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netcdf_io.F90
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!***********************************************************************
!* 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/>.
!***********************************************************************
!> @file
!> @brief Create a netcdf type, which can be extended to meet
!! our various I/O needs.
module netcdf_io_mod
use, intrinsic :: iso_fortran_env
use netcdf
use mpp_mod
use fms_io_utils_mod
implicit none
private
!Module constants.
integer, parameter :: variable_missing = -1
integer, parameter :: dimension_missing = -1
integer, parameter, public :: no_unlimited_dimension = -1 !> No unlimited dimension in file.
character(len=1), parameter :: missing_path = ""
integer, parameter :: missing_ncid = -1
integer, parameter :: missing_rank = -1
integer, parameter, public :: define_mode = 0
integer, parameter, public :: data_mode = 1
integer, parameter, public :: max_num_restart_vars = 200
integer, parameter, public :: unlimited = nf90_unlimited !> Wrapper to specify unlimited dimension.
integer, parameter :: dimension_not_found = 0
integer, parameter, public :: max_num_compressed_dims = 10 !> Maximum number of compressed
!! dimensions allowed.
integer, private :: fms2_ncchksz = -1 !< Chunksize (bytes) used in nc_open and nc_create
integer, private :: fms2_nc_format_param = -1 !< Netcdf format type param used in nc_create
character (len = 10), private :: fms2_nc_format !< Netcdf format type used in netcdf_file_open
integer, private :: fms2_header_buffer_val = -1 !< value used in NF__ENDDEF
!> @brief Restart variable.
type :: RestartVariable_t
character(len=256) :: varname !< Variable name.
class(*), pointer :: data0d => null() !< Scalar data pointer.
class(*), dimension(:), pointer :: data1d => null() !< 1d data pointer.
class(*), dimension(:,:), pointer :: data2d => null() !< 2d data pointer.
class(*), dimension(:,:,:), pointer :: data3d => null() !< 3d data pointer.
class(*), dimension(:,:,:,:), pointer :: data4d => null() !< 4d data pointer.
class(*), dimension(:,:,:,:,:), pointer :: data5d => null() !< 5d data pointer.
logical :: was_read !< Flag to support legacy "query_initialized" feature, which
!! keeps track if a file was read.
endtype RestartVariable_t
!> @brief Compressed dimension.
type :: CompressedDimension_t
character(len=256) :: dimname !< Dimension name.
integer, dimension(:), allocatable :: npes_corner !< Array of starting
!! indices for each rank.
integer, dimension(:), allocatable :: npes_nelems !< Number of elements
!! associated with each
!! rank.
integer :: nelems !< Total size of the dimension.
endtype CompressedDimension_t
!> @brief Netcdf file type.
type, public :: FmsNetcdfFile_t
character(len=256) :: path !< File path.
logical :: is_readonly !< Flag telling if the file is readonly.
integer :: ncid !< Netcdf file id.
character(len=256) :: nc_format !< Netcdf file format.
integer, dimension(:), allocatable :: pelist !< List of ranks who will
!! communicate.
integer :: io_root !< I/O root rank of the pelist.
logical :: is_root !< Flag telling if the current rank is the
!! I/O root.
logical :: is_restart !< Flag telling if the this file is a restart
!! file (that has internal pointers to data).
logical :: mode_is_append !! true if file is open in "append" mode
logical, allocatable :: is_open !< Allocated and set to true if opened.
type(RestartVariable_t), dimension(:), allocatable :: restart_vars !< Array of registered
!! restart variables.
integer :: num_restart_vars !< Number of registered restart variables.
type(CompressedDimension_t), dimension(:), allocatable :: compressed_dims !< "Compressed" dimension.
integer :: num_compressed_dims !< Number of compressed dimensions.
logical :: is_diskless !< Flag telling whether this is a diskless file.
character (len=20) :: time_name
endtype FmsNetcdfFile_t
!> @brief Range type for a netcdf variable.
type, public :: Valid_t
logical :: has_range !< Flag that's true if both min/max exist for a variable.
logical :: has_min !< Flag that's true if min exists for a variable.
logical :: has_max !< Flag that's true if max exists for a variable.
logical :: has_fill !< Flag that's true a user defined fill value.
logical :: has_missing !< Flag that's true a user defined missing value.
real(kind=real64) :: fill_val !< Unpacked fill value for a variable.
real(kind=real64) :: min_val !< Unpacked minimum value allowed for a variable.
