-
Notifications
You must be signed in to change notification settings - Fork 139
/
Copy pathmpp_io.F90
1134 lines (1079 loc) · 47.3 KB
/
mpp_io.F90
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
!***********************************************************************
!* GNU Lesser General Public License
!*
!* This file is part of the GFDL Flexible Modeling System (FMS).
!*
!* FMS is free software: you can redistribute it and/or modify it under
!* the terms of the GNU Lesser General Public License as published by
!* the Free Software Foundation, either version 3 of the License, or (at
!* your option) any later version.
!*
!* FMS is distributed in the hope that it will be useful, but WITHOUT
!* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
!* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
!* for more details.
!*
!* You should have received a copy of the GNU Lesser General Public
!* License along with FMS. If not, see <http://www.gnu.org/licenses/>.
!***********************************************************************
!-----------------------------------------------------------------------
! Parallel I/O for message-passing codes
!
! AUTHOR: V. Balaji (vb@gfdl.gov)
! SGI/GFDL Princeton University
!
!-----------------------------------------------------------------------
!> @defgroup mpp_io_mod mpp_io_mod
!> @ingroup mpp
!> @brief a set of simple calls for parallel I/O on
!! distributed systems. It is geared toward the writing of data in netCDF
!! format
!> @author V. Balaji <"vb@gfdl.noaa.gov">
!!
!> In massively parallel environments, an often difficult problem is
!! the reading and writing of data to files on disk. MPI-IO and MPI-2 IO
!! are moving toward providing this capability, but are currently not
!! widely implemented. Further, it is a rather abstruse
!! API. @ref mpp_io_mod is an attempt at a simple API encompassing a
!! certain variety of the I/O tasks that will be required. It does not
!! attempt to be an all-encompassing standard such as MPI, however, it
!! can be implemented in MPI if so desired. It is equally simple to add
!! parallel I/O capability to @ref mpp_io_mod based on vendor-specific
!! APIs while providing a layer of insulation for user codes.
!!
!! The @ref mpp_io_mod parallel I/O API built on top of the <LINK
!! SRC="mpp_domains.html">mpp_domains_mod</LINK> and <LINK
!! SRC="mpp.html">mpp_mod</LINK> API for domain decomposition and
!! message passing. Features of @ref mpp_io_mod include:
!!
!! 1) Simple, minimal API, with free access to underlying API for more
!! complicated stuff.<BR/>
!! 2) Self-describing files: comprehensive header information
!! (metadata) in the file itself.<BR/>
!! 3) Strong focus on performance of parallel write: the climate models
!! for which it is designed typically read a minimal amount of data
!! (typically at the beginning of the run); but on the other hand, tend
!! to write copious amounts of data during the run. An interface for
!! reading is also supplied, but its performance has not yet been optimized.<BR/>
!! 4) Integrated netCDF capability: <LINK SRC
!! ="http://www.unidata.ucar.edu/packages/netcdf/">netCDF</LINK> is a
!! data format widely used in the climate/weather modeling
!! community. netCDF is considered the principal medium of data storage
!! for @ref mpp_io_mod. But I provide a raw unformatted
!! fortran I/O capability in case netCDF is not an option, either due to
!! unavailability, inappropriateness, or poor performance.<BR/>
!! 5) May require off-line post-processing: a tool for this purpose,
!! <TT>mppnccombine</TT>, is available. GFDL users may use
!! <TT>~hnv/pub/mppnccombine</TT>. Outside users may obtain the
!! source <LINK SRC
!! ="ftp://ftp.gfdl.gov/perm/hnv/mpp/mppnccombine.c">here</LINK>. It
!! can be compiled on any C compiler and linked with the netCDF
!! library. The program is free and is covered by the <LINK SRC
!! ="ftp://ftp.gfdl.gov/perm/hnv/mpp/LICENSE">GPL license</LINK>.
!!
!! The internal representation of the data being written out is
!! assumed be the default real type, which can be 4 or 8-byte. Time data
!! is always written as 8-bytes to avoid overflow on climatic time scales
!! in units of seconds.
!!
!! <LINK SRC="modes"></LINK><H4>I/O modes in @ref mpp_io_mod</H4>
!!
!! The I/O activity critical to performance in the models for which
!! @ref mpp_io_mod is designed is typically the writing of large
!! datasets on a model grid volume produced at intervals during
!! a run. Consider a 3D grid volume, where model arrays are stored as
!! <TT>(i,j,k)</TT>. The domain decomposition is typically along
!! <TT>i</TT> or <TT>j</TT>: thus to store data to disk as a global
!! volume, the distributed chunks of data have to be seen as
!! non-contiguous. If we attempt to have all PEs write this data into a
!! single file, performance can be seriously compromised because of the
!! data reordering that will be required. Possible options are to have
!! one PE acquire all the data and write it out, or to have all the PEs
!! write independent files, which are recombined offline. These three
!! modes of operation are described in the @ref mpp_io_mod terminology
!! in terms of two parameters, <I>threading</I> and <I>fileset</I>,
!! as follows:
!!
!! <I>Single-threaded I/O:</I> a single PE acquires all the data
!! and writes it out.<BR/>
!! <I>Multi-threaded, single-fileset I/O:</I> many PEs write to a
!! single file.<BR/>
!! <I>Multi-threaded, multi-fileset I/O:</I> many PEs write to
!! independent files. This is also called <I>distributed I/O</I>.
!!
!! The middle option is the most difficult to achieve performance. The
!! choice of one of these modes is made when a file is opened for I/O, in
!! <LINK SRC="#mpp_open">mpp_open</LINK>.
!!
