Download and Install Models
This page contains instructions on how to download and install ecosystem models that have been or are being coupled to PEcAn. These instructions have been tested on the PEcAn unbuntu VM. Commands may vary on other operating systems. Also, some model downloads require permissions before downloading, making them unavailable to the general public. Please contact the PEcAn team if you would like access to a model that is not already installed on the default PEcAn VM.
Install instructions
ED2
ED2.2 r46 (used in PEcAn manuscript)
# ----------------------------------------------------------------------
# Get version r46 with a few patches for ubuntu
cd
curl -o ED.r46.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r46.tgz
tar zxf ED.r46.tgz
rm ED.r46.tgz
# ----------------------------------------------------------------------
# configure and compile ed
cd ~/ED.r46/ED/build/bin
curl -o include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`
make OPT=VM
sudo cp ../ed_2.1-VM /usr/local/bin/ed2.r46
Perform a test run using pre configured ED settings for ED2.2 r46
# ----------------------------------------------------------------------
# Create sample run
cd
mkdir testrun.ed.r46
cd testrun.ed.r46
curl -o ED2IN http://isda.ncsa.illinois.edu/~kooper/EBI/ED2IN.r46
sed -i -e "s#\$HOME#$HOME#" ED2IN
curl -o config.xml http://isda.ncsa.illinois.edu/~kooper/EBI/config.r46.xml
# execute test run
time ed2.r46
ED 2.2 r82
cd
curl -o ED.r82.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.tgz
tar zxf ED.r82.tgz
rm ED.r82.tgz
cd ED.r82
curl -o ED.r82.patch http://isda.ncsa.illinois.edu/~kooper/EBI/ED.r82.patch
patch -p1 < ED.r82.patch
cd ED/build/bin
curl -o include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`
make OPT=VM
sudo cp ../ed_2.1-VM /usr/local/bin/ed2.r82
Perform a test run using pre configured ED settings for ED2.2 r82
cd
mkdir testrun.ed.r82
cd testrun.ed.r82
curl -o ED2IN http://isda.ncsa.illinois.edu/~kooper/EBI/ED2IN.r82
sed -i -e "s#\$HOME#$HOME#" ED2IN
curl -o config.xml http://isda.ncsa.illinois.edu/~kooper/EBI/config.r82.xml
# execute test run
time ed2.r82
ED 2.2 bleeding edge
cd
git clone https://github.com/EDmodel/ED2.git
cd ED2/ED/build/bin
curl -o include.mk.VM http://isda.ncsa.illinois.edu/~kooper/EBI/include.mk.opt.`uname -s`
./generate_deps.sh
make OPT=VM
sudo cp ../ed_2.1-VM /usr/local/bin/ed2.git
SIPNET
Sipnet Installation
cd
curl -o sipnet_unk.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/sipnet_unk.tar.gz
tar zxf sipnet_unk.tar.gz
rm sipnet_unk.tar.gz
cd sipnet_unk
make
sudo cp sipnet /usr/local/bin/sipnet.runk
SIPNET testrun
cd
curl -o testrun.sipnet.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.sipnet.tar.gz
tar zxf testrun.sipnet.tar.gz
rm testrun.sipnet.tar.gz
cd testrun.sipnet
sipnet.runk
BioCro
Installation
# Public
echo 'devtools::install_github("ebimodeling/biocro")' | R --vanilla
# Development:
echo 'devtools::install_github("ebimodeling/biocro-dev")' | R --vanilla
BioCro Developers: request from @dlebauer on GitHub
Linkages
Installation
# Public
echo 'devtools::install_github("araiho/linkages_package")' | R --vanilla
DALEC
Installation
cd
curl -o dalec_EnKF_pub.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/dalec_EnKF_pub.tgz
tar zxf dalec_EnKF_pub.tgz
rm dalec_EnKF_pub.tgz
cd dalec_EnKF_pub
make dalec_EnKF
make dalec_seqMH
sudo cp dalec_EnKF dalec_seqMH /usr/local/bin
LINKAGES
Installation
#FORTRAN VERSION
cd
git clone https://github.com/araiho/Linkages.git
cd Linkages
gfortran -o linkages linkages.f
sudo cp linkages /usr/local/bin/linkages.git
#R Version
git clone https://github.com/araiho/linkages_package.git
R CMD INSTALL --no-multiarch --with-keep.source linkages_package
CLM 4.5
The version of CLM installed on PEcAn is the ORNL branch provided by Dan Ricciuto. This version includes Dan's point-level CLM processing scripts
Download the code (~300M compressed), input data (1.7GB compressed and expands to 14 GB), and a few misc inputs.
