITICAL
622	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_size_local', local_sizes ), istop )
623	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_position_first', start_pos ), istop )
624	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_halo_size_start', halo_start ), istop )
625	CALL check_nf90( nf90_get_att( ncid, nf90_global, 'DOMAIN_halo_size_end', halo_end ), istop )
626	CALL check_nf90( nf90_inquire_variable( ncid, jv, varname, xtype, ndims, dimids, natts ), istop )
627	CALL check_nf90( nf90_inquire( ncid, unlimitedDimId = unlimitedDimId ), istop )
628	!$OMP END CRITICAL
629
630	! set defaults for rebuilding so that i is 1st, j 2nd
631	di=1
632	dj=2
633
634	IF( rbdims == 1 ) THEN
635	! override defaults above and set other variables
636	start_pos(2) = 1
637	local_sizes(2) = outdimlens(3-dimids(2))
638	halo_end(2) = 0
639	halo_start(2) = 0
640	di=rebuild_dims(1)
641	dj=3-di
642	ENDIF
643
644	!3.3.1 Generate local domain interior sizes from local_sizes and halo sizes
645	! idomain defines the 1st and last interior points in the i direction and
646	! jdomain defines the 1st and last interior points in the j direction
647
648	idomain(1) = 1 + halo_start(di)
649	idomain(2) = local_sizes(di) - halo_end(di)
650	jdomain(1) = 1 + halo_start(dj)
651	jdomain(2) = local_sizes(dj) - halo_end(dj)
652
653	!3.3.2 For rbdims or more dimensions put the data array from this input file into the correct
654	! part of the output data array. Assume the first dimensions are those to be rebuilt.
655
656	IF( ndims == 1 ) THEN
657
658	IF( rebuild_dims(1) == 1 ) THEN
659	dr = di
660	rdomain = idomain
661	ELSE
662	dr = dj
663	rdomain = jdomain
664	ENDIF
665
666	SELECT CASE( xtype )
667	CASE( NF90_BYTE )
668	ALLOCATE(localdata_1d_i1(local_sizes(dr)))
669	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_i1 ), istop )
670	DO jr = rdomain(1), rdomain(2)
671	globaldata_1d_i1(start_pos(dr) + jr - 1) = localdata_1d_i1(jr)
672	END DO
673	DEALLOCATE(localdata_1d_i1)
674	CASE( NF90_SHORT )
675	ALLOCATE(localdata_1d_i2(local_sizes(dr)))
676	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_i2 ), istop )
677	DO jr = rdomain(1), rdomain(2)
678	globaldata_1d_i2(start_pos(dr) + jr - 1) = localdata_1d_i2(jr)
679	END DO
680	DEALLOCATE(localdata_1d_i2)
681	CASE( NF90_INT )
682	ALLOCATE(localdata_1d_i4(local_sizes(dr)))
683	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_i4 ), istop )
684	DO jr = rdomain(1), rdomain(2)
685	globaldata_1d_i4(start_pos(dr) + jr - 1) = localdata_1d_i4(jr)
686	END DO
687	DEALLOCATE(localdata_1d_i4)
688	CASE( NF90_FLOAT )
689	ALLOCATE(localdata_1d_sp(local_sizes(dr)))
690	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_sp ), istop )
691	DO jr = rdomain(1), rdomain(2)
692	globaldata_1d_sp(start_pos(dr) + jr - 1) = localdata_1d_sp(jr)
693	END DO
694	DEALLOCATE(localdata_1d_sp)
695	CASE( NF90_DOUBLE )
696	ALLOCATE(localdata_1d_dp(local_sizes(dr)))
697	CALL check_nf90( nf90_get_var( ncid, jv, localdata_1d_dp ), istop )
698	DO jr = rdomain(1), rdomain(2)
699	globaldata_1d_dp(start_pos(dr) + jr - 1) = localdata_1d_dp(jr)
700	END DO
701	DEALLOCATE(localdata_1d_dp)
702	CASE DEFAULT
703	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
704	istop = istop + 1
705	END SELECT
706
707	ELSEIF( ndims == 2 ) THEN
708
709	SELECT CASE( xtype )
710	CASE( NF90_BYTE )
711	ALLOCATE(localdata_2d_i1(local_sizes(di),local_sizes(dj)))
712	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_i1 ), istop )
713	DO jj = jdomain(1), jdomain(2)
714	DO ji = idomain(1), idomain(2)
715	globaldata_2d_i1(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_i1(ji,jj)
716	END DO
717	END DO
718	DEALLOCATE(localdata_2d_i1)
719	CASE( NF90_SHORT )
720	ALLOCATE(localdata_2d_i2(local_sizes(di),local_sizes(dj)))
721	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_i2 ), istop )
722	DO jj = jdomain(1), jdomain(2)
723	DO ji = idomain(1), idomain(2)
724	globaldata_2d_i2(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_i2(ji,jj)
725	END DO
726	END DO
727	DEALLOCATE(localdata_2d_i2)
728	CASE( NF90_INT )
729	ALLOCATE(localdata_2d_i4(local_sizes(di),local_sizes(dj)))
