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Commit c9f2ea54 authored by WAUTELET Philippe's avatar WAUTELET Philippe
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Philippe 01/08/2019: cdf2cdf: allow merge of entire Z-split files 

(cherry picked from commit bc1461b3)
parent cf799e3b
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LIBTOOLS/tools/lfi2cdf/src/mode_options.f90
+ 0
− 6
View file @ c9f2ea54
......@@ -278,12 +278,6 @@ subroutine check_options(options,infile,runmode)
call help()
end if
!Merge flag only supported if -v is set
if (options(OPTMERGE)%set .AND. .NOT.options(OPTVAR)%set) then
print *,'Error: merge option must be used with var option'
call help()
end if
!Split flag only supported if -v is set
if (options(OPTSPLIT)%set .AND. .NOT.options(OPTVAR)%set) then
options(OPTSPLIT)%set = .false.
......
LIBTOOLS/tools/lfi2cdf/src/mode_util.f90
+ 139
− 30
View file @ c9f2ea54
......@@ -7,9 +7,10 @@
! P. Wautelet 07/02/2019: force TYPE to a known value for IO_FILE_ADD2LIST
! P. Wautelet 10/04/2019: use IO_Err_handle_nc4 to handle netCDF errors
! P. Wautelet 25/06/2019: add support for 3D integer arrays
! P. Wautelet 01/08/2019: allow merge of entire Z-split files
!-----------------------------------------------------------------
MODULE mode_util
USE MODD_IO, ONLY: TFILE_ELT
USE MODD_IO, ONLY: TFILEDATA, TFILE_ELT
USE MODD_NETCDF, ONLY: DIMCDF, CDFINT
USE MODD_PARAMETERS, ONLY: JPVEXT, NLFIMAXCOMMENTLENGTH, NMNHNAMELGTMAX
use modd_precision, only: LFIINT
......@@ -95,6 +96,7 @@ CONTAINS
LOGICAL :: ladvan
LOGICAL :: GOK
TYPE(TLFIDATE),DIMENSION(MAXDATES) :: TLFIDATES
type(TFILEDATA) :: tzfile
CALL PRINT_MSG(NVERB_DEBUG,'IO','parse_infiles','called')
......@@ -229,6 +231,7 @@ CONTAINS
!If we are merging, maybe it is one of the split variable
!In that case, the 1st part of the variable is in the 1st split file with a 0001 suffix
kcdf_id2 = INFILES(1)%TFILE%TFILES_IOZ(1)%TFILE%NNCID
tzfile = INFILES(1)%TFILE%TFILES_IOZ(1)%TFILE
status = NF90_INQ_VARID(kcdf_id2,trim(yrecfm)//'0001',var_id)
IF (status == NF90_NOERR) THEN
tpreclist(ji)%LSPLIT = .true.
......@@ -243,11 +246,12 @@ CONTAINS
call IO_Err_handle_nc4( status, 'parse_infiles', 'NF90_INQ_VARID', trim(yrecfm) )
ELSE
kcdf_id2 = kcdf_id
tzfile = INFILES(1)%TFILE
ENDIF
!
IF (status == NF90_NOERR) THEN
tpreclist(ji)%found = .true.
CALL IO_Metadata_get_nc4(kcdf_id2,var_id,tpreclist(ji))
CALL IO_Metadata_get_nc4(tzfile,var_id,tpreclist(ji))
END IF
END IF
......@@ -340,7 +344,7 @@ END DO
if ( status /= NF90_NOERR ) &
call IO_Err_handle_nc4( status, 'parse_infiles', 'NF90_INQUIRE_VARIABLE', tpreclist(ji)%name )
tpreclist(ji)%found = .TRUE.
CALL IO_Metadata_get_nc4(kcdf_id,var_id,tpreclist(ji))
CALL IO_Metadata_get_nc4(INFILES(1)%TFILE,var_id,tpreclist(ji))
END DO
END IF
......@@ -698,6 +702,7 @@ END DO
REAL, DIMENSION(:,:,:), ALLOCATABLE :: XTAB3D, XTAB3D2
REAL, DIMENSION(:,:,:,:), ALLOCATABLE :: XTAB4D, XTAB4D2
TYPE(DATE_TIME) :: TZDATE
TYPE(TFILEDATA) :: TZFILE
CALL PRINT_MSG(NVERB_DEBUG,'IO','fill_files','called')
......@@ -847,7 +852,16 @@ END DO
CASE (3)
ALLOCATE(XTAB3D(IDIMLEN(1),IDIMLEN(2),IDIMLEN(3)))
IF (tpreclist(ji)%calc) ALLOCATE(XTAB3D2(IDIMLEN(1),IDIMLEN(2),IDIMLEN(3)))
CALL IO_Field_read(INFILES(1)%TFILE,tpreclist(ISRC)%TFIELD,XTAB3D)
!Hack not very clean: 3D LB fields are not split
!If NSUBFILES_IOZ is set to 0, IO_READ_FIELD will read it as a non-split field
!CAUTION: there are no guarantee the IO_READ_FIELD will continue to use this information that way...