real(kind=real64) :: max_val !< Unpacked maximum value allowed for a variable.
real(kind=real64) :: missing_val !< Unpacked missing value for a variable.
endtype Valid_t
public :: netcdf_io_init
public :: netcdf_file_open
public :: netcdf_file_close
public :: netcdf_add_dimension
public :: netcdf_add_variable
public :: netcdf_add_restart_variable
public :: global_att_exists
public :: variable_att_exists
public :: register_global_attribute
public :: register_variable_attribute
public :: get_global_attribute
public :: get_variable_attribute
public :: get_num_dimensions
public :: get_dimension_names
public :: dimension_exists
public :: is_dimension_unlimited
public :: get_dimension_size
public :: get_num_variables
public :: get_variable_names
public :: variable_exists
public :: get_variable_num_dimensions
public :: get_variable_dimension_names
public :: get_variable_size
public :: get_variable_unlimited_dimension_index
public :: netcdf_read_data
public :: netcdf_write_data
public :: compressed_write
public :: netcdf_save_restart
public :: netcdf_restore_state
public :: get_valid
public :: is_valid
public :: get_unlimited_dimension_name
public :: netcdf_file_open_wrap
public :: netcdf_file_close_wrap
public :: netcdf_add_variable_wrap
public :: netcdf_save_restart_wrap
public :: compressed_write_0d_wrap
public :: compressed_write_1d_wrap
public :: compressed_write_2d_wrap
public :: compressed_write_3d_wrap
public :: compressed_write_4d_wrap
public :: compressed_write_5d_wrap
public :: compressed_read_0d
public :: compressed_read_1d
public :: compressed_read_2d
public :: compressed_read_3d
public :: compressed_read_4d
public :: compressed_read_5d
public :: register_compressed_dimension
public :: netcdf_add_restart_variable_0d_wrap
public :: netcdf_add_restart_variable_1d_wrap
public :: netcdf_add_restart_variable_2d_wrap
public :: netcdf_add_restart_variable_3d_wrap
public :: netcdf_add_restart_variable_4d_wrap
public :: netcdf_add_restart_variable_5d_wrap
public :: compressed_start_and_count
public :: get_fill_value
public :: get_variable_sense
public :: get_variable_missing
public :: get_variable_units
public :: get_time_calendar
public :: is_registered_to_restart
public :: set_netcdf_mode
public :: check_netcdf_code
public :: check_if_open
public :: set_fileobj_time_name
interface netcdf_add_restart_variable
module procedure netcdf_add_restart_variable_0d
module procedure netcdf_add_restart_variable_1d
module procedure netcdf_add_restart_variable_2d
module procedure netcdf_add_restart_variable_3d
module procedure netcdf_add_restart_variable_4d
module procedure netcdf_add_restart_variable_5d
end interface netcdf_add_restart_variable
interface netcdf_read_data
module procedure netcdf_read_data_0d
module procedure netcdf_read_data_1d
module procedure netcdf_read_data_2d
module procedure netcdf_read_data_3d
module procedure netcdf_read_data_4d
module procedure netcdf_read_data_5d
end interface netcdf_read_data
interface netcdf_write_data
module procedure netcdf_write_data_0d
module procedure netcdf_write_data_1d
module procedure netcdf_write_data_2d
module procedure netcdf_write_data_3d
module procedure netcdf_write_data_4d
module procedure netcdf_write_data_5d
end interface netcdf_write_data
interface compressed_write
module procedure compressed_write_0d
module procedure compressed_write_1d
module procedure compressed_write_2d
module procedure compressed_write_3d
module procedure compressed_write_4d
module procedure compressed_write_5d
end interface compressed_write
interface register_global_attribute
module procedure register_global_attribute_0d
module procedure register_global_attribute_1d
end interface register_global_attribute
interface register_variable_attribute
module procedure register_variable_attribute_0d
module procedure register_variable_attribute_1d
end interface register_variable_attribute
interface get_global_attribute
module procedure get_global_attribute_0d
module procedure get_global_attribute_1d
end interface get_global_attribute
interface get_variable_attribute
module procedure get_variable_attribute_0d
module procedure get_variable_attribute_1d
end interface get_variable_attribute
contains
!> @brief Accepts the namelist fms2_io_nml variables relevant to netcdf_io_mod
subroutine netcdf_io_init (chksz, header_buffer_val, netcdf_default_format)
integer, intent(in) :: chksz
character (len = 10), intent(in) :: netcdf_default_format
integer, intent(in) :: header_buffer_val
fms2_ncchksz = chksz
fms2_header_buffer_val = header_buffer_val
if (string_compare(netcdf_default_format, "64bit", .true.)) then
fms2_nc_format_param = nf90_64bit_offset
call string_copy(fms2_nc_format, "64bit")
elseif (string_compare(netcdf_default_format, "classic", .true.)) then
fms2_nc_format_param = nf90_classic_model
call string_copy(fms2_nc_format, "classic")
elseif (string_compare(netcdf_default_format, "netcdf4", .true.)) then
fms2_nc_format_param = nf90_netcdf4
call string_copy(fms2_nc_format, "netcdf4")
else
call error("unrecognized netcdf file format "//trim(netcdf_default_format)// &
'. The acceptable values are "64bit", "classic", "netcdf4". Check fms2_io_nml: netcdf_default_format')
endif
end subroutine netcdf_io_init
!> @brief Check for errors returned by netcdf.
