Configuring ROGER for BioCro runs - Githubissues

ebimodeling / biocro_regional

Enabling BioCro to run regionally, starting with midwest miscanthus

University of Illinois/NCSA Open Source License

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Configuring ROGER for BioCro runs #6

Closed dlebauer closed 9 years ago

dlebauer commented 9 years ago

Running BioCro regional runs

[x] setup account for username dlebauer
[x] setup shared directory (for inputs / outputs)
[x] install R, netCDF-4, udunits2
- this is a list of modules that I currently use:

module load nco/4.4.8
module load netcdf/4.3.3.1
module load parallel-netcdf/1.4.1
module load gdal/1.11.2
module load udunits/2.1.24
module load R/3.1.1

[ ] R packages:

install.packages( c('ncdf4', 'rgdal', 'DBI', 'XML', 'udunits2', 'RPostgreSQL', 
                                'rPython','minpack.lm','geonames', 'Rcpp'), 
                             repos="http://cran.rstudio.com/")

if you have any difficulty with these, please let me or @robkooper know, and record any specific configuration arguments (most often this is a matter of either making sure the relevant *.so files are in the $PATH, appropriate modules are loaded, or the *.so file is specified as an argument to install.packages).
Second
[x] Install BioCro

install.packages("devtools")
library(devtools)
install_github("ebimodeling/biocro-dev")

Resources

[x] Install HipChat, NCSA opensource, use PEcAn room
[x] Keep notes below; eventually to be added to PEcAn Wiki