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Michael Dietze edited this page Jan 6, 2014 · 3 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 ED)
  • 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:

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

Computer Requirements

  • Fortran compiler (recommended ifort or gfortran)
  • C compiler (recommended icc or gcc)
  • MPI
  • HDF5
ED currently requires that the code be run through MPI even for serial runs, thus it is important that a version of the MPI exacutables and the MPI libraries be installed. ED also uses the HDF5 libraries for the reading and writing of most files.

Compilation

  • Check out most recent code using bazaar following instructions here 
> mkdir <newdir> #optional e.g. for keeping multiple versions 
> cd <newdir>/ #also optional
> bzr branch /home/mdietze/EDBRAMS
  • First you need to set the .../ED/build/bin/paths.mk file such that the ED_ROOT variable points to your ED directory (e.g. ED_ROOT=/home/mdietze/ED)
> cd <newdir>/EDBRAMS/ED/build/bin/
> sed -i 's/mdietze\/r31/<user>/g' paths.mk 
#if going to <newdir> 
>sed -i 's/mdietze\/r31/<user>\/<newdir>/g' paths.mk
  • Create or edit an include.mk file for your project (e.g. myincludefile.mk.opt). There are a number of examples in the build/bin directory for different architectures and compilers. A key set of variables to specify are the HDF5 paths and flags (USE_HDF5, HDF5_INCS, HDF5_LIBS). Once your include file is ready, create a link to include.mk.opt .
> ln -s myincludefile.mk.opt include.mk.opt
  • From the EDBRAMS/ED/build/bin/ directory type
> ./install.sh

This will create the executable in the ED/build directory (usually ed_2.1-opt).

  • This is an example moving from one revision subfolder to a new revision subfolder:
>  mkdir aged47a2
>  cd aged47a2/
>  bzr branch /home/mdietze/r47A/EDBRAMS
>  cd EDBRAMS/ED/build/bin/
>  sed -i 's/mdietze\/r47A/dlebauer\/aged47a2/g' paths.mk
>  ln -s include.mk.ebi include.mk.opt
>  ./install.sh

Running

Serial run

Single polygon runs must be run in serial mode. To run this, simply copy or link the executable to the same directory where the ED2IN file you modified is located, then type: 

> ./ed_2.1-opt

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

> ./ed_2.1-opt -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_2.1-opt

where <n></n> is the number of processors to use. The -f option also works in parallel simulations.

Additional information about running on specific systems

University of Illinois EBI Cluster

Harvard Portal

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