Changeset 2364 for branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC
- Timestamp:
- 2010-11-05T16:22:12+01:00 (13 years ago)
- Location:
- branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC
- Files:
-
- 8 edited
-
DIA/diaptr.F90 (modified) (2 diffs)
-
DIA/diawri.F90 (modified) (10 diffs)
-
DOM/domain.F90 (modified) (3 diffs)
-
IOM/in_out_manager.F90 (modified) (1 diff)
-
IOM/iom_nf90.F90 (modified) (9 diffs)
-
IOM/restart.F90 (modified) (2 diffs)
-
TRD/trdmld.F90 (modified) (2 diffs)
-
TRD/trdvor.F90 (modified) (2 diffs)
Legend:
- Unmodified
- Added
- Removed
-
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/DIA/diaptr.F90
r2287 r2364 728 728 ! Horizontal grid : zphi() 729 729 CALL histbeg(clhstnam, 1, zfoo, jpj, zphi, & 730 1, 1, 1, jpj, niter, zjulian, zdt*nf_ptr, nhoridz, numptr, domain_id=nidom_ptr )730 1, 1, 1, jpj, niter, zjulian, zdt*nf_ptr, nhoridz, numptr, domain_id=nidom_ptr, snc4chunks=snc4set) 731 731 ! Vertical grids : gdept_0, gdepw_0 732 732 CALL histvert( numptr, "deptht", "Vertical T levels", & … … 880 880 ENDIF 881 881 882 CALL histend( numptr )882 CALL histend( numptr, snc4set ) 883 883 884 884 END IF -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/DIA/diawri.F90
r2329 r2364 273 273 CALL histbeg( clhstnam, jpi, glamt, jpj, gphit, & ! Horizontal grid: glamt and gphit 274 274 & iimi, iima-iimi+1, ijmi, ijma-ijmi+1, & 275 & nit000-1, zjulian, zdt, nh_T, nid_T, domain_id=nidom )275 & nit000-1, zjulian, zdt, nh_T, nid_T, domain_id=nidom, snc4chunks=snc4set ) 276 276 CALL histvert( nid_T, "deptht", "Vertical T levels", & ! Vertical grid: gdept 277 277 & "m", ipk, gdept_0, nz_T, "down" ) … … 286 286 CALL histbeg( clhstnam, jpi, glamu, jpj, gphiu, & ! Horizontal grid: glamu and gphiu 287 287 & iimi, iima-iimi+1, ijmi, ijma-ijmi+1, & 288 & nit000-1, zjulian, zdt, nh_U, nid_U, domain_id=nidom )288 & nit000-1, zjulian, zdt, nh_U, nid_U, domain_id=nidom, snc4chunks=snc4set ) 289 289 CALL histvert( nid_U, "depthu", "Vertical U levels", & ! Vertical grid: gdept 290 290 & "m", ipk, gdept_0, nz_U, "down" ) … … 299 299 CALL histbeg( clhstnam, jpi, glamv, jpj, gphiv, & ! Horizontal grid: glamv and gphiv 300 300 & iimi, iima-iimi+1, ijmi, ijma-ijmi+1, & 301 & nit000-1, zjulian, zdt, nh_V, nid_V, domain_id=nidom )301 & nit000-1, zjulian, zdt, nh_V, nid_V, domain_id=nidom, snc4chunks=snc4set ) 302 302 CALL histvert( nid_V, "depthv", "Vertical V levels", & ! Vertical grid : gdept 303 303 & "m", ipk, gdept_0, nz_V, "down" ) … … 312 312 CALL histbeg( clhstnam, jpi, glamt, jpj, gphit, & ! Horizontal grid: glamt and gphit 313 313 & iimi, iima-iimi+1, ijmi, ijma-ijmi+1, & 314 & nit000-1, zjulian, zdt, nh_W, nid_W, domain_id=nidom )314 & nit000-1, zjulian, zdt, nh_W, nid_W, domain_id=nidom, snc4chunks=snc4set ) 315 315 CALL histvert( nid_W, "depthw", "Vertical W levels", & ! Vertical grid: gdepw 316 316 & "m", ipk, gdepw_0, nz_W, "down" ) … … 404 404 #endif 405 405 406 CALL histend( nid_T )406 CALL histend( nid_T, snc4chunks=snc4set ) 407 407 408 408 ! !!! nid_U : 3D … … 417 417 & jpi, jpj, nh_U, 1 , 1, 1 , - 99, 32, clop, zsto, zout ) 418 418 419 CALL histend( nid_U )419 CALL histend( nid_U, snc4chunks=snc4set ) 420 420 421 421 ! !!! nid_V : 3D … … 430 430 & jpi, jpj, nh_V, 1 , 1, 1 , - 99, 32, clop, zsto, zout ) 431 431 432 CALL histend( nid_V )432 CALL histend( nid_V, snc4chunks=snc4set ) 433 433 434 434 ! !!! nid_W : 3D … … 458 458 #endif 459 459 460 CALL histend( nid_W )460 CALL histend( nid_W, snc4chunks=snc4set ) 461 461 462 462 IF(lwp) WRITE(numout,*) … … 624 624 zjulian = zjulian - adatrj ! set calendar origin to the beginning of the experiment 625 625 CALL histbeg( clname, jpi, glamt, jpj, gphit, & 626 1, jpi, 1, jpj, nit000-1, zjulian, zdt, nh_i, id_i, domain_id=nidom )! Horizontal grid : glamt and gphit626 1, jpi, 1, jpj, nit000-1, zjulian, zdt, nh_i, id_i, domain_id=nidom, snc4chunks=snc4set ) ! Horizontal grid : glamt and gphit 627 627 CALL histvert( id_i, "deptht", "Vertical T levels", & ! Vertical grid : gdept 628 628 "m", jpk, gdept_0, nz_i, "down") … … 658 658 CALL lim_wri_state_2( kt, id_i, nh_i ) 659 659 #else 660 CALL histend( id_i )660 CALL histend( id_i, snc4chunks=snc4set ) 661 661 #endif 662 662 -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/DOM/domain.F90
r2287 r2364 106 106 !! - namdom namelist 107 107 !! - namcla namelist 108 !! - namnc4 namelist ! "key_netcdf4" only 108 109 !!---------------------------------------------------------------------- 109 110 USE ioipsl … … 115 116 & rn_rdtmax, rn_rdth , nn_baro , nn_closea 116 117 NAMELIST/namcla/ nn_cla 118 #if defined key_netcdf4 119 NAMELIST/namnc4/ nn_nchunks_i, nn_nchunks_j, nn_nchunks_k, ln_nc4zip 120 #endif 117 121 !!---------------------------------------------------------------------- 118 122 … … 232 236 IF( lk_mpp_rep .AND. n_cla /= 0 ) CALL ctl_stop( ' Reproductibility tests (nbit_cmp=1) require n_cla = 0' ) 233 237 ! 238 239 #if defined key_netcdf4 240 241 REWIND( numnam ) ! Namelist namnc4 : netcdf4 chunking parameters 242 READ ( numnam, namnc4 ) 243 IF(lwp) THEN 244 WRITE(numout,*) 245 WRITE(numout,*) ' Namelist namnc4 - Netcdf4 chunking parameters' 246 WRITE(numout,*) ' number of chunks in i-dimension nn_nchunks_i = ', nn_nchunks_i 247 WRITE(numout,*) ' number of chunks in j-dimension nn_nchunks_j = ', nn_nchunks_j 248 WRITE(numout,*) ' number of chunks in k-dimension nn_nchunks_k = ', nn_nchunks_k 249 WRITE(numout,*) ' apply netcdf4/hdf5 chunking & compression ln_nc4zip = ', ln_nc4zip 250 ENDIF 251 252 ! Put the netcdf4 settings into a simple structure (snc4set, defined in in_out_manager module) 253 ! Note the chunk size in the unlimited (time) dimension will be fixed at 1 254 snc4set%ni = nn_nchunks_i 255 snc4set%nj = nn_nchunks_j 256 snc4set%nk = nn_nchunks_k 257 snc4set%luse = ln_nc4zip 258 259 #else 260 261 snc4set%luse = .FALSE. 262 263 #endif 234 264 END SUBROUTINE dom_nam 235 265 -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/IOM/in_out_manager.F90
r2287 r2364 45 45 LOGICAL :: ln_clobber = .FALSE. !: clobber (overwrite) an existing file 46 46 INTEGER :: nn_chunksz = 0 !: chunksize (bytes) for NetCDF file (working only with iom_nf90 routines) 47 #if defined key_netcdf4 48 !!---------------------------------------------------------------------- 49 !! namnc4 namelist parameters 50 !!