!! <LINK name="metadata"></LINK><H4>Metadata in @ref mpp_io_mod</H4>
!!
!! A requirement of the design of @ref mpp_io_mod is that the file must
!! be entirely self-describing: comprehensive header information
!! describing its contents is present in the header of every file. The
!! header information follows the model of netCDF. Variables in the file
!! are divided into <I>axes</I> and <I>fields</I>. An axis describes a
!! co-ordinate variable, e.g <TT>x,y,z,t</TT>. A field consists of data in
!! the space described by the axes. An axis is described in
!! @ref mpp_io_mod using the defined type <TT>axistype</TT>:
!!
!! <PRE>
!! type, public :: axistype
!! sequence
!! character(len=128) :: name
!! character(len=128) :: units
!! character(len=256) :: longname
!! character(len=8) :: cartesian
!! integer :: len
!! integer :: sense !+/-1, depth or height?
!! type(domain1D), pointer :: domain
!! real, dimension(:), pointer :: data
!! integer :: id, did
!! integer :: type ! external NetCDF type format for axis data
!! integer :: natt
!! type(atttype), pointer :: Att(:) ! axis attributes
!! end type axistype
!! </PRE>
!!
!! A field is described using the type <TT>fieldtype</TT>:
!!
!! <PRE>
!! type, public :: fieldtype
!! sequence
!! character(len=128) :: name
!! character(len=128) :: units
!! character(len=256) :: longname
!! real :: min, max, missing, fill, scale, add
!! integer :: pack
!! type(axistype), dimension(:), pointer :: axes
!! integer, dimension(:), pointer :: size
!! integer :: time_axis_index
!! integer :: id
!! integer :: type ! external NetCDF format for field data
!! integer :: natt, ndim
!! type(atttype), pointer :: Att(:) ! field metadata
!! end type fieldtype
!! </PRE>
!!
!! An attribute (global, field or axis) is described using the <TT>atttype</TT>:
!!
!! <PRE>
!! type, public :: atttype
!! sequence
!! integer :: type, len
!! character(len=128) :: name
!! character(len=256) :: catt
!! real(r4_kind), pointer :: fatt(:)
!! end type atttype
!! </PRE>
!!
!! <LINK name="packing"></LINK>This default set of field attributes corresponds
!! closely to various conventions established for netCDF files. The
!! <TT>pack</TT> attribute of a field defines whether or not a
!! field is to be packed on output. Allowed values of
!! <TT>pack</TT> are 1,2,4 and 8. The value of
!! <TT>pack</TT> is the number of variables written into 8
!! bytes. In typical use, we write 4-byte reals to netCDF output; thus
!! the default value of <TT>pack</TT> is 2. For
!! <TT>pack</TT> = 4 or 8, packing uses a simple-minded linear
!! scaling scheme using the <TT>scale</TT> and <TT>add</TT>
!! attributes. There is thus likely to be a significant loss of dynamic
!! range with packing. When a field is declared to be packed, the
!! <TT>missing</TT> and <TT>fill</TT> attributes, if
!! supplied, are packed also.
!!
!! Please note that the pack values are the same even if the default
!! real is 4 bytes, i.e <TT>PACK=1</TT> still follows the definition
!! above and writes out 8 bytes.
!!
!! A set of <I>attributes</I> for each variable is also available. The
!! variable definitions and attribute information is written/read by calling
!! <LINK SRC="#mpp_write_meta">mpp_write_meta</LINK> or <LINK SRC="#mpp_read_meta">mpp_read_meta</LINK>. A typical
!! calling sequence for writing data might be:
!!
!! <PRE>
!! ...
!! type(domain2D), dimension(:), allocatable, target :: domain
!! type(fieldtype) :: field
!! type(axistype) :: x, y, z, t
!! ...
!! call mpp_define_domains( (/1,nx,1,ny/), domain )
!! allocate( a(domain(pe)%x%data%start_index:domain(pe)%x%data%end_index, &
!! domain(pe)%y%data%start_index:domain(pe)%y%data%end_index,nz) )
!! ...
!! call mpp_write_meta( unit, x, 'X', 'km', 'X distance', &
!! domain=domain(pe)%x, data=(/(float(i),i=1,nx)/) )
!! call mpp_write_meta( unit, y, 'Y', 'km', 'Y distance', &
!! domain=domain(pe)%y, data=(/(float(i),i=1,ny)/) )
!! call mpp_write_meta( unit, z, 'Z', 'km', 'Z distance', &
!! data=(/(float(i),i=1,nz)/) )
!! call mpp_write_meta( unit, t, 'Time', 'second', 'Time' )
!!
!! call mpp_write_meta( unit, field, (/x,y,z,t/), 'a', '(m/s)', AAA', &
!! missing=-1e36 )
!! ...
!! call mpp_write( unit, x )
!! call mpp_write( unit, y )
!! call mpp_write( unit, z )
!! ...
!! </PRE>
!!
!! In this example, <TT>x</TT> and <TT>y</TT> have been
!! declared as distributed axes, since a domain decomposition has been
!! associated. <TT>z</TT> and <TT>t</TT> are undistributed
!! axes. <TT>t</TT> is known to be a <I>record</I> axis (netCDF
!! terminology) since we do not allocate the <TT>data</TT> element
!! of the <TT>axistype</TT>. <I>Only one record axis may be
!! associated with a file.</I> The call to <LINK
!! SRC="#mpp_write_meta">mpp_write_meta</LINK> initializes
!! the axes, and associates a unique variable ID with each axis. The call
!! to <TT>mpp_write_meta</TT> with argument <TT>field</TT>
!! declared <TT>field</TT> to be a 4D variable that is a function
!! of <TT>(x,y,z,t)</TT>, and a unique variable ID is associated
!! with it. A 3D field will be written at each call to
!! <TT>mpp_write(field)</TT>.
