8.1. I/O framework

JULES version 3.1 saw a complete rewrite of the I/O code to use a more modular and flexible structure. This section attempts to give a brief description of the low-level I/O framework, and explains how to make some commonly required changes.

Warning

This section requires a good knowledge of Fortran.

8.1.1. Overview

The JULES I/O code is comprised of several ‘layers’ with clearly defined responsibilities that communicate with each other, as shown in the figure Modular structure of the JULES I/O code (the relevant Fortran modules for each layer are also given). The blocks in orange are the JULES specific pieces of code - in theory, the rest of the code could be used with other models if different implementations of these modules were provided.

Modular structure of the JULES I/O code

The core component in the I/O framework is the common file handling API. This layer provides a common interface for different file formats that is then used by the rest of the code. The drivers for ASCII and NetCDF files implement this interface. The interface is based around the concepts of dimensions and variables, much like NetCDF (except that nothing is inferred from metadata - all information about variables and dimensions must be prescribed), but adds the concept of a “record” to that:

Dimension

A file has one or more dimensions. Each regular dimension has a name and a size.

One dimension is special, and is referred to as the record dimension. It has a name but has no defined size. A typical use of the record dimension is to represent time.

Variable

A file has one or more variables. The size of each variable is defined using the dimensions previously defined in the file. Each variable can opt to use the record dimension or not - if a variable uses the record dimension it must be the last dimension that the variable has.

Record

A record is the collection of all variables at a certain value of the record dimension. The figure Records in a file gives an example of this:

Records in a file

In the figure, each variable has dimensions x, y and n, where n is the record dimension. Each green box represents the (2D plane of) values of a variable for a certain value of n. A record is then the collection of all variables at a certain value of n.

A good analogy is the lines in an ASCII file, where each column represents a variable and each line is a record (in fact, this is a generalisation to multiple dimensions of that exact concept).

Files keep track of the record they are currently pointing at (it is the responsibility of the file-type drivers to do this in the way that best suits the file format they implement). When a file receives a read or write request for a particular variable, the values are read from or written to the current record.

The record abstraction also allows two useful operations - seek and advance. When a file receives an instruction to seek to a particular record, it sets its internal pointer so that read/write requests access the given record (a use of this within JULES is looping the input files round spin-up cycles). An advance instruction just moves the internal pointer on to the next record.

The routines in file_mod define the interface that each file-type driver must implement, and are responsible for deciding which driver to defer to. Support for a file format is provided by implementing this interface and declaring the implementation in file_mod. This is discussed in further detail in Implementing a new file format.

The gridded file API then imposes the concept of reading and writing cubes of gridded data (i.e. x and y dimensions for the grid, plus zero or more ‘levels’ dimensions) on top of the common file handling API. The underlying files may have a 1D or 2D grid (see Input files for JULES), and this layer handles the grid dimensions transparently. It is this layer that handles the extraction of a subgrid from a larger grid (see file_gridded_read_var and file_gridded_write_var).

The time series file API builds on the gridded file API by explicitly presenting the record dimension as a time dimension. It provides an interface that allows users to treat multiple files (e.g. monthly files, yearly files) as if they were a single file (i.e. seek and advance will automatically open and close files if required).

The input and output layers interact with the model via an interface provided by model_interface_mod. model_interface_mod allows the input and output layers to read values from and write values to the internal model variables. This is discussed in more detail in Implementing new variables for input and output. The input and output layers use the time series file API to read from and write to file.

This should provide a reasonable introduction to the JULES I/O framework, but looking at the code is the best way to learn about it.

8.1.2. Implementing new variables for input and output

The only I/O code that needs to be modified to add new variables for input and output is in model_interface_mod (the routines in src/io/model_interface). All interaction between the I/O code and the model happens in this module (apart from reading and writing dump files).

Before adding any code to model_interface_mod, the variable the user wishes to make available for input and/or output must be accessible to model_interface_mod. This is usually accomplished by placing the variable in a module and importing the module into model_interface_mod where required, e.g.:

! Declare the variable in a module
MODULE my_module

  REAL, ALLOCATABLE :: my_var(:)

  ! ...
END MODULE my_module


! ... Later, in model_interface_mod
USE my_module, ONLY : my_var

model_interface_mod contains several routines:

• Two routines that populate and extract data from the relevant model variables. These are populate_var and extract_var respectively.

• Routines that provide various pieces of information (e.g. string identifiers, number and size of ‘levels’ dimensions) about the available variables to the input and output layers. Internally, a metadata array that contains information about the available variables is used to implement these ‘information providing’ routines.