730	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_i4 ), istop )
731	DO jj = jdomain(1), jdomain(2)
732	DO ji = idomain(1), idomain(2)
733	globaldata_2d_i4(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_i4(ji,jj)
734	END DO
735	END DO
736	DEALLOCATE(localdata_2d_i4)
737	CASE( NF90_FLOAT )
738	ALLOCATE(localdata_2d_sp(local_sizes(di),local_sizes(dj)))
739	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_sp ), istop )
740	DO jj = jdomain(1), jdomain(2)
741	DO ji = idomain(1), idomain(2)
742	globaldata_2d_sp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_sp(ji,jj)
743	END DO
744	END DO
745	DEALLOCATE(localdata_2d_sp)
746	CASE( NF90_DOUBLE )
747	ALLOCATE(localdata_2d_dp(local_sizes(di),local_sizes(dj)))
748	CALL check_nf90( nf90_get_var( ncid, jv, localdata_2d_dp ), istop )
749	DO jj = jdomain(1), jdomain(2)
750	DO ji = idomain(1), idomain(2)
751	globaldata_2d_dp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1) = localdata_2d_dp(ji,jj)
752	END DO
753	END DO
754	DEALLOCATE(localdata_2d_dp)
755	CASE DEFAULT
756	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
757	istop = istop + 1
758	END SELECT
759
760	ELSEIF( ndims == 3 ) THEN
761
762	SELECT CASE( xtype )
763	CASE( NF90_BYTE )
764	ALLOCATE(localdata_3d_i1(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
765	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_i1 ), istop )
766	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
767	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_i1,localdata_3d_i1,di,dj)
768	DO jk = 1, indimlens(dimids(3))
769	DO jj = jdomain(1), jdomain(2)
770	DO ji = idomain(1), idomain(2)
771	globaldata_3d_i1(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_i1(ji,jj,jk)
772	END DO
773	END DO
774	END DO
775	!$OMP END PARALLEL DO
776	DEALLOCATE(localdata_3d_i1)
777	CASE( NF90_SHORT )
778	ALLOCATE(localdata_3d_i2(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
779	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_i2 ), istop )
780	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
781	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_i2,localdata_3d_i2,di,dj)
782	DO jk = 1, indimlens(dimids(3))
783	DO jj = jdomain(1), jdomain(2)
784	DO ji = idomain(1), idomain(2)
785	globaldata_3d_i2(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_i2(ji,jj,jk)
786	END DO
787	END DO
788	END DO
789	!$OMP END PARALLEL DO
790	DEALLOCATE(localdata_3d_i2)
791	CASE( NF90_INT )
792	ALLOCATE(localdata_3d_i4(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
793	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_i4 ), istop )
794	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
795	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_i4,localdata_3d_i4,di,dj)
796	DO jk = 1, indimlens(dimids(3))
797	DO jj = jdomain(1), jdomain(2)
798	DO ji = idomain(1), idomain(2)
799	globaldata_3d_i4(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_i4(ji,jj,jk)
800	END DO
801	END DO
802	END DO
803	!$OMP END PARALLEL DO
804	DEALLOCATE(localdata_3d_i4)
805	CASE( NF90_FLOAT )
806	ALLOCATE(localdata_3d_sp(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
807	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_sp ), istop )
808	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
809	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_sp,localdata_3d_sp,di,dj)
810	DO jk = 1, indimlens(dimids(3))
811	DO jj = jdomain(1), jdomain(2)
812	DO ji = idomain(1), idomain(2)
813	globaldata_3d_sp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_sp(ji,jj,jk)
814	END DO
815	END DO
816	END DO
817	!$OMP END PARALLEL DO
818	DEALLOCATE(localdata_3d_sp)
819	CASE( NF90_DOUBLE )
820	ALLOCATE(localdata_3d_dp(local_sizes(di),local_sizes(dj),indimlens(dimids(3))))
821	CALL check_nf90( nf90_get_var( ncid, jv, localdata_3d_dp ), istop )
822	!$OMP PARALLEL DO DEFAULT(NONE) PRIVATE(ji,jj,jk) &
823	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_3d_dp,localdata_3d_dp,di,dj)
824	DO jk = 1, indimlens(dimids(3))
825	DO jj = jdomain(1), jdomain(2)
826	DO ji = idomain(1), idomain(2)
827	globaldata_3d_dp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk) = localdata_3d_dp(ji,jj,jk)