!!
!! The data to any variable, including axes, is written by
!! <TT>mpp_write</TT>.
!!
!! Any additional attributes of variables can be added through
!! subsequent <TT>mpp_write_meta</TT> calls, using the variable ID as a
!! handle. <I>Global</I> attributes, associated with the dataset as a
!! whole, can also be written thus. See the <LINK
!! SRC="#mpp_write_meta">mpp_write_meta</LINK> call syntax below
!! for further details.
!!
!! You cannot interleave calls to <TT>mpp_write</TT> and
!! <TT>mpp_write_meta</TT>: the first call to
!! <TT>mpp_write</TT> implies that metadata specification is
!! complete.
!!
!! A typical calling sequence for reading data might be:
!!
!! <PRE>
!! ...
!! integer :: unit, natt, nvar, ntime
!! type(domain2D), dimension(:), allocatable, target :: domain
!! type(fieldtype), allocatable, dimension(:) :: fields
!! type(atttype), allocatable, dimension(:) :: global_atts
!! real, allocatable, dimension(:) :: times
!! ...
!! call mpp_define_domains( (/1,nx,1,ny/), domain )
!!
!! call mpp_read_meta(unit)
!! call mpp_get_info(unit,natt,nvar,ntime)
!! allocate(global_atts(natt))
!! call mpp_get_atts(unit,global_atts)
!! allocate(fields(nvar))
!! call mpp_get_vars(unit, fields)
!! allocate(times(ntime))
!! call mpp_get_times(unit, times)
!!
!! allocate( a(domain(pe)%x%data%start_index:domain(pe)%x%data%end_index, &
!! domain(pe)%y%data%start_index:domain(pe)%y%data%end_index,nz) )
!! ...
!! do i=1, nvar
!! if (fields(i)%name == 'a') call mpp_read(unit,fields(i),domain(pe), a,
!! tindex)
!! enddo
!! ...
!! </PRE>
!!
!! In this example, the data are distributed as in the previous
!! example. The call to <LINK
!! SRC="#mpp_read_meta">mpp_read_meta</LINK> initializes
!! all of the metadata associated with the file, including global
!! attributes, variable attributes and non-record dimension data. The
!! call to <TT>mpp_get_info</TT> returns the number of global
!! attributes (<TT>natt</TT>), variables (<TT>nvar</TT>) and
!! time levels (<TT>ntime</TT>) associated with the file
!! identified by a unique ID (<TT>unit</TT>).
!! <TT>mpp_get_atts</TT> returns all global attributes for
!! the file in the derived type <TT>atttype(natt)</TT>.
!! <TT>mpp_get_vars</TT> returns variable types
!! (<TT>fieldtype(nvar)</TT>). Since the record dimension data are not allocated for calls to
!! <LINK SRC="#mpp_write">mpp_write</LINK>, a separate call to <TT>mpp_get_times</TT> is required to access record
!! dimension data. Subsequent calls to
!! <TT>mpp_read</TT> return the field data arrays corresponding to
!! the fieldtype. The <TT>domain</TT> type is an optional
!! argument. If <TT>domain</TT> is omitted, the incoming field
!! array should be dimensioned for the global domain, otherwise, the
!! field data is assigned to the computational domain of a local array.
!!
!! <I>Multi-fileset</I> reads are not supported with <TT>mpp_read</TT>.
!!
!! </DESCRIPTION>
!! @endhtmlonly
!> @file
!> @brief File for @ref mpp_io_mod
!> @addtogroup mpp_io_mod
!> @{
module mpp_io_mod
#define _MAX_FILE_UNITS 1024
#ifdef use_netCDF
use netcdf
use netcdf_nf_data
use netcdf_nf_interfaces
use netcdf4_nf_interfaces
#endif
use mpp_parameter_mod, only : MPP_WRONLY, MPP_RDONLY, MPP_APPEND, MPP_OVERWR, MPP_ASCII
use mpp_parameter_mod, only : MPP_IEEE32, MPP_NATIVE, MPP_NETCDF, MPP_SEQUENTIAL
use mpp_parameter_mod, only : MPP_DIRECT, MPP_SINGLE, MPP_MULTI, MPP_DELETE, MPP_COLLECT
use mpp_parameter_mod, only : MPP_DEBUG, MPP_VERBOSE, NULLUNIT, NULLTIME, ALL_PES
use mpp_parameter_mod, only : CENTER, EAST, NORTH, CORNER
use mpp_parameter_mod, only : MAX_FILE_SIZE, GLOBAL_ROOT_ONLY, XUPDATE, YUPDATE
use mpp_mod, only : mpp_error, FATAL, WARNING, NOTE, stdin, stdout, stderr, stdlog
use mpp_mod, only : mpp_pe, mpp_root_pe, mpp_npes, lowercase, mpp_transmit, mpp_sync_self
use mpp_mod, only : mpp_init, mpp_sync, mpp_clock_id, mpp_clock_begin, mpp_clock_end
use mpp_mod, only : MPP_CLOCK_SYNC, MPP_CLOCK_DETAILED, CLOCK_ROUTINE
use mpp_mod, only : input_nml_file, mpp_gather, mpp_broadcast
use mpp_mod, only : mpp_send, mpp_recv, mpp_sync_self, EVENT_RECV, COMM_TAG_1
use mpp_domains_mod, only : domain1d, domain2d, NULL_DOMAIN1D, mpp_domains_init
use mpp_domains_mod, only : mpp_get_global_domain, mpp_get_compute_domain