In most cases, the following edits will be sufficient to add a variable for input and/or output:

model_interface_mod.F90

Note

Required for both input and output variables.

Increment the constant N_VARS. This PARAMETER indicates how many elements are in the metadata array. If you forget to do this, the module will fail to compile.

populate_var.inc

Note

Required for input variables only.

populate_var takes a variable identifier and a cube of data on the full model grid, and populates the associated model variable using that data. This is done using a SELECT statement, to which a case must be added for the new variable.

extract_var.inc

Note

Required for output variables only.

extract_var takes a variable identifier, extracts the values from the associated model variable, and returns those values as a cube of data on the full model grid. This is done using a SELECT statement, to which a case must be added for the new variable.

variable_metadata.inc

Note

Required for both input and output variables.

This file contains the DATA definition for the variable metadata array. The metadata array contains objects of the derived type var_metadata, which is defined in model_interface_mod.F90. A typical entry in this array will look something like:

!-----------------------------------------------------------------------------
! Metadata for latitude
!-----------------------------------------------------------------------------
DATA metadata(1) / var_metadata(                                              &
! String identifier
    'latitude',                                                               &
! Variable type
    VAR_TYPE_SURFACE,                                                         &
! Long name
    "Gridbox latitude",                                                       &
! Units
    "degrees"                                                                 &
  ) /

This allows us to define all the static information about a variable in one place:

String identifier

This is the name used to identify the variable in namelists (as seen elsewhere in the User Guide)

Variable type

This indicates the number and size of the ‘levels’ dimensions for the variable. For a full list of types see the file get_var_levs_dims.inc; some of the available types are:

Type	Number and size of ‘levels’ dimension(s)
VAR_TYPE_SURFACE	No levels dimension
VAR_TYPE_PFT	Single levels dimension of size npft
VAR_TYPE_NVG	Single levels dimension of size nnvg
VAR_TYPE_TYPE	Single levels dimension of size ntype (npft + nnvg)
VAR_TYPE_TILE	Single levels dimension of size nsurft (1 if l_aggregate = TRUE, ntype otherwise)
VAR_TYPE_SOIL	Single levels dimension of size sm_levels
VAR_TYPE_SCPOOL	Single levels dimension of size dim_cs1 (number of soil carbon pools, i.e. 4 if l_triffid = TRUE, 1 otherwise)
VAR_TYPE_SNOW	Two levels dimensions: the first of size nsurft and the second of size nsmax

Adding a new type is a relatively simple procedure:

1. A new PARAMETER must be added for the type in model_interface_mod.F90

2. A new CASE must be added to the SELECT statement in get_var_levs_dims.inc that correctly returns the number, names and sizes of the levels dimensions.

Long name

This is the name used in the long_name attribute for the variable in output files.

Units

This is the units given in the units attribute for the variable in output files.

map_from_land and map_to_land are provided as utilities for use with variables that are defined on land points only. tiles_to_gbm is used to provide gridbox mean diagnostics for model variables that have one value per surface tile.

As always, the best way to go about implementing new variables for input and output is to follow the examples that are already there.

8.1.3. Implementing a new file format

To understand how to implement a new file format, it first helps to understand how the common file handling layer works under the hood.

Each of the routines in file_mod (see files in src/io/file_handling/core) takes a file_handle as its first argument. The file_handle is a Fortran derived type that contains a flag indicating the format of the file it represents, and each of the routines in file_mod contains a SELECT statement that defers to the correct implementation of the routine based on that flag.

file_handles are created in file_open. Each file format implementation defines a list of recognised file extensions, and the appropriate file opening routine is deferred to by comparing the extension of the given file name to the recognised extensions for each file format.

To implement a new file format, an implementation of each of the routines in file_mod must first be provided (the implementations for ASCII and NetCDF formats should be used as a reference). A new CASE deferring to the new implementation should then be added to the SELECT statement in each of the routines in file_mod. The recognised file extensions for the new format should also be added to the checks in file_open to allow the new the file opening routine to be called.

Implementations of these routines for ASCII and NetCDF file formats are given in driver_ascii (see src/io/file_handling/core/drivers/ascii) and driver_ncdf (see src/io/file_handling/core/drivers/ncdf) respectively. These should be used as examples of how to implement a file format.

These two file formats suffer from opposite problems when implementing the concepts of dimensions, variables and records. For NetCDF, the concepts of dimensions and variables already exist, but the idea of a record has to be imposed. For ASCII, the concept of a record is a natural fit (think lines in a file), but the concepts of dimensions and variables have to be imposed. Between them, these implementations should provide sufficient examples of how to implement a new file format.