configure-roger.md

Dependencies:

System Utilities

modules: netcdf4, udunits2, R/3.2.0, ... XML: libxml2/2.9.1

• (older versions of libxml cause segfault PecanProject/pecan#476)

Add to ~/.bash_profile (example)

export R_LIBS_USER=~/R/library
module load netcdf4 gdal R udunits2

Git Repositories

need to setup ssh-key, and be able to access either

• github.com/ebimodeling/biocro (public, has miscanthus, switchgrass)
• github.com/ebimodeling/biocro-dev (private, also has willow, sugarcane)

All of the following are public, but to use the git@ url, need to setup an ssh key ...

git clone [email protected]:ebimodeling/biocro
git clone [email protected]:pecanproject/pecan
git clone [email protected]:ebimodeling/regional_biocro

Alternatively, can use git clone https://github.com/path-to/repository/

R dependencies

netcdf and udunits packages are tricky. Install them first:

install.packages('ncdf4', configure.args = "--with-nc-config=/sw/netcdf-4.3.3.1/bin/nc-config")

install.packages("udunits2", configure.args='--with-udunits2=/sw/udunits-2.1.24/ --with-udunits2-include=/sw/udunits-2.1.24/include')

cd path/to/pecan
./scripts/install.dependencies.R
./scripts/build.sh