mkdir models
cd models
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clm4_5_1_r085.tar.gz
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clm/ccsm_inputdata.tar.gz
tar -xvzf clm4_5*
tar -xvzf ccsm_inputdata.tar.gz
#Parameter file:
mkdir /home/carya/models/ccsm_inputdata/lnd/clm2/paramdata
cd /home/carya/models/ccsm_inputdata/lnd/clm2/paramdata
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clm_params.c130821.nc
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clm_params.c140423.nc
#Domain file:
cd /home/carya/models/ccsm_inputdata/share/domains/domain.clm/
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/domain.lnd.1x1pt_US-UMB_navy.nc
#Aggregated met data file:
cd /home/carya/models/ccsm_inputdata/atm/datm7/CLM1PT_data/1x1pt_US-UMB
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/all_hourly.nc
## lightning database
cd /home/carya/models/ccsm_inputdata/atm/datm7/NASA_LIS/
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clmforc.Li_2012_climo1995-2011.T62.lnfm_Total_c140423.nc
## surface data
cd /home/carya/models/ccsm_inputdata/lnd/clm2/surfdata
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clm/surfdata_360x720cru_simyr1850_c130927.nc
cd /home/carya/models/ccsm_inputdata/lnd/clm2/surfdata_map
wget ftp://nacp.ornl.gov/synthesis/2008/firenze/site/clm/surfdata_1x1pt_US-UMB_I1850CLM45CN_simyr1850.nc_new
mv surfdata_1x1pt_US-UMB_I1850CLM45CN_simyr1850.nc_new surfdata_1x1pt_US-UMB_I1850CLM45CN_simyr1850.nc
Required libraries
sudo apt-get install mercurial csh tcsh subversion cmake
sudo ln -s /usr/bin/make /usr/bin/gmake
Compile and build default inputs
cd ~/carya/models/clm4_5_1_r085/scripts
python runCLM.py --site US-UMB ––compset I1850CLM45CN --mach ubuntu --ccsm_input /home/carya/models/ccsm_inputdata --tstep 1 --nopointdata --coldstart --cpl_bypass --clean_build
CLM Test Run
You will see a new directory in scripts: US-UMB_I1850CLM45CN Enter this directory and run (you shouldn’t have to do this normally, but there is a bug with the python script and doing this ensures all files get to the right place):
./US-UMB_I1850CLM45CN.build
Next you are ready to go to the run directory:
/home/carya/models/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/run
Open to edit file: datm.streams.txt.CLM1PT.CLM_USRDAT and check file paths such that all paths start with /home/carya/models/ccsm_inputdata
From this directory, launch the executable that resides in the bld directory:
/home/carya/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/bld/cesm.exe
not sure this was the right location, but wherever the executable is
You should begin to see output files that look like this: US-UMB_I1850CLM45CN.clm2.h0.yyyy-mm.nc (yyyy is year, mm is month) These are netcdf files containing monthly averages of lots of variables.
The lnd_in file in the run directory can be modified to change the output file frequency and variables.
JULES
INSTALL STEPS: 1) Download JULES and FCM JULES: Model requires registration to download. Not to be put on PEcAn VM Registration: https://jules.jchmr.org/software-and-documentation Documentation: http://jules-lsm.github.io/vn4.2/index.html
FCM:
https://github.com/metomi/fcm/
wget https://github.com/metomi/fcm/archive/2015.05.0.tar.gz
2) edit makefile
open etc/fcm-make/make.cfg
set JULES_NETCDF = actual instead of dummy
set path (e.g. /usr/) and lib_path /lib64 to netCDF libraries
3) compile JULES
cd etc/fcm-make/
{path.to.fcm}/fcm make -f etc/fcm-make/make.cfg --new
UBUNTU VERSION: installed without having to add any perl libraries
#perl stuff that I had to install on pecan2 not PEcAN VM
sudo yum install perl-Digest-SHA
sudo yum install perl-Time-modules
sudo yum install cpan
curl -L http://cpanmin.us | perl - --sudo App::cpanminus
sudo cpanm Time/Piece.pm
sudo cpanm IO/Uncompress/Gunzip.pm
Executable is under build/bin/jules.exe
Example rundir: examples/point_loobos
MAESPA
Navigate to a directory you would like store MAESPA and run the following:
git clone https://bitbucket.org/remkoduursma/maespa.git
cd maespa
make
maespa.out is your executable. Example input files can be found in the inpufiles directory. Executing measpa.out from within one of the example directories will produce output.
MAESPA developers have also developed a wrapper package called Maeswrap. The usual R package installation method install.packages may present issues with downloading an unpacking a dependency package called rgl. Here are a couple of solutions:
Solution 1
### From the Command Line
sudo apt-get install r-cran-rgl
then from within R
install.packages("Maeswrap")
Solution 2
### From the Command line
sudo apt-get install libglu1-mesa-dev
then from within R
install.packages("Maeswrap")
GDAY
Navigate to a directory you would like to store GDAY and run the following:
git clone https://github.com/mdekauwe/GDAY.git
cd GDAY
cd src
make
gday is your executable.
LPJ-GUESS
Instructions to download source code
wget http://stormbringerii.nateko.lu.se/public/guess_download/guess_3.1.tar.gz
tar -xvzf guess_3.1.tar.gz