if ( tpreclist(ji)%tfield%clbtype /= 'NONE' .or. tpreclist(ji)%name(1:2) == 'LB' ) then
tzfile = infiles(1)%tfile
tzfile%nsubfiles_ioz=0
call IO_Field_read(tzfile,tpreclist(isrc)%tfield,xtab3d)
else
call IO_Field_read(infiles(1)%tfile,tpreclist(isrc)%tfield,xtab3d)
end if
CASE (4)
ALLOCATE(XTAB4D(IDIMLEN(1),IDIMLEN(2),IDIMLEN(3),IDIMLEN(4)))
IF (tpreclist(ji)%calc) ALLOCATE(XTAB4D2(IDIMLEN(1),IDIMLEN(2),IDIMLEN(3),IDIMLEN(4)))
......@@ -1194,31 +1208,114 @@ END DO
END SUBROUTINE CLOSE_FILES
SUBROUTINE IO_Metadata_get_nc4(KFILE_ID,KVAR_ID,TPREC)
SUBROUTINE IO_Metadata_get_nc4(TPFILE,KVAR_ID,TPREC)
USE MODD_DIM_n, ONLY: NKMAX
USE MODD_PARAMETERS, ONLY: JPVEXT
INTEGER(KIND=CDFINT), INTENT(IN) :: KFILE_ID
TYPE(TFILEDATA), INTENT(IN) :: TPFILE
INTEGER(KIND=CDFINT), INTENT(IN) :: KVAR_ID
TYPE(workfield), INTENT(INOUT) :: TPREC
character(len=:), allocatable :: YSPLIT
character(len=:), allocatable :: YTIMEDEP
integer :: iblocks
INTEGER :: ILENG
INTEGER :: JDIM
INTEGER(KIND=CDFINT) :: ISTATUS
INTEGER(KIND=CDFINT) :: IFILE_ID
INTEGER(KIND=CDFINT) :: IVAR_ID
INTEGER(KIND=CDFINT),DIMENSION(NF90_MAX_VAR_DIMS) :: IDIMS_ID
LOGICAL :: GSPLIT_AT_ENTRY
CALL PRINT_MSG(NVERB_DEBUG,'IO','IO_Metadata_get_nc4','called')
ISTATUS = NF90_INQUIRE_VARIABLE(KFILE_ID,KVAR_ID,NDIMS = TPREC%NDIMS_FILE, &
!Necessary to know if we already are in a split file for determining correct number of dimensions
GSPLIT_AT_ENTRY = TPREC%LSPLIT
IFILE_ID = TPFILE%NNCID
iblocks = -1
ISTATUS = NF90_INQUIRE_VARIABLE(IFILE_ID, KVAR_ID, NDIMS = TPREC%NDIMS_FILE, &
XTYPE = TPREC%NTYPE_FILE, DIMIDS = IDIMS_ID)
if ( istatus /= NF90_NOERR ) call IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_INQUIRE_VARIABLE', '' )
!split_variable and other attributes were added in MesoNH > 5.4.2
ISTATUS = NF90_INQUIRE_ATTRIBUTE(IFILE_ID, KVAR_ID, 'split_variable', LEN=ILENG)
IF (ISTATUS == NF90_NOERR) THEN
IF (GSPLIT_AT_ENTRY) CALL PRINT_MSG(NVERB_ERROR,'IO','IO_GET_METADATA_NC4','split variable delcaration inside a split file')
ALLOCATE(CHARACTER(LEN=ILENG) :: YSPLIT)
ISTATUS = NF90_GET_ATT(IFILE_ID, KVAR_ID, 'split_variable', YSPLIT)
IF (istatus /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_GET_ATT', 'split_variable' )
IF ( YSPLIT == 'yes' ) then
TPREC%LSPLIT = .true.