use mpp_domains_mod, only : mpp_get_data_domain, mpp_get_memory_domain, mpp_get_pelist
use mpp_domains_mod, only : mpp_update_domains, mpp_global_field, mpp_domain_is_symmetry
use mpp_domains_mod, only : operator( .NE. ), mpp_get_domain_shift, mpp_get_UG_compute_domains
use mpp_domains_mod, only : mpp_get_io_domain, mpp_domain_is_tile_root_pe, mpp_get_domain_tile_root_pe
use mpp_domains_mod, only : mpp_get_tile_id, mpp_get_tile_npes, mpp_get_io_domain_layout
use mpp_domains_mod, only : mpp_get_domain_name, mpp_get_domain_npes
use mpp_parameter_mod, only : MPP_FILL_DOUBLE,MPP_FILL_INT
use mpp_mod, only : mpp_chksum
!----------
!ug support
use mpp_domains_mod, only: domainUG, &
mpp_get_UG_io_domain, &
mpp_domain_UG_is_tile_root_pe, &
mpp_get_UG_domain_tile_id, &
mpp_get_UG_domain_npes, &
mpp_get_io_domain_UG_layout, &
mpp_get_UG_compute_domain, &
mpp_get_UG_domain_pelist
use platform_mod
!----------
implicit none
private
!--- public parameters -----------------------------------------------
public :: MPP_WRONLY, MPP_RDONLY, MPP_APPEND, MPP_OVERWR, MPP_ASCII, MPP_IEEE32
public :: MPP_NATIVE, MPP_NETCDF, MPP_SEQUENTIAL, MPP_DIRECT, MPP_SINGLE
public :: MPP_MULTI, MPP_DELETE, MPP_COLLECT
public :: FILE_TYPE_USED
public :: MAX_FILE_SIZE
!--- public data type ------------------------------------------------
public :: axistype, atttype, fieldtype, validtype, filetype
!--- public data -----------------------------------------------------
public :: default_field, default_axis, default_att
!--- public interface from mpp_io_util.h ----------------------
public :: mpp_get_id, mpp_get_ncid, mpp_is_valid
public :: mpp_get_info, mpp_get_atts, mpp_get_fields
public :: mpp_get_times, mpp_get_axes, mpp_get_recdimid, mpp_get_axis_data, mpp_get_axis_by_name
public :: mpp_io_set_stack_size, mpp_get_field_index, mpp_get_axis_index
public :: mpp_get_field_name, mpp_get_att_value, mpp_get_att_length
public :: mpp_get_att_type, mpp_get_att_name, mpp_get_att_real, mpp_get_att_char
public :: mpp_get_att_real_scalar, mpp_get_axis_length, mpp_is_dist_ioroot
public :: mpp_get_file_name, mpp_file_is_opened, mpp_attribute_exist
public :: mpp_io_clock_on, mpp_get_time_axis, mpp_get_default_calendar
public :: mpp_get_dimension_length, mpp_get_axis_bounds
!--- public interface from mpp_io_misc.h ----------------------
public :: mpp_io_init, mpp_io_exit, netcdf_err, mpp_flush, mpp_get_maxunits, do_cf_compliance
!--- public interface from mpp_io_write.h ---------------------
public :: mpp_write, mpp_write_meta, mpp_copy_meta, mpp_modify_meta, mpp_write_axis_data, mpp_def_dim
!--- public interface from mpp_io_read.h ---------------------
public :: mpp_read, mpp_read_meta, mpp_get_tavg_info
public :: mpp_read_compressed, mpp_write_compressed, mpp_read_distributed_ascii, mpp_write_unlimited_axis
!--- public interface from mpp_io_switch.h ---------------------
public :: mpp_open, mpp_close
public :: fillin_fieldtype
!-----------------------------------------------------------------------------
!--- mpp_io data types
!-----------------------------------------------------------------------------
integer FILE_TYPE_USED
integer, parameter :: MAX_ATT_LENGTH = 1280
!> @}
!> @ingroup mpp_io_mod
type :: atttype
private
integer :: type, len
character(len=128) :: name
character(len=MAX_ATT_LENGTH) :: catt
real, pointer :: fatt(:) =>NULL() ! just use type conversion for integers
end type atttype
!> @ingroup mpp_io_mod
type :: axistype
private
character(len=128) :: name
character(len=128) :: name_bounds
character(len=128) :: units
character(len=256) :: longname
character(len=8) :: cartesian
character(len=256) :: compressed
character(len=24) :: calendar
integer :: sense, len !+/-1, depth or height?
type(domain1D) :: domain !if pointer is associated, it is a distributed data axis
real, pointer :: data(:) =>NULL() !axis values (not used if time axis)
real, pointer :: data_bounds(:) =>NULL() !axis bounds values
integer, pointer :: idata(:) =>NULL() !compressed axis valuesi
integer :: id, did, type, natt !id is the "variable ID", did is the "dimension ID":
!netCDF requires 2 IDs for axes
integer :: shift !normally is 0. when domain is symmetry, its value maybe 1.