---------------------------------------------------------------------- 51 !: ========================================================================= 52 !: The following four values determine the partitioning of the output fields 53 !: into netcdf4 chunks. They are unrelated to the nn_chunk_sz setting which is 54 !: for runtime optimisation. The individual netcdf4 chunks can be optionally 55 !: gzipped (recommended) leading to significant reductions in I/O volumes 56 INTEGER :: nn_nchunks_i = 1 !: number of chunks required in the i-dimension (only with iom_nf90 routines and key_netcdf4) 57 INTEGER :: nn_nchunks_j = 1 !: number of chunks required in the j-dimension (only with iom_nf90 routines and key_netcdf4) 58 INTEGER :: nn_nchunks_k = 1 !: number of chunks required in the k-dimension (only with iom_nf90 routines and key_netcdf4) 59 INTEGER :: nn_nchunks_t = 1 !: number of chunks required in the t-dimension (only with iom_nf90 routines and key_netcdf4) 60 LOGICAL :: ln_nc4zip = .TRUE. !: netcdf4 usage. (T): chunk and compress output datasets using the HDF5 sublayers of netcdf4 61 !: (F): ignore chunking request and use the netcdf4 library to produce netcdf3-compatible files 62 #endif 63 64 !$AGRIF_DO_NOT_TREAT 65 TYPE, PUBLIC :: snc4_ctl !: netcdf4 chunking control structure (always needed for decision making) 66 SEQUENCE 67 INTEGER :: ni 68 INTEGER :: nj 69 INTEGER :: nk 70 LOGICAL :: luse 71 END TYPE snc4_ctl 72 73 TYPE(snc4_ctl) :: snc4set !: netcdf4 chunking control structure (always needed for decision making) 74 !$AGRIF_END_DO_NOT_TREAT 75 47 76 48 77 !! conversion of DOCTOR norm namelist name into model name -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/IOM/iom_nf90.F90
r2351 r2364 39 39 MODULE PROCEDURE iom_nf90_rp0123d 40 40 END INTERFACE 41 42 #if ! defined key_netcdf4 43 !!-------------------------------------------------------------------- 44 !! NOT 'key_netcdf4' Defines dummy routines for netcdf4 45 !! calls when compiling without netcdf4 libraries 46 !!-------------------------------------------------------------------- 47 PUBLIC NF90_DEF_VAR_CHUNKING, NF90_DEF_VAR_DEFLATE ! contained below 48 INTEGER :: NF90_HDF5 49 #endif 41 50 !!---------------------------------------------------------------------- 42 51 !! NEMO/OPA 3.3 , NEMO Consortium (2010) … … 67 76 INTEGER :: jl ! loop variable 68 77 INTEGER :: ichunk ! temporary storage of nn_chunksz 69 INTEGER :: imode ! creation mode flag: NF90_CLOBBER or NF90_NOCLOBBER 78 INTEGER :: imode ! creation mode flag: NF90_CLOBBER or NF90_NOCLOBBER or NF90_HDF5 70 79 LOGICAL :: llclobber ! local definition of ln_clobber 71 80 !--------------------------------------------------------------------- … … 82 91 IF( ldwrt ) THEN ! ... in write mode 83 92 IF(lwp) WRITE(numout,*) TRIM(clinfo)//' open existing file: '//TRIM(cdname)//' in WRITE mode' 84 CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id, chunksize = ichunk ), clinfo) 93 IF( snc4set%luse ) THEN 94 CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id ), clinfo) 95 ELSE 96 CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id, chunksize = ichunk ), clinfo) 97 ENDIF 85 98 CALL iom_nf90_check(NF90_SET_FILL( if90id, NF90_NOFILL, idmy ), clinfo) 86 99 ELSE ! ... in read mode … … 101 114 ELSE ; imode = IOR( NF90_64BIT_OFFSET, NF90_NOCLOBBER ) 102 115 ENDIF 103 CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id, chunksize = ichunk ), clinfo) 116 IF( snc4set%luse ) THEN 117 