828	END DO
829	END DO
830	END DO
831	!$OMP END PARALLEL DO
832	DEALLOCATE(localdata_3d_dp)
833	CASE DEFAULT
834	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
835	istop = istop + 1
836	END SELECT
837
838	ELSEIF (ndims == 4) THEN
839
840	SELECT CASE( xtype )
841	CASE( NF90_BYTE )
842	ALLOCATE(localdata_4d_i1(local_sizes(di),local_sizes(dj), &
843	& indimlens(dimids(3)),ntchunk))
844	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i1, start=(/1,1,1,nt/) ), istop )
845	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
846	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i1,localdata_4d_i1,di,dj,nt,ntchunk)
847	DO jl = 1, ntchunk
848	!$OMP DO
849	DO jk = 1, indimlens(dimids(3))
850	DO jj = jdomain(1), jdomain(2)
851	DO ji = idomain(1), idomain(2)
852	globaldata_4d_i1(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_i1(ji,jj,jk,jl)
853	END DO
854	END DO
855	END DO
856	!$OMP END DO nowait
857	END DO
858	!$OMP END PARALLEL
859	DEALLOCATE(localdata_4d_i1)
860	CASE( NF90_SHORT )
861	ALLOCATE(localdata_4d_i2(local_sizes(di),local_sizes(dj), &
862	& indimlens(dimids(3)),ntchunk))
863	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i2, start=(/1,1,1,nt/) ), istop )
864	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
865	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i2,localdata_4d_i2,di,dj,nt,ntchunk)
866	DO jl = 1, ntchunk
867	!$OMP DO
868	DO jk = 1, indimlens(dimids(3))
869	DO jj = jdomain(1), jdomain(2)
870	DO ji = idomain(1), idomain(2)
871	globaldata_4d_i2(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_i2(ji,jj,jk,jl)
872	END DO
873	END DO
874	END DO
875	!$OMP END DO nowait
876	END DO
877	!$OMP END PARALLEL
878	DEALLOCATE(localdata_4d_i2)
879	CASE( NF90_INT )
880	ALLOCATE(localdata_4d_i4(local_sizes(di),local_sizes(dj), &
881	& indimlens(dimids(3)),ntchunk))
882	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i4, start=(/1,1,1,nt/) ), istop )
883	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
884	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i4,localdata_4d_i4,di,dj,nt,ntchunk)
885	DO jl = 1, ntchunk
886	!$OMP DO
887	DO jk = 1, indimlens(dimids(3))
888	DO jj = jdomain(1), jdomain(2)
889	DO ji = idomain(1), idomain(2)
890	globaldata_4d_i4(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_i4(ji,jj,jk,jl)
891	END DO
892	END DO
893	END DO
894	!$OMP END DO nowait
895	END DO
896	!$OMP END PARALLEL
897	DEALLOCATE(localdata_4d_i4)
898	CASE( NF90_FLOAT )
899	ALLOCATE(localdata_4d_sp(local_sizes(di),local_sizes(dj), &
900	& indimlens(dimids(3)),ntchunk))
901	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_sp, start=(/1,1,1,nt/) ), istop )
902	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
903	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_sp,localdata_4d_sp,di,dj,nt,ntchunk)
904	DO jl = 1, ntchunk
905	!$OMP DO
906	DO jk = 1, indimlens(dimids(3))
907	DO jj = jdomain(1), jdomain(2)
908	DO ji = idomain(1), idomain(2)
909	globaldata_4d_sp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_sp(ji,jj,jk,jl)
910	END DO
911	END DO
912	END DO
913	!$OMP END DO nowait
914	END DO
915	!$OMP END PARALLEL
916	DEALLOCATE(localdata_4d_sp)
917	CASE( NF90_DOUBLE )
918	ALLOCATE(localdata_4d_dp(local_sizes(di),local_sizes(dj), &
919	& indimlens(dimids(3)),ntchunk))
920	CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_dp, start=(/1,1,1,nt/) ), istop )
921	!$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) &
922	!$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_dp,localdata_4d_dp,di,dj,nt,ntchunk)
923	DO jl = 1, ntchunk
924	!$OMP DO
925	DO jk = 1, indimlens(dimids(3))
926	DO jj = jdomain(1), jdomain(2)
927	DO ji = idomain(1), idomain(2)
928	globaldata_4d_dp(start_pos(di) + ji - 1, start_pos(dj) + jj - 1, jk, jl) = localdata_4d_dp(ji,jj,jk,jl)
929	END DO
930	END DO
931	END DO
932	!$OMP END DO nowait
933	END DO
934	!$OMP END PARALLEL
935	DEALLOCATE(localdata_4d_dp)
936	CASE DEFAULT
937	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
938	istop = istop + 1
939	END SELECT
940
941	ENDIF ! l_noRebuild false
942
943	!3.4 Work out if the valid_min and valid_max attributes exist for this variable.