type(atttype), pointer :: Att(:) =>NULL()
end type axistype
!> @ingroup mpp_io_mod
type :: validtype
private
logical :: is_range ! if true, then the data represent the valid range
real :: min,max ! boundaries of the valid range or missing value
end type validtype
!> @ingroup mpp_io_mod
type :: fieldtype
private
character(len=128) :: name
character(len=128) :: units
character(len=256) :: longname
character(len=256) :: standard_name ! CF standard name
real :: min, max, missing, fill, scale, add
integer :: pack
integer(i8_kind), dimension(3) :: checksum
type(axistype), pointer :: axes(:) =>NULL() !axes associated with field size, time_axis_index redundantly
!hold info already contained in axes. it's clunky and inelegant,
!but required so that axes can be shared among multiple files
integer, pointer :: size(:) =>NULL()
integer :: time_axis_index
integer :: id, type, natt, ndim
type(atttype), pointer :: Att(:) =>NULL()
integer :: position ! indicate the location of the data ( CENTER, NORTH, EAST, CORNER )
end type fieldtype
!> @ingroup mpp_io_mod
type :: filetype
private
character(len=256) :: name
integer :: action, format, access, threading, fileset, record, ncid
logical :: opened, initialized, nohdrs
integer :: time_level
real(r8_kind) :: time
logical :: valid
logical :: write_on_this_pe ! indicate if will write out from this pe
logical :: read_on_this_pe ! indicate if will read from this pe
logical :: io_domain_exist ! indicate if io_domain exist or not.
integer :: id !variable ID of time axis associated with file (only one time axis per file)
integer :: recdimid !dim ID of time axis associated with file (only one time axis per file)
real(r8_kind), pointer :: time_values(:) =>NULL() ! time axis values are stored here instead of axis%data
! since mpp_write assumes these values are not time values.
! Not used in mpp_write
! additional elements of filetype for mpp_read (ignored for mpp_write)
integer :: ndim, nvar, natt ! number of dimensions, non-dimension variables and global attributes
! redundant axis types stored here and in associated fieldtype
! some axes are not used by any fields, i.e. "edges"
type(axistype), pointer :: axis(:) =>NULL()
type(fieldtype), pointer :: var(:) =>NULL()
type(atttype), pointer :: att(:) =>NULL()
type(domain2d), pointer :: domain =>NULL()
!----------
!ug support
type(domainUG),pointer :: domain_ug => null() !Is this actually pointed to?
!----------
end type filetype
!> @addtogroup mpp_io_mod
!> @{
!***********************************************************************
!
! public interface from mpp_io_util.h
!
!***********************************************************************
interface mpp_get_id
module procedure mpp_get_axis_id
module procedure mpp_get_field_id
end interface
! <INTERFACE NAME="mpp_get_atts">
! <OVERVIEW>
! Get file global metdata.
! </OVERVIEW>
! <DESCRIPTION>
! Get file global metdata.
! </DESCRIPTION>
! <TEMPLATE>
! call mpp_get_atts( unit, global_atts)
! </TEMPLATE>
! <IN NAME="unit"></IN>
! <IN NAME="global_atts"></IN>
! </INTERFACE>
!> @brief Get file global metadata.
!!
!> <br>Example usage:
!! call mpp_get_atts( unit, global_atts)
interface mpp_get_atts
module procedure mpp_get_global_atts
module procedure mpp_get_field_atts
module procedure mpp_get_axis_atts
end interface
interface mpp_get_att_value
module procedure mpp_get_field_att_text
end interface
!***********************************************************************
!
! public interface from mpp_io_read.h
!
!***********************************************************************
! <INTERFACE NAME="mpp_read">
! <OVERVIEW>
! Read from an open file.
! </OVERVIEW>
! <DESCRIPTION>
! <TT>mpp_read</TT> is used to read data to the file on an I/O unit
! using the file parameters supplied by <LINK
! SRC="#mpp_open"><TT>mpp_open</TT></LINK>. There are two
! forms of <TT>mpp_read</TT>, one to read
! distributed field data, and one to read non-distributed field
! data. <I>Distributed</I> data refer to arrays whose two
! fastest-varying indices are domain-decomposed. Distributed data must
! be 2D or 3D (in space). Non-distributed data can be 0-3D.
!
! The <TT>data</TT> argument for distributed data is expected by
! <TT>mpp_read</TT> to contain data specified on the <I>data</I> domain,
! and will read the data belonging to the <I>compute</I> domain,
! fetching data as required by the parallel I/O <LINK
! SRC="#modes">mode</LINK> specified in the <TT>mpp_open</TT> call. This
! is consistent with our definition of <LINK
! SRC="http:mpp_domains.html#domains">domains</LINK>, where all arrays are
! expected to be dimensioned on the data domain, and all operations
! performed on the compute domain.
! </DESCRIPTION>
! <TEMPLATE>
! call mpp_read( unit, field, data, time_index )
! </TEMPLATE>
! <TEMPLATE>
! call mpp_read( unit, field, domain, data, time_index )
! </TEMPLATE>
! <IN NAME="unit"></IN>
! <IN NAME="field"></IN>
! <INOUT NAME="data"></INOUT>
! <IN NAME="domain"></IN>
! <IN NAME="time_index">
! time_index is an optional argument. It is to be omitted if the
! field was defined not to be a function of time. Results are
! unpredictable if the argument is supplied for a time- independent
! field, or omitted for a time-dependent field.
! </IN>
! <NOTE>
! The type of read performed by <TT>mpp_read</TT> depends on
! the file characteristics on the I/O unit specified at the <LINK
! SRC="#mpp_open"><TT>mpp_open</TT></LINK> call. Specifically, the
! format of the input data (e.g netCDF or IEEE) and the
! <TT>threading</TT> flags, etc., can be changed there, and
! require no changes to the <TT>mpp_read</TT>
! calls. (<TT>fileset</TT> = MPP_MULTI is not supported by
! <TT>mpp_read</TT>; IEEE is currently not supported).
!
! Packed variables are unpacked using the <TT>scale</TT> and
! <TT>add</TT> attributes.
!