ISTATUS = NF90_GET_ATT(IFILE_ID, KVAR_ID, 'ndims', TPREC%NDIMS_FILE)
IF (istatus /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_GET_ATT', 'ndims' )
IF ( TPREC%NDIMS_FILE/=3 ) CALL PRINT_MSG(NVERB_ERROR,'IO','IO_GET_METADATA_NC4', &
'split variable with ndims/=3 not supported')
ISTATUS = NF90_INQUIRE_ATTRIBUTE(IFILE_ID, KVAR_ID, 'time_dependent', LEN=ILENG)
IF (istatus /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_INQUIRE_ATTRIBUTE', &
'time_dependent' )
ALLOCATE(CHARACTER(LEN=ILENG) :: YTIMEDEP)
ISTATUS = NF90_GET_ATT(IFILE_ID, KVAR_ID, 'time_dependent', YTIMEDEP)
IF (istatus /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_GET_ATT', 'time_dependent' )
IF ( YTIMEDEP == 'yes' ) then
TPREC%TFIELD%LTIMEDEP = .TRUE.
ELSE IF ( YTIMEDEP == 'no' ) THEN
TPREC%TFIELD%LTIMEDEP = .FALSE.
ELSE
CALL PRINT_MSG(NVERB_WARNING,'IO','IO_GET_METADATA_NC4','unknown value '//trim(YTIMEDEP)// &
' for time_dependent attribute' )
END IF
ISTATUS = NF90_GET_ATT(IFILE_ID, KVAR_ID, 'split_nblocks', iblocks)
IF (istatus /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_GET_ATT', 'split_nblocks' )
!PW: todo:check tfiles_ioz exist
IFILE_ID = TPFILE%TFILES_IOZ(1)%TFILE%NNCID
istatus = NF90_INQ_VARID(IFILE_ID,trim(TPREC%NAME)//'0001',ivar_id)
IF (ISTATUS /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_INQ_VARID', &
trim(TPREC%NAME)//'0001' )
ISTATUS = NF90_INQUIRE_VARIABLE(IFILE_ID, IVAR_ID, DIMIDS = IDIMS_ID)
IF (ISTATUS /= NF90_NOERR) CALL IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_INQUIRE_VARIABLE',&
trim(TPREC%NAME)//'0001' )
DEALLOCATE(YTIMEDEP)
ELSE IF ( YSPLIT /= 'no' ) THEN
CALL PRINT_MSG(NVERB_WARNING,'IO','IO_GET_METADATA_NC4','unknown value '//trim(YSPLIT)//' for split_variable attribute' )
END IF
DEALLOCATE(YSPLIT)
END IF
ISTATUS = NF90_GET_ATT(IFILE_ID,KVAR_ID,'grid',TPREC%NGRID_FILE)
!On MesoNH versions < 5.4.0, the grid number was stored in 'GRID' instead of 'grid'
IF (ISTATUS /= NF90_NOERR) ISTATUS = NF90_GET_ATT(IFILE_ID,KVAR_ID,'GRID',TPREC%NGRID_FILE)
IF (ISTATUS /= NF90_NOERR) TPREC%NGRID_FILE = 0
ISTATUS = NF90_GET_ATT(IFILE_ID,KVAR_ID,'units',TPREC%CUNITS_FILE)
IF (ISTATUS /= NF90_NOERR) TPREC%CUNITS_FILE = ''
IF (.NOT.TPREC%LSPLIT) THEN
ALLOCATE(TPREC%NDIMSIZES_FILE(TPREC%NDIMS_FILE))
ALLOCATE(TPREC%CDIMNAMES_FILE(TPREC%NDIMS_FILE))
ELSE
ALLOCATE(TPREC%NDIMSIZES_FILE(TPREC%NDIMS_FILE+1))
ALLOCATE(TPREC%CDIMNAMES_FILE(TPREC%NDIMS_FILE+1))
IF ( GSPLIT_AT_ENTRY ) THEN
ALLOCATE(TPREC%NDIMSIZES_FILE(TPREC%NDIMS_FILE+1))
ALLOCATE(TPREC%CDIMNAMES_FILE(TPREC%NDIMS_FILE+1))
ELSE
IF (TPREC%TFIELD%LTIMEDEP) THEN
ALLOCATE(TPREC%NDIMSIZES_FILE(TPREC%NDIMS_FILE+1))
ALLOCATE(TPREC%CDIMNAMES_FILE(TPREC%NDIMS_FILE+1))
ELSE
ALLOCATE(TPREC%NDIMSIZES_FILE(TPREC%NDIMS_FILE))
ALLOCATE(TPREC%CDIMNAMES_FILE(TPREC%NDIMS_FILE))
END IF
END IF
END IF
IF (TPREC%NDIMS_FILE == 0) THEN
......@@ -1228,7 +1325,7 @@ END DO