944	! If they do then calculate the extrema over all input files.
945
946	DO attid = 1, natts
947	CALL check_nf90( nf90_inq_attname( ncid, jv, attid, attname ), istop )
948	IF( INDEX( attname, "valid_min" ) == 1 ) THEN
949	CALL check_nf90( nf90_get_att( ncid, jv, attname, InMin), istop )
950	l_valid = .true.
951	ENDIF
952	IF( INDEX( attname, "valid_max" ) == 1 ) THEN
953	CALL check_nf90( nf90_get_att( ncid, jv, attname, InMax ), istop )
954	l_valid = .true.
955	ENDIF
956	END DO
957
958	IF (l_valid) THEN
959	!$OMP CRITICAL
960	IF( InMin < ValMin ) ValMin = InMin
961	IF( InMax > ValMax ) ValMax = InMax
962	!$OMP END CRITICAL
963	ENDIF
964
965	!3.5 Abort if failure and only 1 thread
966
967	IF( nthreads == 1 .AND. istop /= nf90_noerr ) THEN
968	WRITE(numerr,) ' NEMO rebuild failed! *'
969	STOP
970	ENDIF
971
972	END DO ! loop over files
973	!$OMP END PARALLEL DO
974
975	!3.6 Abort if any of the OMP threads failed
976	IF( istop /= nf90_noerr ) THEN
977	WRITE(numerr,) ' NEMO rebuild failed! *'
978	STOP
979	ENDIF
980
981	ENDIF ! ndims > 2
982
983	!---------------------------------------------------------------------------
984	!4. Write data to output file
985
986	IF (l_verbose) WRITE(numout,*) 'Writing variable '//TRIM(varname)//'...'
987
988	!4.1 If the valid min and max attributes exist then update them in the file
989
990	IF( l_valid ) THEN
991	CALL check_nf90( nf90_put_att( outid, jv, "valid_min", ValMin ) )
992	CALL check_nf90( nf90_put_att( outid, jv, "valid_max", ValMax ) )
993	ENDIF
994
995	!4.2 Write the data to the output file depending on how many dimensions it has
996
997	IF( ndims == 0 ) THEN
998
999	SELECT CASE( xtype )
1000	CASE( NF90_BYTE )
1001	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_i1 ) )
1002	CASE( NF90_SHORT )
1003	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_i2 ) )
1004	CASE( NF90_INT )
1005	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_i4 ) )
1006	CASE( NF90_FLOAT )
1007	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_sp ) )
1008	CASE( NF90_DOUBLE )
1009	CALL check_nf90( nf90_put_var( outid, jv, globaldata_0d_dp ) )
1010	END SELECT
1011
1012	ELSEIF( ndims == 1 ) THEN
1013
1014	SELECT CASE( xtype )
1015	CASE( NF90_BYTE )
1016	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_i1 ) )
1017	DEALLOCATE(globaldata_1d_i1)
1018	CASE( NF90_SHORT )
1019	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_i2 ) )
1020	DEALLOCATE(globaldata_1d_i2)
1021	CASE( NF90_INT )
1022	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_i4 ) )
1023	DEALLOCATE(globaldata_1d_i4)
1024	CASE( NF90_FLOAT )
1025	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_sp ) )
1026	DEALLOCATE(globaldata_1d_sp)
1027	CASE( NF90_DOUBLE )
1028	CALL check_nf90( nf90_put_var( outid, jv, globaldata_1d_dp ) )
1029	DEALLOCATE(globaldata_1d_dp)
1030	END SELECT
1031
1032	ELSEIF( ndims == 2 ) THEN
1033
1034	SELECT CASE( xtype )
1035	CASE( NF90_BYTE )
1036	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_i1 ) )
1037	DEALLOCATE(globaldata_2d_i1)
1038	CASE( NF90_SHORT )
1039	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_i2 ) )
1040	DEALLOCATE(globaldata_2d_i2)
1041	CASE( NF90_INT )
1042	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_i4 ) )
1043	DEALLOCATE(globaldata_2d_i4)
1044	CASE( NF90_FLOAT )
1045	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_sp ) )
1046	DEALLOCATE(globaldata_2d_sp)
1047	CASE( NF90_DOUBLE )
1048	CALL check_nf90( nf90_put_var( outid, jv, globaldata_2d_dp ) )