! <TT>mpp_read_meta</TT> must be called prior to calling <TT>mpp_read.</TT>
! </NOTE>
! </INTERFACE>
interface mpp_read
module procedure mpp_read_2ddecomp_r2d_r4
module procedure mpp_read_2ddecomp_r3d_r4
module procedure mpp_read_2ddecomp_r4d_r4
module procedure mpp_read_2ddecomp_r2d_r8
module procedure mpp_read_2ddecomp_r3d_r8
module procedure mpp_read_2ddecomp_r4d_r8
module procedure mpp_read_region_r2D_r4
module procedure mpp_read_region_r3D_r4
module procedure mpp_read_region_r2D_r8
module procedure mpp_read_region_r3D_r8
module procedure mpp_read_r0D_r4
module procedure mpp_read_r1D_r4
module procedure mpp_read_r2D_r4
module procedure mpp_read_r3D_r4
module procedure mpp_read_r4D_r4
module procedure mpp_read_r0D_r8
module procedure mpp_read_r1D_r8
module procedure mpp_read_r2D_r8
module procedure mpp_read_r3D_r8
module procedure mpp_read_r4D_r8
module procedure mpp_read_text
end interface
!***********************************************************************
!
! public interfaces from mpp_io_read_distributed_ascii.inc
!
!***********************************************************************
! <INTERFACE NAME="mpp_read_distributed_ascii">
! <OVERVIEW>
! Read from an opened, ascii file, translating data to the desired format
! </OVERVIEW>
! <DESCRIPTION>
! These routines are part of the mpp_read family. It is intended to
! provide a general purpose, distributed, list directed read
! </DESCRIPTION>
! <TEMPLATE>
! call mpp_read_distributed_ascii(unit,fmt,ssize,data,iostat)
! </TEMPLATE>
! <IN NAME="unit"></IN>
! <IN NAME="fmt"></IN>
! <IN NAME="ssize"></IN>
! <INOUT NAME="data"></IN>
! <OUT NAME="iostat">
! </IN>
! <NOTE>
! <TT>mpp_read_distributed_ascii</TT>
! The stripe size must be greater than or equal to 1. The stripe
! size does not have to be a common denominator of the number of
! MPI ranks.
! </NOTE>
! </INTERFACE>
interface mpp_read_distributed_ascii
module procedure mpp_read_distributed_ascii_r1d
module procedure mpp_read_distributed_ascii_i1d
module procedure mpp_read_distributed_ascii_a1d
end interface
!***********************************************************************
!
! public interfaces from mpp_io_read_compressed.h
!
!***********************************************************************
! <INTERFACE NAME="mpp_read_compressed">
! <OVERVIEW>
! Read from an opened, sparse data, compressed file (e.g. land_model)
! </OVERVIEW>
! <DESCRIPTION>
! These routines are similar to mpp_read except that they are designed
! to handle sparse, compressed vectors of data such as from the
! land model. Currently, the sparse vector may vary in z. Hence
! the need for the rank 2 treatment.
! </DESCRIPTION>
! <TEMPLATE>
! call mpp_read_compressed( unit, field, domain, data, time_index )
! </TEMPLATE>
! <IN NAME="unit"></IN>
! <IN NAME="field"></IN>
! <IN NAME="domain"></IN>
! <INOUT NAME="data"></INOUT>
! <IN NAME="time_index">
! time_index is an optional argument. It is to be omitted if the
! field was defined not to be a function of time. Results are
! unpredictable if the argument is supplied for a time- independent
! field, or omitted for a time-dependent field.
! </IN>
! <NOTE>
! <TT>mpp_read_meta</TT> must be called prior to calling
! <TT>mpp_read_compressed.</TT>
! Since in general, the vector is distributed across the io-domain
! The read expects the io_domain to be defined.
! </NOTE>
! </INTERFACE>
interface mpp_read_compressed
module procedure mpp_read_compressed_r1d_r4
module procedure mpp_read_compressed_r2d_r4
module procedure mpp_read_compressed_r3d_r4
module procedure mpp_read_compressed_r1d_r8
module procedure mpp_read_compressed_r2d_r8
module procedure mpp_read_compressed_r3d_r8
end interface mpp_read_compressed
!***********************************************************************
!
! public interface from mpp_io_write.h
!
!***********************************************************************
! <INTERFACE NAME="mpp_write_meta">
! <OVERVIEW>
! Write metadata.
! </OVERVIEW>
! <DESCRIPTION>
! This routine is used to write the <LINK SRC="#metadata">metadata</LINK>
! describing the contents of a file being written. Each file can contain
! any number of fields, which are functions of 0-3 space axes and 0-1
! time axes. (Only one time axis can be defined per file). The basic
! metadata defined <LINK SRC="#metadata">above</LINK> for <TT>axistype</TT>
! and <TT>fieldtype</TT> are written in the first two forms of the call
! shown below. These calls will associate a unique variable ID with each
! variable (axis or field). These can be used to attach any other real,
! integer or character attribute to a variable. The last form is used to
! define a <I>global</I> real, integer or character attribute that
! applies to the dataset as a whole.
! </DESCRIPTION>
! <TEMPLATE>
! call mpp_write_meta( unit, axis, name, units, longname,
! cartesian, sense, domain, data )
! </TEMPLATE>
! <NOTE>
! The first form defines a time or space axis. Metadata corresponding to the type
! above are written to the file on <unit>. A unique ID for subsequen
! references to this axis is returned in axis%id. If the <domain>
! element is present, this is recognized as a distributed data axis
! and domain decomposition information is also written if required (the
! domain decomposition info is required for multi-fileset multi-threaded
! I/O). If the <data> element is allocated, it is considered to be a
! space axis, otherwise it is a time axis with an unlimited dimension. Only
! one time axis is allowed per file.