IF(lwp) WRITE(numout,*) TRIM(clinfo)//' creating file: '//TRIM(cdname)//' in hdf5 (netcdf4) mode' 118 IF( llclobber ) THEN ; imode = IOR(NF90_HDF5, NF90_CLOBBER) 119 ELSE ; imode = IOR(NF90_HDF5, NF90_NOCLOBBER) 120 ENDIF 121 CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id ), clinfo) 122 ELSE 123 CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id, chunksize = ichunk ), clinfo) 124 ENDIF 104 125 CALL iom_nf90_check(NF90_SET_FILL( if90id, NF90_NOFILL, idmy ), clinfo) 105 126 ! define dimensions … … 378 399 INTEGER :: idmy ! dummy variable 379 400 INTEGER :: itype ! variable type 401 INTEGER, DIMENSION(4) :: ichunksz ! NetCDF4 chunk sizes. Will be computed using 402 ! nn_nchunks_[i,j,k,t] namelist parameters 403 INTEGER :: ichunkalg, ishuffle,& 404 ideflate, ideflate_level 405 ! NetCDF4 internally fixed parameters 406 LOGICAL :: lchunk ! logical switch to activate chunking and compression 407 ! when appropriate (currently chunking is applied to 4d fields only) 380 408 !--------------------------------------------------------------------- 381 409 ! … … 408 436 ! =============== 409 437 IF( kvid <= 0 ) THEN 438 ! 439 ! NetCDF4 chunking and compression fixed settings 440 ichunkalg = 0 441 ishuffle = 1 442 ideflate = 1 443 ideflate_level = 1 444 ! 410 445 idvar = iom_file(kiomid)%nvars + 1 411 446 ! are we in define mode? … … 438 473 & iom_file(kiomid)%nvid(idvar) ), clinfo) 439 474 ENDIF 475 lchunk = .false. 476 IF( snc4set%luse .AND. idims.eq.4 ) lchunk = .true. 440 477 ! update informations structure related the new variable we want to add... 441 478 iom_file(kiomid)%nvars = idvar … … 449 486 DO jd = 1, idims 450 487 CALL iom_nf90_check(NF90_INQUIRE_DIMENSION( if90id, idimid(jd), len = iom_file(kiomid)%dimsz(jd,idvar) ), clinfo) 488 IF ( lchunk ) ichunksz(jd) = iom_file(kiomid)%dimsz(jd,idvar) 451 489 END DO 490 IF ( lchunk ) THEN 491 ! Calculate chunk sizes by partitioning each dimension as requested in namnc4 namelist 492 ! Disallow very small chunk sizes and prevent chunk sizes larger than each individual dimension 493 ichunksz(1) = MIN( ichunksz(1),MAX( (ichunksz(1)-1)/snc4set%ni + 1 ,16 ) ) ! Suggested default nc4set%ni=4 494 ichunksz(2) = MIN( ichunksz(2),MAX( (ichunksz(2)-1)/snc4set%nj + 1 ,16 ) ) ! Suggested default nc4set%nj=2 495 ichunksz(3) = MIN( ichunksz(3),MAX( (ichunksz(3)-1)/snc4set%nk + 1 , 1 ) ) ! Suggested default nc4set%nk=6 496 ichunksz(4) = 1 ! Do not allow chunks to span the 497 ! unlimited dimension 498 CALL iom_nf90_check(NF90_DEF_VAR_CHUNKING(if90id, idvar, ichunkalg, ichunksz), clinfo) 499 CALL iom_nf90_check(NF90_DEF_VAR_DEFLATE(if90id, idvar, ishuffle, ideflate, ideflate_level), clinfo) 500 IF(lwp) WRITE(numout,*) TRIM(clinfo)//' chunked ok. Chunks sizes: ', ichunksz 501 ENDIF 452 502 IF(lwp) WRITE(numout,*) TRIM(clinfo)//' defined ok' 453 503 ELSE … … 529 579 END SUBROUTINE iom_nf90_check 530 580 581 #if ! defined key_netcdf4 582 583 !!-------------------------------------------------------------------- 584 !! NOT 'key_netcdf4' Defines dummy routines for netcdf4 585 !! calls when compiling without netcdf4 libraries 586 !!-------------------------------------------------------------------- 587 588 INTEGER FUNCTION NF90_DEF_VAR_CHUNKING(idum1, idum2, idum3, iarr1) 589 !!