!! @internal
subroutine check_netcdf_code(err)
integer, intent(in) :: err !< Code returned by netcdf.
character(len=80) :: buf
if (err .ne. nf90_noerr) then
buf = nf90_strerror(err)
call error(trim(buf))
endif
end subroutine check_netcdf_code
!> @brief Switch to the correct netcdf mode.
!! @internal
subroutine set_netcdf_mode(ncid, mode)
integer, intent(in) :: ncid !< Netcdf file id.
integer, intent(in) :: mode !< Netcdf file mode.
integer :: err
if (mode .eq. define_mode) then
err = nf90_redef(ncid)
if (err .eq. nf90_eindefine .or. err .eq. nf90_eperm) then
return
endif
elseif (mode .eq. data_mode) then
if (fms2_header_buffer_val == -1) call error("set_netcdf_mode: fms2_header_buffer_val not set, call fms2_io_init")
err = nf90_enddef(ncid, h_minfree=fms2_header_buffer_val)
if (err .eq. nf90_enotindefine .or. err .eq. nf90_eperm) then
return
endif
else
call error("mode must be either define_mode or data_mode.")
endif
call check_netcdf_code(err)
end subroutine set_netcdf_mode
!> @brief Get the id of a dimension from its name.
!! @return Dimension id, or dimension_missing if it doesn't exist.
!! @internal
function get_dimension_id(ncid, dimension_name, allow_failure) &
result(dimid)
integer, intent(in) :: ncid !< Netcdf file id.
character(len=*), intent(in) :: dimension_name !< Dimension name.
logical, intent(in), optional :: allow_failure !< Flag that prevents
!! crash if dimension
!! does not exist.
integer :: dimid
integer :: err
err = nf90_inq_dimid(ncid, trim(dimension_name), dimid)
if (present(allow_failure)) then
if (allow_failure .and. err .eq. nf90_ebaddim) then
dimid = dimension_missing
return
endif
endif
call check_netcdf_code(err)
end function get_dimension_id
!> @brief Get the id of a variable from its name.
!! @return Variable id, or variable_missing if it doesn't exist.
!! @internal
function get_variable_id(ncid, variable_name, allow_failure) &
result(varid)
integer, intent(in) :: ncid !< Netcdf file object.
character(len=*), intent(in) :: variable_name !< Variable name.
logical, intent(in), optional :: allow_failure !< Flag that prevents
!! crash if variable does
!! not exist.
integer :: varid
integer :: err
err = nf90_inq_varid(ncid, trim(variable_name), varid)
if (present(allow_failure)) then
if (allow_failure .and. err .eq. nf90_enotvar) then
varid = variable_missing
return
endif
endif
call check_netcdf_code(err)
end function get_variable_id
!> @brief Determine if an attribute exists.
!! @return Flag telling if the attribute exists.
!! @internal
function attribute_exists(ncid, varid, attribute_name) &
result(att_exists)
integer, intent(in) :: ncid !< Netcdf file id.
integer, intent(in) :: varid !< Variable id.
character(len=*), intent(in) :: attribute_name !< Attribute name.
logical :: att_exists
integer :: err
err = nf90_inquire_attribute(ncid, varid, trim(attribute_name))
if (err .eq. nf90_enotatt) then
att_exists = .false.
else
call check_netcdf_code(err)
att_exists = .true.
endif
end function attribute_exists
!> @brief Get the type of a netcdf attribute.
