Fortran Examples

These examples are based on the CMOR repository’s examples/fortran directory. They use the same shared CMIP7 user input file as the Python examples and load CMIP7 tables from a local clone of WCRP-CMIP/cmip7-cmor-tables.

Create and activate a Conda or Mamba environment with CMOR and a Fortran compiler:

mamba create -n cmor-fortran -c conda-forge cmor fortran-compiler udunits2
mamba activate cmor-fortran

If you use Conda instead of Mamba, use the same package list:

conda create -n cmor-fortran -c conda-forge cmor fortran-compiler udunits2
conda activate cmor-fortran

Install the CMIP7 tables in the working directory where you will run the examples:

git clone https://github.com/WCRP-CMIP/cmip7-cmor-tables.git

Run the examples from a working directory that contains the cmip7-cmor-tables repository using the run_examples.sh script:

chmod a+x run_examples.sh
./run_examples.sh

The examples expect tables under ./cmip7-cmor-tables/tables in the directory where you run the script. To use a different table location, set CMOR_TABLES_PATH to the directory containing the CMIP7 table JSON files. To use a different user input file, set CMOR_INPUT_PATH.

Each example builds the CMIP7 compound variable name and uses it to read CMIP7_cell_measures.json and CMIP7_long_name_overrides.json before writing data. The fixed-field example overrides frequency from the shared user input file to fx.

CMOR Input Files

Click to expand shared JSON input

{
  "_AXIS_ENTRY_FILE": "CMIP7_coordinate.json",
  "_FORMULA_VAR_FILE": "CMIP7_formula_terms.json",
  "_cmip7_option": 1,
  "_controlled_vocabulary_file": "../tables-cvs/cmor-cvs.json",
  "activity_id": "CMIP",
  "archive_id": "WCRP",
  "calendar": "360_day",
  "experiment_id": "amip",
  "forcing_index": "f1",
  "frequency": "mon",
  "grid_label": "g999",
  "host_collection": "CMIP7",
  "initialization_index": "i1",
  "institution_id": "MOHC",
  "license_id": "CC-BY-4.0",
  "nominal_resolution": "100 km",
  "outpath": "output",
  "physics_index": "p1",
  "realization_index": "r1",
  "region": "glb",
  "source_id": "ACCESS-ESM1-6"
}

Common Fortran Utilities

Click to expand common Fortran code

module cmip7_fortran_common
  use cmor_users_functions
  implicit none

  integer, parameter :: nlon = 4
  integer, parameter :: nlat = 3
  integer, parameter :: ntimes = 2
  real, parameter :: missing_value = 1.0e20

contains

  subroutine get_example_args(tables_path, input_path, output_dir)
    character(len=*), intent(out) :: tables_path
    character(len=*), intent(out) :: input_path
    character(len=*), intent(out) :: output_dir

    call get_command_argument(1, tables_path)
    call get_command_argument(2, input_path)
    call get_command_argument(3, output_dir)

    if (len_trim(tables_path) == 0) tables_path = "./cmip7-cmor-tables/tables"
    if (len_trim(input_path) == 0) input_path = "./CMIP7_input_example.json"
    if (len_trim(output_dir) == 0) output_dir = "output"
  end subroutine get_example_args

  subroutine load_shared_user_input(input_path, output_dir, frequency, &
       realization_index, forcing_index)
    character(len=*), intent(in) :: input_path
    character(len=*), intent(in) :: output_dir
    character(len=*), intent(in), optional :: frequency
    character(len=*), intent(in), optional :: realization_index
    character(len=*), intent(in), optional :: forcing_index
    integer :: ierr

    ierr = cmor_dataset_json(trim(input_path))
    call check_status("cmor_dataset_json", ierr)

    ierr = cmor_set_cur_dataset_attribute("outpath", trim(output_dir), 1)
    call check_status("cmor_set_cur_dataset_attribute(outpath)", ierr)

    if (present(frequency)) then
      ierr = cmor_set_cur_dataset_attribute("frequency", trim(frequency), 1)
      call check_status("cmor_set_cur_dataset_attribute(frequency)", ierr)
    endif

    if (present(realization_index)) then
      ierr = cmor_set_cur_dataset_attribute("realization_index", &
           trim(realization_index), 1)
      call check_status("cmor_set_cur_dataset_attribute(realization_index)", ierr)
    endif

    if (present(forcing_index)) then
      ierr = cmor_set_cur_dataset_attribute("forcing_index", &
           trim(forcing_index), 1)
      call check_status("cmor_set_cur_dataset_attribute(forcing_index)", ierr)
    endif
  end subroutine load_shared_user_input

  subroutine check_status(call_name, ierr)
    character(len=*), intent(in) :: call_name
    integer, intent(in) :: ierr

    if (ierr /= 0) then
      write(*, '(a, i0)') trim(call_name)//" failed with status ", ierr
      stop 1
    endif
  end subroutine check_status