! </NOTE>
! <TEMPLATE>
! call mpp_write_meta( unit, field, axes, name, units, longname,
! min, max, missing, fill, scale, add, pack )
! </TEMPLATE>
! <NOTE>
! The second form defines a field. Metadata corresponding to the type
! above are written to the file on <unit>. A unique ID for subsequen
! references to this field is returned in field%id. At least one axis
! must be associated, 0D variables are not considered. mpp_write_meta
! must previously have been called on all axes associated with this
! field.
! </NOTE>
! <TEMPLATE>
! call mpp_write_meta( unit, id, name, rval=rval, pack=pack )
! </TEMPLATE>
! <TEMPLATE>
! call mpp_write_meta( unit, id, name, ival=ival )
! </TEMPLATE>
! <TEMPLATE>
! call mpp_write_meta( unit, id, name, cval=cval )
! </TEMPLATE>
! <NOTE>
! The third form (3 - 5) defines metadata associated with a previously defined
! axis or field, identified to mpp_write_meta by its unique ID <id>.
! The attribute is named <name> and can take on a real, integer
! or character value. <rval> and <ival> can be scalar or 1D arrays.
! This need not be called for attributes already contained in
! the type.
! </NOTE>
! <TEMPLATE>
! call mpp_write_meta( unit, name, rval=rval, pack=pack )
! </TEMPLATE>
! <TEMPLATE>
! call mpp_write_meta( unit, name, ival=ival )
! </TEMPLATE>
! <TEMPLATE>
! call mpp_write_meta( unit, name, cval=cval )
! </TEMPLATE>
! <NOTE>
! The last form (6 - 8) defines global metadata associated with the file as a
! whole. The attribute is named <name> and can take on a real, integer
! or character value. <rval> and <ival> can be scalar or 1D arrays.
! </NOTE>
! <IN NAME="unit"></IN>
! <OUT NAME="axis"></OUT>
! <IN NAME="name"></IN>
! <IN NAME="units"></IN>
! <IN NAME="longname"></IN>
! <IN NAME="cartesian"></IN>
! <IN NAME="sense"></IN>
! <IN NAME="domain"></IN>
! <IN NAME="data"></IN>
! <OUT NAME="field"></OUT>
! <IN NAME="min, max"></IN>
! <IN NAME="missing"></IN>
! <IN NAME="fill"></IN>
! <IN NAME="scale"></IN>
! <IN NAME="add"></IN>
! <IN NAME="pack"></IN>
! <IN NAME="id"></IN>
! <IN NAME="cval"></IN>
! <IN NAME="ival"></IN>
! <IN NAME="rval"></IN>
! <NOTE>
! Note that <TT>mpp_write_meta</TT> is expecting axis data on the
! <I>global</I> domain even if it is a domain-decomposed axis.
!
! You cannot interleave calls to <TT>mpp_write</TT> and
! <TT>mpp_write_meta</TT>: the first call to
! <TT>mpp_write</TT> implies that metadata specification is complete.
! </NOTE>
! </INTERFACE>
interface mpp_write_meta
module procedure mpp_write_meta_var
module procedure mpp_write_meta_scalar_r
module procedure mpp_write_meta_scalar_i
module procedure mpp_write_meta_axis_r1d
module procedure mpp_write_meta_axis_i1d
module procedure mpp_write_meta_axis_unlimited
module procedure mpp_write_meta_field
module procedure mpp_write_meta_global
module procedure mpp_write_meta_global_scalar_r
module procedure mpp_write_meta_global_scalar_i
end interface
interface mpp_copy_meta
module procedure mpp_copy_meta_axis
module procedure mpp_copy_meta_field
module procedure mpp_copy_meta_global
end interface
interface mpp_modify_meta
! module procedure mpp_modify_att_meta
module procedure mpp_modify_field_meta
module procedure mpp_modify_axis_meta
end interface
! <INTERFACE NAME="mpp_write">
! <OVERVIEW>
! Write to an open file.
! </OVERVIEW>
! <DESCRIPTION>
! <TT>mpp_write</TT> is used to write data to the file on an I/O unit
! using the file parameters supplied by <LINK
! SRC="#mpp_open"><TT>mpp_open</TT></LINK>. Axis and field definitions must
! have previously been written to the file using <LINK
! SRC="#mpp_write_meta"><TT>mpp_write_meta</TT></LINK>. There are three
! forms of <TT>mpp_write</TT>, one to write axis data, one to write
! distributed field data, and one to write non-distributed field
! data. <I>Distributed</I> data refer to arrays whose two
! fastest-varying indices are domain-decomposed. Distributed data must
! be 2D or 3D (in space). Non-distributed data can be 0-3D.
!
! The <TT>data</TT> argument for distributed data is expected by
! <TT>mpp_write</TT> to contain data specified on the <I>data</I> domain,
! and will write the data belonging to the <I>compute</I> domain,
! fetching or sending data as required by the parallel I/O <LINK
! SRC="#modes">mode</LINK> specified in the <TT>mpp_open</TT> call. This
! is consistent with our definition of <LINK
! SRC="http:mpp_domains.html#domains">domains</LINK>, where all arrays are
! expected to be dimensioned on the data domain, and all operations
! performed on the compute domain.
!
! The type of the <TT>data</TT> argument must be a <I>default
! real</I>, which can be 4 or 8 byte.