!! @return The netcdf type of the attribute.
!! @internal
function get_attribute_type(ncid, varid, attname) &
result(xtype)
integer, intent(in) :: ncid !< Netcdf file id.
integer, intent(in) :: varid !< Variable id.
character(len=*), intent(in) :: attname !< Attribute name.
integer :: xtype
integer :: err
err = nf90_inquire_attribute(ncid, varid, attname, xtype=xtype)
call check_netcdf_code(err)
end function get_attribute_type
!> @brief Get the type of a netcdf variable.
!! @return The netcdf type of the variable.
!! @internal
function get_variable_type(ncid, varid) &
result(xtype)
integer, intent(in) :: ncid !< Netcdf file id.
integer, intent(in) :: varid !< Variable id.
integer :: xtype
integer :: err
err = nf90_inquire_variable(ncid, varid, xtype=xtype)
call check_netcdf_code(err)
end function get_variable_type
!> @brief Open a netcdf file.
!! @return .true. if open succeeds, or else .false.
function netcdf_file_open(fileobj, path, mode, nc_format, pelist, is_restart, dont_add_res_to_filename) &
result(success)
class(FmsNetcdfFile_t), intent(inout) :: fileobj !< File object.
character(len=*), intent(in) :: path !< File path.
character(len=*), intent(in) :: mode !< File mode. Allowed values are:
!! "read", "append", "write", or
!! "overwrite".
character(len=*), intent(in), optional :: nc_format !< Netcdf format that
!! new files are written
!! as. Allowed values
!! are: "64bit", "classic",
!! or "netcdf4". Defaults to
!! "64bit". This overwrites
!! the value set in the fms2io
!! namelist
integer, dimension(:), intent(in), optional :: pelist !< List of ranks associated
!! with this file. If not
!! provided, only the current
!! rank will be able to
!! act on the file.
logical, intent(in), optional :: is_restart !< Flag telling if this file
!! is a restart file. Defaults
!! to false.
logical, intent(in), optional :: dont_add_res_to_filename !< Flag indicating not to add
!! ".res" to the filename
logical :: success
integer :: nc_format_param
integer :: err
character(len=256) :: buf
logical :: is_res
logical :: dont_add_res !< flag indicated to not add ".res" to the filename
if (allocated(fileobj%is_open)) then
if (fileobj%is_open) then
success = .true.
return
endif
endif
!< Only add ".res" to the file path if is_restart is set to true
!! and dont_add_res_to_filename is set to false.
is_res = .false.
if (present(is_restart)) then
is_res = is_restart
endif
dont_add_res = .false.
if (present(dont_add_res_to_filename)) then
dont_add_res = dont_add_res_to_filename
endif
if (is_res .and. .not. dont_add_res) then
call restart_filepath_mangle(buf, trim(path))
else
call string_copy(buf, trim(path))
endif
!Check if the file exists.
success = .true.
if (string_compare(mode, "read", .true.) .or. string_compare(mode, "append", .true.)) then
success = file_exists(buf)
if (.not. success) then
return
endif
endif
!Store properties in the derived type.
call string_copy(fileobj%path, trim(buf))
if (present(pelist)) then
allocate(fileobj%pelist(size(pelist)))
fileobj%pelist(:) = pelist(:)
else
allocate(fileobj%pelist(1))
fileobj%pelist(1) = mpp_pe()
endif
fileobj%io_root = fileobj%pelist(1)
fileobj%is_root = mpp_pe() .eq. fileobj%io_root
!Open the file with netcdf if this rank is the I/O root.
if (fileobj%is_root) then
if (fms2_ncchksz == -1) call error("netcdf_file_open:: fms2_ncchksz not set.")
if (fms2_nc_format_param == -1) call error("netcdf_file_open:: fms2_nc_format_param not set.")
if (present(nc_format)) then
if (string_compare(nc_format, "64bit", .true.)) then
nc_format_param = nf90_64bit_offset
elseif (string_compare(nc_format, "classic", .true.)) then
nc_format_param = nf90_classic_model
elseif (string_compare(nc_format, "netcdf4", .true.)) then
nc_format_param = nf90_netcdf4
else
call error("unrecognized netcdf file format "//trim(nc_format)//".")