  subroutine check_id(call_name, cmor_id)
    character(len=*), intent(in) :: call_name
    integer, intent(in) :: cmor_id

    if (cmor_id < 0) then
      write(*, '(a, i0)') trim(call_name)//" failed with id ", cmor_id
      stop 1
    endif
  end subroutine check_id

  subroutine check_grid_id(call_name, cmor_id)
    character(len=*), intent(in) :: call_name
    integer, intent(in) :: cmor_id

    if (cmor_id > -CMOR_MAX_GRIDS) then
      write(*, '(a, i0)') trim(call_name)//" failed with grid id ", cmor_id
      stop 1
    endif
  end subroutine check_grid_id

  subroutine apply_cmip7_variable_metadata(var_id, tables_path, realm, &
       table_entry, frequency, region)
    integer, intent(in) :: var_id
    character(len=*), intent(in) :: tables_path
    character(len=*), intent(in) :: realm
    character(len=*), intent(in) :: table_entry
    character(len=*), intent(in) :: frequency
    character(len=*), intent(in) :: region
    character(len=2048) :: compound_name
    character(len=2048) :: cell_measures
    character(len=2048) :: long_name
    integer :: ierr
    logical :: found

    call cmip7_compound_name(realm, table_entry, frequency, region, &
         compound_name)

    cell_measures = ""
    call lookup_json_string(trim(tables_path)//"/CMIP7_cell_measures.json", &
         trim(compound_name), cell_measures, found)
    ierr = cmor_set_variable_attribute(var_id, "cell_measures", &
         trim(cell_measures))
    call check_status("cmor_set_variable_attribute(cell_measures)", ierr)

    long_name = ""
    call lookup_json_string(trim(tables_path)//"/CMIP7_long_name_overrides.json", &
         trim(compound_name), long_name, found)
    if (found) then
      ierr = cmor_set_variable_attribute(var_id, "long_name", trim(long_name))
      call check_status("cmor_set_variable_attribute(long_name)", ierr)
    endif
  end subroutine apply_cmip7_variable_metadata

  subroutine cmip7_compound_name(realm, table_entry, frequency, region, &
       compound_name)
    character(len=*), intent(in) :: realm
    character(len=*), intent(in) :: table_entry
    character(len=*), intent(in) :: frequency
    character(len=*), intent(in) :: region
    character(len=*), intent(out) :: compound_name
    character(len=1024) :: normalized_entry
    integer :: i

    normalized_entry = table_entry
    do i = 1, len_trim(normalized_entry)
      if (normalized_entry(i:i) == "_") normalized_entry(i:i) = "."
    enddo

    compound_name = trim(realm)//"."//trim(normalized_entry)//"."// &
         trim(frequency)//"."//trim(region)
  end subroutine cmip7_compound_name

  subroutine lookup_json_string(path, key, value, found)
    character(len=*), intent(in) :: path
    character(len=*), intent(in) :: key
    character(len=*), intent(out) :: value
    logical, intent(out) :: found
    character(len=8192) :: line
    character(len=2050) :: search_key
    integer :: colon_pos
    integer :: ierr
    integer :: quote_1
    integer :: quote_2
    integer :: start_pos
    integer :: unit

    value = ""
    found = .false.
    search_key = '"'//trim(key)//'"'

    open(newunit=unit, file=trim(path), status="old", action="read", &
         iostat=ierr)
    if (ierr /= 0) then
      write(*, '(a)') "Could not open CMIP7 metadata table: "//trim(path)
      stop 1
    endif

    do
      read(unit, '(a)', iostat=ierr) line
      if (ierr /= 0) exit
      if (index(line, trim(search_key)) == 0) cycle

      colon_pos = index(line, ":")
      if (colon_pos == 0) exit

      quote_1 = index(line(colon_pos + 1:), '"')
      if (quote_1 == 0) exit

      start_pos = colon_pos + quote_1
      quote_2 = index(line(start_pos + 1:), '"')
      if (quote_2 == 0) exit

      value = line(start_pos + 1:start_pos + quote_2 - 1)
      found = .true.
      exit
    enddo

    close(unit)
  end subroutine lookup_json_string

end module cmip7_fortran_common

Click to expand runner script

#!/usr/bin/env bash
set -euo pipefail

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
RUN_DIR="${RUN_DIR:-$PWD}"
TABLES_PATH="${CMOR_TABLES_PATH:-$RUN_DIR/cmip7-cmor-tables/tables}"
INPUT_PATH="${CMOR_INPUT_PATH:-$RUN_DIR/CMIP7_input_example.json}"
OUTPUT_ROOT="$SCRIPT_DIR/output"
BUILD_DIR="${BUILD_DIR:-$SCRIPT_DIR/build}"

cd "$SCRIPT_DIR"

if [[ -z "${CONDA_PREFIX:-}" ]]; then
  echo "Activate your conda environment or run: conda run -n <env-name> $0" >&2
  exit 2
fi

