- Timestamp:
- 2011-10-28T17:00:02+02:00 (13 years ago)
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- 1 edited
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branches/2011/dev_r2802_UKMET3_rebuild/NEMOGCM/TOOLS/REBUILD_NEMO/src/rebuild_nemo.f90
r3019 r3025 14 14 !! * works for 1,2,3 and 4d arrays or types for all valid NetCDF types 15 15 !! * utilises OMP shared memory parallelisation where applicable 16 !! * time 'chunking' for lower memory use 17 !! (only for 4D vars with unlimited dimension) 16 18 !! 17 19 !! Ed Blockley - August 2011 … … 36 38 !! and errors are written to numerr (default 0 - stderr). 37 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 !! 38 44 !!------------------------------------------------------------------------------- 39 45 … … 61 67 CHARACTER(LEN=nf90_max_name), DIMENSION(2) :: dims 62 68 63 INTEGER :: ndomain, ifile, ndomain_file 69 INTEGER :: ndomain, ifile, ndomain_file, nchunksize 64 70 INTEGER :: ncid, outid, idim, istop 65 71 INTEGER :: natts, attid, xtype, varid, rbdims 66 72 INTEGER :: jv, ndims, nvars, dimlen, dimids(4) 67 73 INTEGER :: dimid, unlimitedDimId, di, dj, dr 74 INTEGER :: nmax_unlimited, nt, ntchunk 68 75 INTEGER :: chunksize = 32000000 69 76 INTEGER :: nthreads = 1 … … 145 152 LOGICAL :: l_findDims = .true. 146 153 147 NAMELIST/nam_rebuild/ filebase, ndomain, dims 154 NAMELIST/nam_rebuild/ filebase, ndomain, dims, nchunksize 148 155 149 156 !End of definitions … … 163 170 164 171 dims(:) = "" 172 nchunksize = 0 165 173 OPEN( UNIT=numnam, FILE='nam_rebuild', FORM='FORMATTED', STATUS='OLD' ) 166 174 READ( numnam, nam_rebuild ) … … 249 257 IF( idim == unlimitedDimId ) THEN 250 258 CALL check_nf90( nf90_def_dim( outid, dimname, nf90_unlimited, dimid) ) 259 nmax_unlimited = dimlen 251 260 ELSE 252 261 CALL check_nf90( nf90_def_dim( outid, dimname, dimlen, dimid) ) … … 336 345 l_valid = .false. 337 346 istop = nf90_noerr 347 nt = 1 348 ntchunk = nmax_unlimited 349 IF( nchunksize == 0 ) nchunksize = nmax_unlimited 338 350 339 351 !3.2 Inquire variable to find out name and how many dimensions it has … … 349 361 ENDIF 350 362 363 !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 370 351 371 IF (l_noRebuild) THEN 352 372 353 IF (l_verbose) WRITE(numout,*) 'Copying data from variable '//TRIM(varname)//'...' 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 354 379 355 380 !3.2.1 If rebuilding not required then just need to read in variable … … 452 477 CASE( NF90_BYTE ) 453 478 ALLOCATE(globaldata_4d_i1(indimlens(dimids(1)),indimlens(dimids(2)), & 454 & indimlens(dimids(3)), indimlens(dimids(4))))455 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i1 ) )479 & indimlens(dimids(3)),ntchunk)) 480 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i1, start=(/1,1,1,nt/) ) ) 456 481 CASE( NF90_SHORT ) 457 482 ALLOCATE(globaldata_4d_i2(indimlens(dimids(1)),indimlens(dimids(2)), & 458 & indimlens(dimids(3)), indimlens(dimids(4))))459 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i2 ) )483 & indimlens(dimids(3)),ntchunk)) 484 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i2, start=(/1,1,1,nt/) ) ) 460 485 CASE( NF90_INT ) 461 486 ALLOCATE(globaldata_4d_i4(indimlens(dimids(1)),indimlens(dimids(2)), & 462 & indimlens(dimids(3)), indimlens(dimids(4))))463 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i4 ) )487 & indimlens(dimids(3)),ntchunk)) 488 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_i4, start=(/1,1,1,nt/) ) ) 464 489 CASE( NF90_FLOAT ) 465 490 ALLOCATE(globaldata_4d_sp(indimlens(dimids(1)),indimlens(dimids(2)), & 466 & indimlens(dimids(3)), indimlens(dimids(4))))467 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_sp ) )491 & indimlens(dimids(3)),ntchunk)) 492 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_sp, start=(/1,1,1,nt/) ) ) 468 493 CASE( NF90_DOUBLE ) 469 494 ALLOCATE(globaldata_4d_dp(indimlens(dimids(1)),indimlens(dimids(2)), & 470 & indimlens(dimids(3)), indimlens(dimids(4))))471 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_dp ) )495 & indimlens(dimids(3)),ntchunk)) 496 CALL check_nf90( nf90_get_var( ncid, jv, globaldata_4d_dp, start=(/1,1,1,nt/) ) ) 472 497 CASE DEFAULT 473 498 WRITE(numerr,*) 'Unknown nf90 type: ', xtype … … 481 506 !3.2.2 For variables that require rebuilding we need to read in from all ndomain files 482 507 ! Here we allocate global variables ahead of looping over files 483 IF (l_verbose) WRITE(numout,*) 'Rebuilding data from variable '//TRIM(varname)//'...' 484 508 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 485 514 IF( ndims == 1 ) THEN 486 515 … … 547 576 CASE( NF90_BYTE ) 548 577 ALLOCATE(globaldata_4d_i1(outdimlens(dimids(1)),outdimlens(dimids(2)), & 549 & outdimlens(dimids(3)), outdimlens(dimids(4))))578 & outdimlens(dimids(3)),ntchunk)) 550 579 CASE( NF90_SHORT ) 551 580 ALLOCATE(globaldata_4d_i2(outdimlens(dimids(1)),outdimlens(dimids(2)), & 552 & outdimlens(dimids(3)), outdimlens(dimids(4))))581 & outdimlens(dimids(3)),ntchunk)) 553 582 CASE( NF90_INT ) 554 583 ALLOCATE(globaldata_4d_i4(outdimlens(dimids(1)),outdimlens(dimids(2)), & 555 & outdimlens(dimids(3)), outdimlens(dimids(4))))584 & outdimlens(dimids(3)),ntchunk)) 556 585 CASE( NF90_FLOAT ) 557 586 ALLOCATE(globaldata_4d_sp(outdimlens(dimids(1)),outdimlens(dimids(2)), & 558 & outdimlens(dimids(3)), outdimlens(dimids(4))))587 & outdimlens(dimids(3)),ntchunk)) 559 588 CASE( NF90_DOUBLE ) 560 589 ALLOCATE(globaldata_4d_dp(outdimlens(dimids(1)),outdimlens(dimids(2)), & 561 & outdimlens(dimids(3)), outdimlens(dimids(4))))590 & outdimlens(dimids(3)),ntchunk)) 562 591 CASE DEFAULT 563 592 WRITE(numerr,*) 'Unknown nf90 type: ', xtype … … 584 613 !$OMP& globaldata_3d_i2,globaldata_3d_i4,globaldata_3d_sp,globaldata_3d_dp, & 585 614 !$OMP& globaldata_4d_i2,globaldata_4d_i4,globaldata_4d_sp,globaldata_4d_dp, & 586 !$OMP& globaldata_1d_i1,globaldata_2d_i1,globaldata_3d_i1,globaldata_4d_i1) 615 !$OMP& globaldata_1d_i1,globaldata_2d_i1,globaldata_3d_i1,globaldata_4d_i1, & 616 !$OMP& ntchunk,nt,nmax_unlimited) 587 617 588 618 DO ifile = 1, ndomain … … 811 841 CASE( NF90_BYTE ) 812 842 ALLOCATE(localdata_4d_i1(local_sizes(di),local_sizes(dj), & 813 & indimlens(dimids(3)), indimlens(dimids(4))))814 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i1 ), istop )843 & indimlens(dimids(3)),ntchunk)) 844 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i1, start=(/1,1,1,nt/) ), istop ) 815 845 !$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) & 816 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i1,localdata_4d_i1,di,dj )817 DO jl = 1, indimlens(dimids(4))846 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i1,localdata_4d_i1,di,dj,nt,ntchunk) 847 DO jl = 1, ntchunk 818 848 !$OMP DO 819 849 DO jk = 1, indimlens(dimids(3)) … … 830 860 CASE( NF90_SHORT ) 831 861 ALLOCATE(localdata_4d_i2(local_sizes(di),local_sizes(dj), & 832 & indimlens(dimids(3)), indimlens(dimids(4))))833 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i2 ), istop )862 & indimlens(dimids(3)),ntchunk)) 863 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i2, start=(/1,1,1,nt/) ), istop ) 834 864 !$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) & 835 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i2,localdata_4d_i2,di,dj )836 DO jl = 1, indimlens(dimids(4))865 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i2,localdata_4d_i2,di,dj,nt,ntchunk) 866 DO jl = 1, ntchunk 837 867 !