1049	DEALLOCATE(globaldata_2d_dp)
1050	CASE DEFAULT
1051	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1052	STOP
1053	END SELECT
1054
1055	ELSEIF( ndims == 3 ) THEN
1056
1057	SELECT CASE( xtype )
1058	CASE( NF90_BYTE )
1059	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_i1 ) )
1060	DEALLOCATE(globaldata_3d_i1)
1061	CASE( NF90_SHORT )
1062	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_i2 ) )
1063	DEALLOCATE(globaldata_3d_i2)
1064	CASE( NF90_INT )
1065	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_i4 ) )
1066	DEALLOCATE(globaldata_3d_i4)
1067	CASE( NF90_FLOAT )
1068	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_sp ) )
1069	DEALLOCATE(globaldata_3d_sp)
1070	CASE( NF90_DOUBLE )
1071	CALL check_nf90( nf90_put_var( outid, jv, globaldata_3d_dp ) )
1072	DEALLOCATE(globaldata_3d_dp)
1073	CASE DEFAULT
1074	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1075	STOP
1076	END SELECT
1077
1078	ELSEIF( ndims == 4 ) THEN
1079
1080	SELECT CASE( xtype )
1081	CASE( NF90_BYTE )
1082	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i1, start=(/1,1,1,nt/) ) )
1083	DEALLOCATE(globaldata_4d_i1)
1084	CASE( NF90_SHORT )
1085	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i2, start=(/1,1,1,nt/) ) )
1086	DEALLOCATE(globaldata_4d_i2)
1087	CASE( NF90_INT )
1088	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i4, start=(/1,1,1,nt/) ) )
1089	DEALLOCATE(globaldata_4d_i4)
1090	CASE( NF90_FLOAT )
1091	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_sp, start=(/1,1,1,nt/) ) )
1092	DEALLOCATE(globaldata_4d_sp)
1093	CASE( NF90_DOUBLE )
1094	CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_dp, start=(/1,1,1,nt/) ) )
1095	DEALLOCATE(globaldata_4d_dp)
1096	CASE DEFAULT
1097	WRITE(numerr,*) 'Unknown nf90 type: ', xtype
1098	STOP
1099	END SELECT
1100
1101	ENDIF
1102
1103	nt = nt + ntchunk
1104
1105	END DO ! WHILE loop
1106
1107	END DO ! loop over variables
1108
1109	!---------------------------------------------------------------------------
1110	!5. Close files
1111
1112	!5.1 Close input files
1113
1114	IF (l_verbose) WRITE(numout,*) 'Closing input files...'
1115	DO ifile = 1, ndomain
1116	ncid = inncids(ifile)
1117	CALL check_nf90( nf90_close( ncid ) )
1118	END DO
1119
1120	!5.2 Close output file
1121
1122	IF (l_verbose) WRITE(numout,*) 'Closing output file...'
1123	CALL check_nf90( nf90_close( outid ) )
1124
1125	IF (l_verbose) WRITE(numout,*) 'NEMO rebuild completed successfully'
1126	IF (l_verbose) WRITE(numout,*)
1127
1128	CONTAINS
1129
1130
1131	SUBROUTINE check_nf90(status, errorFlag)
1132	!---------------------------------------------------------------------
1133	! Checks return code from nf90 library calls and warns if needed
1134	! If errorFlag is present then it just increments this flag (OMP use)
1135	!
1136	!---------------------------------------------------------------------
1137	INTEGER, INTENT(IN ) :: status
1138	INTEGER, INTENT(INOUT), OPTIONAL :: errorFlag
1139	!---------------------------------------------------------------------
1140
1141	IF( status /= nf90_noerr ) THEN
1142	WRITE(numerr,*) 'ERROR! : '//TRIM(nf90_strerror(status))
1143	IF( PRESENT( errorFlag ) ) THEN
1144	errorFlag = errorFlag + status
1145	ELSE
1146	WRITE(numerr,) " NEMO rebuild failed *"
1147	WRITE(numerr,*)
1148	STOP
1149	ENDIF
1150	ENDIF
1151
1152	END SUBROUTINE check_nf90
1153
1154
1155	END PROGRAM rebuild_nemo

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