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Marcos Longo edited this page Jan 29, 2021 · 16 revisions

Table of Contents

Data Requirements for any ED2 simulation

The following data is the minimum necessary to start a simulation with near bare ground, for a single polygon.

  • Meteorology data with sub-daily resolution (recommended between 15 min to 6hr)
  • Radiation data, with sub-daily resolution (recommended between 15 min to 1hr)
  • ED2IN Namelist with the appropriate configuration.

Additional data required for a regional ED2 simulation.

  • Land/sea fraction (only land points are solved by ED2)
  • Soil texture map (homogeneous soil type is an option, but not recommended).

Additional data required for a simulation with initial conditions other than near bare ground.

  • Tree-level inventory data (minimum: species, DBH)
  • Soil Carbon stocks

Optional data (the model will use default values if these are not provided)

  • Soil texture profile (assumed homogeneous if not provided).
  • Leaf phenology data
  • Model & PFT parameters
  • Land use change data (assumed inexistent if not provided).

File Requirements

From the data above you then need to build:

  • Meteorology/Radiation boundary condition files (hdf5)
  • ED2IN settings file
  • Soil texture and depth databases (hdf5) OR Site file (*.site, used when running with IRESTYPE = 3.)
  • Vegetation Initial Condition Files (*.pss, *.css) (optional).
  • XML parameter file (optional)
  • Phenology boundary conditions (optional)
  • Land Use boundary conditions (optional)

Computer Requirements

  • Fortran compiler. We recommend ifort or gfortran.
  • C compiler. We recommend icc or gcc. Make sure that the C compiler is consistent with the Fortran compiler
  • HDF5. The HDF5 libraries must be compatible with the Fortran and C compilers.
  • MPI (optional). MPI libraries are only used in regional (multi-polygon) simulations. If this is your case, make sure that MPI libraries are compatible with the Fortran and C compilers you are using.

Code version

  • Check out most recent code using git following instructions available in this link.

Installing required programs and libraries on Ubuntu

To compile the model on an Ubuntu machine, execute the following commands 

sudo apt-get update            # Updates application information
sudo apt-get install git       # Skip if you have Git already
sudo apt-get install gcc       # You probably want the latest <code>GCC</code>
sudo apt-get install gfortran  # You probably want the latest <code>gfortran</code>
sudo apt-get install libhdf5-openmpi-dev    # In case it fails, try 'sudo apt-cache hdf5' to see what is available.
sudo apt-get install libhdf5-tools          # Installs e.g. h5dump, which you probably want.
In case you want the MPI libraries: 
sudo apt-get libopenmpi-dev    # This should always get the latest version of openmpi, a requirement
sudo apt-get openmpi-doc       # Documentation
sudo apt-get openmpi-bin       # Standalone binaries

Next, move to the directory in which you'd like to install ED and clone the main repo: 

git clone https://github.com/EDmodel/ED2.git

To install ED2, you must have the following library files:

  • libhdf5.a
  • libhdf5_fortran.a
  • libhdf5_hl.a
which should all be found in the same directory, probably /usr/lib/x86_64-linux-gnu/ if you've got a 64-bit machine.

Installing ED2

Preparing the compiler instructions

Once you've cloned the mainline and set up the compilers, HDF5 libraries, and optionally the MPI libraries, navigate to ED2/ED/build/make. In case you are part of a group that already uses ED2, the correct configuration file may be already included in the ED2 distribution:

  • include.mk.bnl. Brookhaven National Labs.
  • include.mk.bu_geo. Boston University.
  • include.mk.cannon. Harvard's Cannon cluster (formerly known as Odyssey).
  • include.mk.sdumont. Santos Dumont Cluster (LNCC).
  • include.mk.ugent. Ghent University.
Otherwise, copy include.mk.gfortran or include.mk.intel to a unique file (e.g. include.mk.mylab), and make sure to edit it. For more information, check the compiler instructions page.

Compiling ED2

To compile ED2, navigate to ED2/ED/build/make, where you should find the install.sh script.

The install.sh calls the Makefile as well as any script needed for compilation. The script accepts the following options.

  • -p [PLATFORM] or --platform [PLATFORM] . This selects with platform (system) to use. There must be an include.mk.[PLATFORM] file in the make directory. In case no platform is provided, the script assumes --platform gfortran.
  • -c or --clean. This removes the compilation defined by the platform.
  • -k [KIND] or --kind [KIND]. For some platforms, there are multiple pre-defined options to compile more strict checks (useful for debugging) or less strict checks (useful for production). Typically KIND = A is the most strict option, and KIND = E is the least strict (fastest) option. If not provided, the installation will assume --kind E.
  • -g or --gitoff. Use this option in case you do not want the git commit label attached to the executable name.
  • -s [STEP] or --step [STEP]. This option is used only when the code is being compiled with interface check settings (normally ifort compiler with --kind A). To thoroughly check interfaces, you must compile the code in 3 steps. 1. Generate interfaces; 2. Clean compilation except for the interface modules; 3. Re-compile, this time checking interfaces.
For example, in case you want to compile the model with fast (not debugging) options using include.mk.intel and attach the GitHub label, type: 
./install.sh -k E -p intel -g

If installation is successful, you should see a message similar to this: 

Finished building === ed_2.2-opt-master-e6xy61a9

Also, note that you can also set multiple working versions. Additional details at Using-Github-with-ED2

Running ED-2

Serial run

Single polygon runs must be run in serial mode. To run this, simply copy or link the executable (for example, ed_2.2-opt-master-e6xy61a9 to the same directory where the ED2IN file you modified is located, then type: 

> ./ed_2.2-opt-master-e6xy61a9

In case your namelist is called anything other than ED2IN, you must provide the correct name using the -f option 

> ./ed_2.2-opt-master-e6xy61a9 -f my-ED2IN

Parallel run

Regional runs can be run using MPI. In this case, you must submit the job with the mpirun command: 

> mpirun -np [n] ./ed_2.2-opt-master-e6xy61a9

where [n] is the number of processors to use. The -f option also works in parallel simulations.

Additional information about running on specific systems

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