endif
call string_copy(fileobj%nc_format, nc_format)
else
call string_copy(fileobj%nc_format, trim(fms2_nc_format))
nc_format_param = fms2_nc_format_param
endif
if (string_compare(mode, "read", .true.)) then
err = nf90_open(trim(fileobj%path), nf90_nowrite, fileobj%ncid, chunksize=fms2_ncchksz)
elseif (string_compare(mode, "append", .true.)) then
err = nf90_open(trim(fileobj%path), nf90_write, fileobj%ncid, chunksize=fms2_ncchksz)
elseif (string_compare(mode, "write", .true.)) then
err = nf90_create(trim(fileobj%path), ior(nf90_noclobber, nc_format_param), fileobj%ncid, chunksize=fms2_ncchksz)
elseif (string_compare(mode,"overwrite",.true.)) then
err = nf90_create(trim(fileobj%path), ior(nf90_clobber, nc_format_param), fileobj%ncid, chunksize=fms2_ncchksz)
else
call error("unrecognized file mode "//trim(mode)//".")
endif
call check_netcdf_code(err)
else
fileobj%ncid = missing_ncid
endif
fileobj%is_diskless = .false.
!Allocate memory.
fileobj%is_restart = is_res
if (fileobj%is_restart) then
allocate(fileobj%restart_vars(max_num_restart_vars))
fileobj%num_restart_vars = 0
endif
fileobj%is_readonly = string_compare(mode, "read", .true.)
fileobj%mode_is_append = string_compare(mode, "append", .true.)
allocate(fileobj%compressed_dims(max_num_compressed_dims))
fileobj%num_compressed_dims = 0
! Set the is_open flag to true for this file object.
if (.not.allocated(fileobj%is_open)) allocate(fileobj%is_open)
fileobj%is_open = .true.
end function netcdf_file_open
!> @brief Close a netcdf file.
subroutine netcdf_file_close(fileobj)
class(FmsNetcdfFile_t),intent(inout) :: fileobj !< File object.
integer :: err
integer :: i
if (fileobj%is_root) then
err = nf90_close(fileobj%ncid)
call check_netcdf_code(err)
endif
if (allocated(fileobj%is_open)) fileobj%is_open = .false.
fileobj%path = missing_path
fileobj%ncid = missing_ncid
if (allocated(fileobj%pelist)) then
deallocate(fileobj%pelist)
endif
fileobj%io_root = missing_rank
fileobj%is_root = .false.
if (allocated(fileobj%restart_vars)) then
deallocate(fileobj%restart_vars)
endif
fileobj%is_restart = .false.
fileobj%num_restart_vars = 0
do i = 1, fileobj%num_compressed_dims
if (allocated(fileobj%compressed_dims(i)%npes_corner)) then
deallocate(fileobj%compressed_dims(i)%npes_corner)
endif
if (allocated(fileobj%compressed_dims(i)%npes_nelems)) then
deallocate(fileobj%compressed_dims(i)%npes_nelems)
endif
enddo
if (allocated(fileobj%compressed_dims)) then
deallocate(fileobj%compressed_dims)
endif
end subroutine netcdf_file_close
!> @brief Get the index of a compressed dimension in a file object.
!! @return Index of the compressed dimension.
!! @internal
function get_compressed_dimension_index(fileobj, dim_name) &
result(dindex)
class(FmsNetcdfFile_t), intent(in) :: fileobj !< File object.
character(len=*), intent(in) :: dim_name !< Dimension name.
integer :: dindex
integer :: i
dindex = dimension_not_found
do i = 1, fileobj%num_compressed_dims
if (string_compare(fileobj%compressed_dims(i)%dimname, dim_name)) then
dindex = i
return
endif
enddo
end function get_compressed_dimension_index
!> @brief Add a compressed dimension to a file object.
!! @internal
subroutine append_compressed_dimension(fileobj, dim_name, npes_corner, &
npes_nelems)
class(FmsNetcdfFile_t), intent(inout) :: fileobj !< File object.
character(len=*), intent(in) :: dim_name !< Dimension name.
integer, dimension(:), intent(in) :: npes_corner !< Array of starting
!! indices for each rank.
integer, dimension(:), intent(in) :: npes_nelems !< Number of elements
!! associated with each
!! rank.
integer :: n
if (get_compressed_dimension_index(fileobj, dim_name) .ne. dimension_not_found) then
call error("dimension "//trim(dim_name)//" already registered" &
//" to file "//trim(fileobj%path)//".")