$OMP DO 838 868 DO jk = 1, indimlens(dimids(3)) … … 849 879 CASE( NF90_INT ) 850 880 ALLOCATE(localdata_4d_i4(local_sizes(di),local_sizes(dj), & 851 & indimlens(dimids(3)), indimlens(dimids(4))))852 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i4 ), istop )881 & indimlens(dimids(3)),ntchunk)) 882 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_i4, start=(/1,1,1,nt/) ), istop ) 853 883 !$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) & 854 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i4,localdata_4d_i4,di,dj )855 DO jl = 1, indimlens(dimids(4))884 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_i4,localdata_4d_i4,di,dj,nt,ntchunk) 885 DO jl = 1, ntchunk 856 886 !$OMP DO 857 887 DO jk = 1, indimlens(dimids(3)) … … 868 898 CASE( NF90_FLOAT ) 869 899 ALLOCATE(localdata_4d_sp(local_sizes(di),local_sizes(dj), & 870 & indimlens(dimids(3)), indimlens(dimids(4))))871 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_sp ), istop )900 & indimlens(dimids(3)),ntchunk)) 901 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_sp, start=(/1,1,1,nt/) ), istop ) 872 902 !$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) & 873 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_sp,localdata_4d_sp,di,dj )874 DO jl = 1, indimlens(dimids(4))903 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_sp,localdata_4d_sp,di,dj,nt,ntchunk) 904 DO jl = 1, ntchunk 875 905 !$OMP DO 876 906 DO jk = 1, indimlens(dimids(3)) … … 887 917 CASE( NF90_DOUBLE ) 888 918 ALLOCATE(localdata_4d_dp(local_sizes(di),local_sizes(dj), & 889 & indimlens(dimids(3)), indimlens(dimids(4))))890 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_dp ), istop )919 & indimlens(dimids(3)),ntchunk)) 920 CALL check_nf90( nf90_get_var( ncid, jv, localdata_4d_dp, start=(/1,1,1,nt/) ), istop ) 891 921 !$OMP PARALLEL DEFAULT(NONE) PRIVATE(ji,jj,jk,jl) & 892 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_dp,localdata_4d_dp,di,dj )893 DO jl = 1, indimlens(dimids(4))922 !$OMP& SHARED(idomain,jdomain,indimlens,dimids,start_pos,globaldata_4d_dp,localdata_4d_dp,di,dj,nt,ntchunk) 923 DO jl = 1, ntchunk 894 924 !$OMP DO 895 925 DO jk = 1, indimlens(dimids(3)) … … 1047 1077 1048 1078 ELSEIF( ndims == 4 ) THEN 1049 1079 1050 1080 SELECT CASE( xtype ) 1051 1081 CASE( NF90_BYTE ) 1052 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i1 ) )1082 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i1, start=(/1,1,1,nt/) ) ) 1053 1083 DEALLOCATE(globaldata_4d_i1) 1054 1084 CASE( NF90_SHORT ) 1055 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i2 ) )1085 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i2, start=(/1,1,1,nt/) ) ) 1056 1086 DEALLOCATE(globaldata_4d_i2) 1057 1087 CASE( NF90_INT ) 1058 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i4 ) )1088 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_i4, start=(/1,1,1,nt/) ) ) 1059 1089 DEALLOCATE(globaldata_4d_i4) 1060 1090 CASE( NF90_FLOAT ) 1061 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_sp ) )1091 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_sp, start=(/1,1,1,nt/) ) ) 1062 1092 DEALLOCATE(globaldata_4d_sp) 1063 1093 CASE( NF90_DOUBLE ) 1064 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_dp ) )1094 CALL check_nf90( nf90_put_var( outid, jv, globaldata_4d_dp, start=(/1,1,1,nt/) ) ) 1065 1095 DEALLOCATE(globaldata_4d_dp) 1066 1096 CASE DEFAULT … … 1070 1100 1071 1101 ENDIF 1102 1103 nt = nt + ntchunk 1104 1105 END DO ! WHILE loop 1072 1106 1073 1107 END DO ! loop over variables
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