! </DESCRIPTION>
! <TEMPLATE>
! mpp_write( unit, axis )
! </TEMPLATE>
! <TEMPLATE>
! mpp_write( unit, field, data, tstamp )
! </TEMPLATE>
! <TEMPLATE>
! mpp_write( unit, field, domain, data, tstamp )
! </TEMPLATE>
! <IN NAME="tstamp">
! <TT>tstamp</TT> is an optional argument. It is to
! be omitted if the field was defined not to be a function of time.
! Results are unpredictable if the argument is supplied for a time-
! independent field, or omitted for a time-dependent field. Repeated
! writes of a time-independent field are also not recommended. One
! time level of one field is written per call. tstamp must be an 8-byte
! real, even if the default real type is 4-byte.
! </IN>
! <NOTE>
! The type of write performed by <TT>mpp_write</TT> depends on the file
! characteristics on the I/O unit specified at the <LINK
! SRC="#mpp_open"><TT>mpp_open</TT></LINK> call. Specifically, the format of
! the output data (e.g netCDF or IEEE), the <TT>threading</TT> and
! <TT>fileset</TT> flags, etc., can be changed there, and require no
! changes to the <TT>mpp_write</TT> calls.
!
! Packing is currently not implemented for non-netCDF files, and the
! <TT>pack</TT> attribute is ignored. On netCDF files,
! <TT>NF_DOUBLE</TT>s (8-byte IEEE floating point numbers) are
! written for <TT>pack</TT>=1 and <TT>NF_FLOAT</TT>s for
! <TT>pack</TT>=2. (<TT>pack</TT>=2 gives the customary
! and default behaviour). We write <TT>NF_SHORT</TT>s (2-byte
! integers) for <TT>pack=4</TT>, or <TT>NF_BYTE</TT>s
! (1-byte integers) for <TT>pack=8</TT>. Integer scaling is done
! using the <TT>scale</TT> and <TT>add</TT> attributes at
! <TT>pack</TT>=4 or 8, satisfying the relation
!
! <PRE>
! data = packed_data*scale + add
! </PRE>
!
! <TT>NOTE: mpp_write</TT> does not check to see if the scaled
! data in fact fits into the dynamic range implied by the specified
! packing. It is incumbent on the user to supply correct scaling
! attributes.
!
! You cannot interleave calls to <TT>mpp_write</TT> and
! <TT>mpp_write_meta</TT>: the first call to
! <TT>mpp_write</TT> implies that metadata specification is
! complete.
! </NOTE>
! </INTERFACE>
interface write_record
module procedure write_record_r8
module procedure write_record_r4
end interface
interface mpp_write
module procedure mpp_write_2ddecomp_r2d_r8
module procedure mpp_write_2ddecomp_r3d_r8
module procedure mpp_write_2ddecomp_r4d_r8
module procedure mpp_write_2ddecomp_r2d_r4
module procedure mpp_write_2ddecomp_r3d_r4
module procedure mpp_write_2ddecomp_r4d_r4
module procedure mpp_write_r0D_r8
module procedure mpp_write_r1D_r8
module procedure mpp_write_r2D_r8
module procedure mpp_write_r3D_r8
module procedure mpp_write_r4D_r8
module procedure mpp_write_r0D_r4
module procedure mpp_write_r1D_r4
module procedure mpp_write_r2D_r4
module procedure mpp_write_r3D_r4
module procedure mpp_write_r4D_r4
module procedure mpp_write_axis
end interface
!***********************************************************************
! <INTERFACE NAME="mpp_write_compressed">
! <OVERVIEW>
! Write to an opened, sparse data, compressed file (e.g. land_model)
! </OVERVIEW>
! <DESCRIPTION>
! These routines are similar to mpp_write except that they are
! designed to handle sparse, compressed vectors of data such
! as from the land model. Currently, the sparse vector may vary in z.
! Hence the need for the rank 2 treatment.
! </DESCRIPTION>
! <TEMPLATE>
! call mpp_write(unit, field, domain, data, nelems_io, tstamp, default_data )
! </TEMPLATE>
! <IN NAME="unit"></IN>
! <IN NAME="field"></IN>
! <IN NAME="domain"></IN>
! <INOUT NAME="data"></INOUT>
! <IN NAME="nelems_io">
! <TT>nelems</TT> is a vector containing the number of elements expected
! from each member of the io_domain. It MUST have the same order as
! the io_domain pelist.
! </IN>
! <IN NAME="tstamp">
! <TT>tstamp</TT> is an optional argument. It is to
! be omitted if the field was defined not to be a function of time.
! Results are unpredictable if the argument is supplied for a time-
! independent field, or omitted for a time-dependent field. Repeated
! writes of a time-independent field are also not recommended. One
! time level of one field is written per call. tstamp must be an 8-byte
! real, even if the default real type is 4-byte.
! </IN>
! <IN NAME="default_data"></IN>
! <NOTE>
! <TT>mpp_write_meta</TT> must be called prior to calling
! <TT>mpp_write_compressed.</TT>
! Since in general, the vector is distributed across the io-domain
! The write expects the io_domain to be defined.
! </NOTE>
! </INTERFACE>
interface mpp_write_compressed
module procedure mpp_write_compressed_r1d_r8
module procedure mpp_write_compressed_r2d_r8
module procedure mpp_write_compressed_r3d_r8
module procedure mpp_write_compressed_r1d_r4
module procedure mpp_write_compressed_r2d_r4
module procedure mpp_write_compressed_r3d_r4
end interface mpp_write_compressed
!***********************************************************************
! <INTERFACE NAME="mpp_write_unlimited_axis">
! <OVERVIEW>
! Write to an opened file along the unlimited axis (e.g. icebergs)
! </OVERVIEW>
! <DESCRIPTION>
! These routines are similar to mpp_write except that they are
! designed to handle data written along the unlimited axis that