endif
fileobj%num_compressed_dims = fileobj%num_compressed_dims + 1
n = fileobj%num_compressed_dims
if (n .gt. max_num_compressed_dims) then
call error("number of compressed dimensions exceeds limit.")
endif
call string_copy(fileobj%compressed_dims(n)%dimname, dim_name)
if (size(npes_corner) .ne. size(fileobj%pelist) .or. &
size(npes_nelems) .ne. size(fileobj%pelist)) then
call error("incorrect size for input npes_corner or npes_nelems arrays.")
endif
allocate(fileobj%compressed_dims(n)%npes_corner(size(fileobj%pelist)))
fileobj%compressed_dims(n)%npes_corner(:) = npes_corner(:)
allocate(fileobj%compressed_dims(n)%npes_nelems(size(fileobj%pelist)))
fileobj%compressed_dims(n)%npes_nelems(:) = npes_nelems(:)
fileobj%compressed_dims(n)%nelems = sum(fileobj%compressed_dims(n)%npes_nelems)
end subroutine append_compressed_dimension
!> @brief Add a dimension to a file.
subroutine netcdf_add_dimension(fileobj, dimension_name, dimension_length, &
is_compressed)
class(FmsNetcdfFile_t), intent(inout) :: fileobj !< File object.
character(len=*), intent(in) :: dimension_name !< Dimension name.
integer, intent(in) :: dimension_length !< Dimension length.
logical, intent(in), optional :: is_compressed !< Changes the meaning of dim_len from
!! referring to the total size of the
!! dimension (when false) to the local
!! size for the current rank (when true).
integer :: dim_len
integer, dimension(:), allocatable :: npes_start
integer, dimension(:), allocatable :: npes_count
integer :: i
integer :: err
integer :: dimid
dim_len = dimension_length
if (present(is_compressed)) then
if (is_compressed) then
!Gather all local dimension lengths on the I/O root pe.
allocate(npes_start(size(fileobj%pelist)))
allocate(npes_count(size(fileobj%pelist)))
do i = 1, size(fileobj%pelist)
if (fileobj%pelist(i) .eq. mpp_pe()) then
npes_count(i) = dim_len
else
call mpp_recv(npes_count(i), fileobj%pelist(i), block=.false.)
call mpp_send(dim_len, fileobj%pelist(i))
endif
enddo
call mpp_sync_self(check=event_recv)
call mpp_sync_self(check=event_send)
npes_start(1) = 1
do i = 1, size(fileobj%pelist)-1
npes_start(i+1) = npes_start(i) + npes_count(i)
enddo
call append_compressed_dimension(fileobj, dimension_name, npes_start, &
npes_count)
dim_len = sum(npes_count)
endif
endif
if (fileobj%is_root .and. .not. fileobj%is_readonly) then
call set_netcdf_mode(fileobj%ncid, define_mode)
err = nf90_def_dim(fileobj%ncid, trim(dimension_name), dim_len, dimid)
call check_netcdf_code(err)
endif
end subroutine netcdf_add_dimension
!> @brief Add a compressed dimension.
subroutine register_compressed_dimension(fileobj, dimension_name, &
npes_corner, npes_nelems)
class(FmsNetcdfFile_t), intent(inout) :: fileobj !< File object.
character(len=*), intent(in) :: dimension_name !< Dimension name.
integer, dimension(:), intent(in) :: npes_corner !< Array of starting
!! indices for each rank.
integer, dimension(:), intent(in) :: npes_nelems !< Number of elements
!! associated with each
!! rank.
integer :: dsize
integer :: fdim_size
call append_compressed_dimension(fileobj, dimension_name, npes_corner, npes_nelems)
dsize = sum(npes_nelems)
if (fileobj%is_readonly) then
call get_dimension_size(fileobj, dimension_name, fdim_size, broadcast=.true.)
if (fdim_size .ne. dsize) then
call error("dimension "//trim(dimension_name)//" does not match" &
//" the size of the associated compressed axis.")
endif
else
call netcdf_add_dimension(fileobj, dimension_name, dsize)
endif
end subroutine register_compressed_dimension
!> @brief Add a variable to a file.
subroutine netcdf_add_variable(fileobj, variable_name, variable_type, dimensions)
class(FmsNetcdfFile_t), intent(in) :: fileobj !< File object.
character(len=*), intent(in) :: variable_name !< Variable name.
character(len=*), intent(in) :: variable_type !< Variable type. Allowed
!! values are: "char", "int", "int64",
!! "float", or "double".