-------------------------------------------------------------------- 590 !! *** SUBROUTINE NF90_DEF_VAR_CHUNKING *** 591 !! 592 !! ** Purpose : Dummy NetCDF4 routine to enable compiling with NetCDF3 libraries 593 !!-------------------------------------------------------------------- 594 INTEGER, INTENT(in) :: idum1, idum2, idum3 595 INTEGER, DIMENSION(4), INTENT(in) :: iarr1 596 IF(lwp) WRITE(numout,*) 'Warning: Attempt to chunk output variable without NetCDF4 support' 597 NF90_DEF_VAR_CHUNKING = -1 598 END FUNCTION NF90_DEF_VAR_CHUNKING 599 600 INTEGER FUNCTION NF90_DEF_VAR_DEFLATE(idum1, idum2, idum3, idum4, idum5) 601 !!-------------------------------------------------------------------- 602 !! *** SUBROUTINE NF90_DEF_VAR_DEFLATE *** 603 !! 604 !! ** Purpose : Dummy NetCDF4 routine to enable compiling with NetCDF3 libraries 605 !!-------------------------------------------------------------------- 606 INTEGER, INTENT(in) :: idum1, idum2, idum3, idum4, idum5 607 IF(lwp) WRITE(numout,*) 'Warning: Attempt to compress output variable without NetCDF4 support' 608 NF90_DEF_VAR_DEFLATE = -1 609 END FUNCTION NF90_DEF_VAR_DEFLATE 610 #endif 531 611 532 612 !!====================================================================== -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/IOM/restart.F90
r2287 r2364 95 95 CASE DEFAULT ; WRITE(numout,*) ' open ocean restart NetCDF file: '//clname 96 96 END SELECT 97 IF ( snc4set%luse ) WRITE(numout,*) ' opened for NetCDF4 chunking and compression' 97 98 IF( kt == nitrst - 1 ) THEN ; WRITE(numout,*) ' kt = nitrst - 1 = ', kt 98 99 ELSE ; WRITE(numout,*) ' kt = ' , kt … … 178 179 CASE ( jprstdimg ) ; WRITE(numout,*) 'rst_read : read oce binary restart file' 179 180 END SELECT 181 IF ( snc4set%luse ) WRITE(numout,*) 'rst_read : configured with NetCDF4 support' 180 182 WRITE(numout,*) '~~~~~~~~' 181 183 ENDIF -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/TRD/trdmld.F90
r2287 r2364 873 873 IF(lwp) WRITE(numout,*) ' Name of NETCDF file ', clhstnam 874 874 CALL histbeg( clhstnam, jpi, glamt, jpj, gphit, & 875 & 1, jpi, 1, jpj, nit000-1, zjulian, rdt, nh_t, nidtrd, domain_id=nidom )875 & 1, jpi, 1, jpj, nit000-1, zjulian, rdt, nh_t, nidtrd, domain_id=nidom, snc4chunks=snc4set ) 876 876 877 877 !-- Define the ML depth variable … … 925 925 926 926 !-- Leave IOIPSL/NetCDF define mode 927 CALL histend( nidtrd )927 CALL histend( nidtrd, snc4set ) 928 928 929 929 #endif /* key_dimgout */ -
branches/nemo_v3_3_beta/NEMOGCM/NEMO/OPA_SRC/TRD/trdvor.F90
r2287 r2364 568 568 IF(lwp) WRITE(numout,*) ' Name of NETCDF file ', clhstnam 569 569 CALL histbeg( clhstnam, jpi, glamf, jpj, gphif,1, jpi, & ! Horizontal grid : glamt and gphit 570 & 1, jpj, nit000-1, zjulian, rdt, nh_t, nidvor, domain_id=nidom )570 & 1, jpj, nit000-1, zjulian, rdt, nh_t, nidvor, domain_id=nidom, snc4chunks=snc4set ) 571 571 CALL wheneq( jpi*jpj, fmask, 1, 1., ndexvor1, ndimvor1 ) ! surface 572 572 … … 598 598 CALL histdef( nidvor, "sovorgap", cvort//"gap", "s-2", & ! gap between 1st and 2 nd mbre 599 599 & jpi,jpj,nh_t,1,1,1,-99,32,clop,zsto,zout) 600 CALL histend( nidvor )600 CALL histend( nidvor, snc4set ) 601 601 602 602 IF( idebug /= 0 ) THEN
Note: See TracChangeset
for help on using the changeset viewer.