detect_fortran_compiler() {
  if [[ -n "${FC:-}" ]]; then
    command -v "$FC" >/dev/null 2>&1 || {
      echo "FC is set to '$FC', but that compiler was not found" >&2
      exit 2
    }
    echo "$FC"
    return
  fi

  local compiler
  for compiler in "$CONDA_PREFIX"/bin/*gfortran "$CONDA_PREFIX"/bin/gfortran; do
    if [[ -x "$compiler" ]]; then
      echo "$compiler"
      return
    fi
  done

  if command -v gfortran >/dev/null 2>&1; then
    command -v gfortran
    return
  fi

  echo "Could not find a Fortran compiler. Install gfortran in the active conda environment or set FC." >&2
  exit 2
}

mkdir -p "$BUILD_DIR" "$OUTPUT_ROOT"

if [[ ! -d "$TABLES_PATH" ]]; then
  echo "Could not find CMIP7 tables under $TABLES_PATH. Clone cmip7-cmor-tables or set CMOR_TABLES_PATH." >&2
  exit 2
fi

if [[ ! -f "$INPUT_PATH" ]]; then
  echo "Could not find CMIP7 user input JSON at $INPUT_PATH. Set CMOR_INPUT_PATH to override it." >&2
  exit 2
fi

FC="$(detect_fortran_compiler)"
CMOR_PREFIX="${CMOR_PREFIX:-$CONDA_PREFIX}"
CMOR_MOD_DIR="${CMOR_MOD_DIR:-$CMOR_PREFIX/include}"

if [[ -n "${CMOR_LIB:-}" ]]; then
  CMOR_LINK_FLAGS=("$CMOR_LIB")
elif [[ -f "$CMOR_PREFIX/lib/libcmor.a" ]]; then
  CMOR_LINK_FLAGS=("$CMOR_PREFIX/lib/libcmor.a")
elif [[ -f "$CMOR_PREFIX/lib/libcmor.dylib" || -f "$CMOR_PREFIX/lib/libcmor.so" ]]; then
  CMOR_LINK_FLAGS=("-L$CMOR_PREFIX/lib" "-lcmor")
else
  echo "Could not find CMOR in $CMOR_PREFIX. Install cmor in the active conda environment or set CMOR_PREFIX/CMOR_LIB." >&2
  exit 2
fi

if [[ ! -f "$CMOR_MOD_DIR/cmor_users_functions.mod" ]]; then
  echo "Could not find cmor_users_functions.mod in $CMOR_MOD_DIR. Install cmor in the active conda environment or set CMOR_MOD_DIR." >&2
  exit 2
fi

FFLAGS_DEFAULT="-g -O2 -ffree-line-length-none"
FFLAGS="${FFLAGS:-$FFLAGS_DEFAULT}"
EXTRA_LDFLAGS="${EXTRA_LDFLAGS:-}"
LINK_DIRS=("$CMOR_PREFIX/lib")
if [[ "$CONDA_PREFIX/lib" != "$CMOR_PREFIX/lib" ]]; then
  LINK_DIRS+=("$CONDA_PREFIX/lib")
fi

LINK_FLAGS=("${CMOR_LINK_FLAGS[@]}")
for link_dir in "${LINK_DIRS[@]}"; do
  LINK_FLAGS+=("-L$link_dir")
done
LINK_FLAGS+=("-lnetcdf" "-ludunits2" "-ljson-c" "-luuid" "-lm")
for link_dir in "${LINK_DIRS[@]}"; do
  if [[ "$(uname -s)" != "Darwin" || "$link_dir" != "$CONDA_PREFIX/lib" ]]; then
    LINK_FLAGS+=("-Wl,-rpath,$link_dir")
  fi
done

INCLUDES=("-I$CMOR_MOD_DIR" "-I$BUILD_DIR" "-I$CONDA_PREFIX/include")
COMMON_SRC="$SCRIPT_DIR/cmip7_fortran_common.f90"

examples=(
  example_01_regular_grid_tos
  example_02_pressure_levels
  example_03_scalar_height_tas
  example_04_basin_axis
  example_05_hybrid_sigma_levels
  example_06_curvilinear_grid
  example_07_fixed_field_rootd
)

for example in "${examples[@]}"; do
  src="$SCRIPT_DIR/$example.f90"
  exe="$BUILD_DIR/$example"
  run_output="$OUTPUT_ROOT/$example"
  mkdir -p "$run_output"

  echo "Compiling $example"
  "$FC" $FFLAGS -J "$BUILD_DIR" "${INCLUDES[@]}" "$COMMON_SRC" "$src" "${LINK_FLAGS[@]}" $EXTRA_LDFLAGS -o "$exe"

  echo "Running $example"
  "$exe" "$TABLES_PATH" "$INPUT_PATH" "$run_output"
done

echo "Wrote CMIP7 example output under $OUTPUT_ROOT"