character(len=*), dimension(:), intent(in), optional :: dimensions !< Dimension names.
integer :: err
integer, dimension(:), allocatable :: dimids
integer :: vtype
integer :: varid
integer :: i
if (fileobj%is_root) then
call set_netcdf_mode(fileobj%ncid, define_mode)
if (string_compare(variable_type, "int", .true.)) then
vtype = nf90_int
elseif (string_compare(variable_type, "int64", .true.)) then
vtype = nf90_int64
elseif (string_compare(variable_type, "float", .true.)) then
vtype = nf90_float
elseif (string_compare(variable_type, "double", .true.)) then
vtype = nf90_double
elseif (string_compare(variable_type, "char", .true.)) then
vtype = nf90_char
if (.not. present(dimensions)) then
call error("string variables require a string length dimension.")
endif
else
call error("unsupported type.")
endif
if (present(dimensions)) then
allocate(dimids(size(dimensions)))
do i = 1, size(dimids)
dimids(i) = get_dimension_id(fileobj%ncid, trim(dimensions(i)))
enddo
err = nf90_def_var(fileobj%ncid, trim(variable_name), vtype, dimids, varid)
deallocate(dimids)
else
err = nf90_def_var(fileobj%ncid, trim(variable_name), vtype, varid)
endif
call check_netcdf_code(err)
endif
end subroutine netcdf_add_variable
!> @brief Given a compressed variable, get the index of the compressed
!! dimension.
!! @return Index of the compressed dimension or dimension_not_found.
function get_variable_compressed_dimension_index(fileobj, variable_name, broadcast) &
result(compressed_dimension_index)
class(FmsNetcdfFile_t), intent(in) :: fileobj !< File object.
character(len=*), intent(in) :: variable_name !< Variable name.
logical, intent(in), optional :: broadcast !< Flag controlling whether or
!! not the data will be
!! broadcasted to non
!! "I/O root" ranks.
!! The broadcast will be done
!! by default.
integer, dimension(2) :: compressed_dimension_index
integer :: ndims
character(len=nf90_max_name), dimension(:), allocatable :: dim_names
integer :: i
integer :: j
compressed_dimension_index = dimension_not_found
if (fileobj%is_root) then
ndims = get_variable_num_dimensions(fileobj, variable_name, broadcast=.false.)
if (ndims .gt. 0) then
allocate(dim_names(ndims))
call get_variable_dimension_names(fileobj, variable_name, dim_names, broadcast=.false.)
do i = 1, size(dim_names)
j = get_compressed_dimension_index(fileobj,dim_names(i))
if (j .ne. dimension_not_found) then
compressed_dimension_index(1) = i
compressed_dimension_index(2) = j
exit
endif
enddo
deallocate(dim_names)
endif
endif
if (present(broadcast)) then
if (.not. broadcast) then
return
endif
endif
call mpp_broadcast(compressed_dimension_index(1), fileobj%io_root, pelist=fileobj%pelist)
end function get_variable_compressed_dimension_index
!> @brief Add a restart variable to a FmsNetcdfFile_t type.
!! @internal
subroutine add_restart_var_to_array(fileobj, variable_name)
class(FmsNetcdfFile_t), intent(inout) :: fileobj !< Netcdf file object.
character(len=*), intent(in) :: variable_name !< Variable name.
integer :: i
if (.not. fileobj%is_restart) then
call error("file "//trim(fileobj%path)//" is not a restart file.")
endif
do i = 1, fileobj%num_restart_vars
if (string_compare(fileobj%restart_vars(i)%varname, variable_name, .true.)) then
call error("variable "//trim(variable_name)//" has already" &
//" been added to restart file "//trim(fileobj%path)//".")
endif
enddo
fileobj%num_restart_vars = fileobj%num_restart_vars + 1
if (fileobj%num_restart_vars .gt. max_num_restart_vars) then
call error("Number of restart variables exceeds limit.")
endif
call string_copy(fileobj%restart_vars(fileobj%num_restart_vars)%varname, &
variable_name)
end subroutine add_restart_var_to_array
!> @brief Loop through registered restart variables and write them to
!! a netcdf file.
subroutine netcdf_save_restart(fileobj, unlim_dim_level)
class(FmsNetcdfFile_t), intent(in) :: fileobj !< File object.
integer, intent(in), optional :: unlim_dim_level !< Unlimited dimension
!! level.