! Fill dimensions info
ILENG = 1
DO JDIM=1,TPREC%NDIMS_FILE
ISTATUS = NF90_INQUIRE_DIMENSION(KFILE_ID,IDIMS_ID(JDIM), &
ISTATUS = NF90_INQUIRE_DIMENSION(IFILE_ID,IDIMS_ID(JDIM), &
len = TPREC%NDIMSIZES_FILE(JDIM), &
name = TPREC%CDIMNAMES_FILE(JDIM) )
if ( istatus /= NF90_NOERR ) call IO_Err_handle_nc4( istatus, 'IO_Metadata_get_nc4', 'NF90_INQUIRE_DIMENSION', '' )
......@@ -1248,29 +1345,41 @@ END DO
IF (TPREC%LSPLIT) THEN
IF( (.NOT.TPREC%TFIELD%LTIMEDEP .AND. TPREC%NDIMS_FILE/=2) &
.OR. ( TPREC%TFIELD%LTIMEDEP .AND. TPREC%NDIMS_FILE/=3) ) &
CALL PRINT_MSG(NVERB_FATAL,'IO','parse_infiles','split variables can only be 3D')
!Split variables are Z-split
ILENG = ILENG * (NKMAX+2*JPVEXT)
!Move time dimension to last (4th) position
IF (TPREC%TFIELD%LTIMEDEP) THEN
TPREC%NDIMSIZES_FILE(4) = TPREC%NDIMSIZES_FILE(3)
TPREC%CDIMNAMES_FILE(4) = TPREC%CDIMNAMES_FILE(3)
END IF
!Add vertical dimension
TPREC%NDIMSIZES_FILE(3) = NKMAX+2*JPVEXT
TPREC%CDIMNAMES_FILE(3) = 'level' !Could also be 'level_w'
CALL PRINT_MSG(NVERB_FATAL,'IO','IO_GET_METADATA_NC4',trim(TPREC%NAME)//': split variables can only be 3D')
!Split variables are Z-split
!Move time dimension to last (4th) position
IF (TPREC%TFIELD%LTIMEDEP) THEN
TPREC%NDIMSIZES_FILE(4) = TPREC%NDIMSIZES_FILE(3)
TPREC%CDIMNAMES_FILE(4) = TPREC%CDIMNAMES_FILE(3)
END IF
END IF
TPREC%NSIZE = ILENG
!Add vertical/3rd dimension
SELECT CASE(TPREC%NGRID_FILE)
CASE (1, 2, 3, 5)
TPREC%CDIMNAMES_FILE(3) = 'level'
CASE (4, 6, 7, 8)
TPREC%CDIMNAMES_FILE(3) = 'level_w'
CASE DEFAULT
TPREC%CDIMNAMES_FILE(3) = 'unknown'
END SELECT
IF (iblocks == -1 ) then
TPREC%NDIMSIZES_FILE(3) = NKMAX+2*JPVEXT
else
ISTATUS = NF90_GET_ATT(KFILE_ID,KVAR_ID,'grid',TPREC%NGRID_FILE)
!On MesoNH versions < 5.4.0, the grid number was stored in 'GRID' instead of 'grid'
IF (ISTATUS /= NF90_NOERR) ISTATUS = NF90_GET_ATT(KFILE_ID,KVAR_ID,'GRID',TPREC%NGRID_FILE)
IF (ISTATUS /= NF90_NOERR) TPREC%NGRID_FILE = 0
if (TPREC%NGRID_FILE/=0 .and. iblocks/=NKMAX+2*JPVEXT) THEN
!If size is not as expected, reset its name
CALL PRINT_MSG(NVERB_WARNING,'IO','IO_GET_METADATA_NC4',trim(TPREC%NAME)//': strange nblocks size')
TPREC%CDIMNAMES_FILE(3) = 'unknown'
end if
TPREC%NDIMSIZES_FILE(3) = iblocks
end if
ILENG = ILENG * TPREC%NDIMSIZES_FILE(3)
END IF
END IF
ISTATUS = NF90_GET_ATT(KFILE_ID,KVAR_ID,'units',TPREC%CUNITS_FILE)
IF (ISTATUS /= NF90_NOERR) TPREC%CUNITS_FILE = ''
TPREC%NSIZE = ILENG
END SUBROUTINE IO_Metadata_get_nc4
......@@ -1311,7 +1420,7 @@ END DO
END IF
IF (TRIM(TPREC%TDIMS(JJ)%name)/='time' .AND. &
TPREC%TDIMS(JJ)%len /= TPREC%NDIMSIZES_FILE(JJ)) THEN
CALL PRINT_MSG(NVERB_WARNING,'IO','parse_infiles','problem with dimensions for '//TPREC%TFIELD%CMNHNAME)
CALL PRINT_MSG(NVERB_WARNING,'IO','IO_FILL_DIMS_NC4','problem with dimensions for '//TPREC%TFIELD%CMNHNAME)
KRESP = -3
EXIT
END IF
......
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