integer :: i
if (.not. fileobj%is_restart) then
call error("file "//trim(fileobj%path)//" is not a restart file.")
endif
do i = 1, fileobj%num_restart_vars
if (associated(fileobj%restart_vars(i)%data0d)) then
call compressed_write(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data0d, &
unlim_dim_level=unlim_dim_level)
elseif (associated(fileobj%restart_vars(i)%data1d)) then
call compressed_write(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data1d, &
unlim_dim_level=unlim_dim_level)
elseif (associated(fileobj%restart_vars(i)%data2d)) then
call compressed_write(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data2d, &
unlim_dim_level=unlim_dim_level)
elseif (associated(fileobj%restart_vars(i)%data3d)) then
call compressed_write(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data3d, &
unlim_dim_level=unlim_dim_level)
elseif (associated(fileobj%restart_vars(i)%data4d)) then
call compressed_write(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data4d, &
unlim_dim_level=unlim_dim_level)
else
call error("this branch should not be reached.")
endif
enddo
end subroutine netcdf_save_restart
!> @brief Loop through registered restart variables and read them from
!! a netcdf file.
subroutine netcdf_restore_state(fileobj, unlim_dim_level)
type(FmsNetcdfFile_t), intent(inout) :: fileobj !< File object.
integer, intent(in), optional :: unlim_dim_level !< Unlimited dimension
!! level.
integer :: i
if (.not. fileobj%is_restart) then
call error("file "//trim(fileobj%path)//" is not a restart file.")
endif
do i = 1, fileobj%num_restart_vars
if (associated(fileobj%restart_vars(i)%data0d)) then
call netcdf_read_data(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data0d, &
unlim_dim_level=unlim_dim_level, &
broadcast=.true.)
elseif (associated(fileobj%restart_vars(i)%data1d)) then
call netcdf_read_data(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data1d, &
unlim_dim_level=unlim_dim_level, &
broadcast=.true.)
elseif (associated(fileobj%restart_vars(i)%data2d)) then
call netcdf_read_data(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data2d, &
unlim_dim_level=unlim_dim_level, &
broadcast=.true.)
elseif (associated(fileobj%restart_vars(i)%data3d)) then
call netcdf_read_data(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data3d, &
unlim_dim_level=unlim_dim_level, &
broadcast=.true.)
elseif (associated(fileobj%restart_vars(i)%data4d)) then
call netcdf_read_data(fileobj, fileobj%restart_vars(i)%varname, &
fileobj%restart_vars(i)%data4d, &
unlim_dim_level=unlim_dim_level, &
broadcast=.true.)
else
call error("this branch should not be reached.")
endif
enddo
end subroutine netcdf_restore_state
!> @brief Determine if a global attribute exists.
!! @return Flag telling if a global attribute exists.
function global_att_exists(fileobj, attribute_name, broadcast) &
result(att_exists)
class(FmsNetcdfFile_t), intent(in) :: fileobj !< File object.
character(len=*), intent(in) :: attribute_name !< Attribute name.
logical, intent(in), optional :: broadcast !< Flag controlling whether or
!! not the data will be
!! broadcasted to non
!! "I/O root" ranks.
!! The broadcast will be done
!! by default.
logical :: att_exists
if (fileobj%is_root) then
att_exists = attribute_exists(fileobj%ncid, nf90_global, trim(attribute_name))
endif
if (present(broadcast)) then
if (.not. broadcast) then
return
endif
endif
call mpp_broadcast(att_exists, fileobj%io_root, pelist=fileobj%pelist)
end function global_att_exists
!> @brief Determine if a variable's attribute exists.
!! @return Flag telling if the variable's attribute exists.
function variable_att_exists(fileobj, variable_name, attribute_name, &
broadcast) &
result(att_exists)
class(FmsNetcdfFile_t), intent(in) :: fileobj !< File object.
character(len=*), intent(in) :: variable_name !< Variable name.
character(len=*), intent(in) :: attribute_name !< Attribute name.
logical, intent(in), optional :: broadcast !< Flag controlling whether or
!! not the data will be
!! broadcasted to non
!! "I/O root" ranks.
!! The broadcast will be done
!! by default.
logical :: att_exists
integer :: varid
att_exists = .false.
if (fileobj%is_root) then
varid = get_variable_id(fileobj%ncid, trim(variable_name))
att_exists = attribute_exists(fileobj%ncid, varid, trim(attribute_name))
endif