23.5 OS Specific Installations

23.5.1 Ubuntu

These are specific notes for installing PEcAn on Ubuntu (14.04) and will be referenced from the main installing PEcAn page. You will at least need to install the build environment and Postgres sections. If you want to access the database/PEcAn using a web browser you will need to install Apache. To access the database using the BETY interface, you will need to have Ruby installed.

This document also contains information on how to install the Rstudio server edition as well as any other packages that can be helpful.

23.5.1.1 Install build environment

sudo -s

# point to latest R
echo "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -s -c`/" > /etc/apt/sources.list.d/R.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

# update package list
apt-get -y update

# install packages needed for PEcAn
apt-get -y install build-essential gfortran git r-base-core r-base-dev jags liblapack-dev libnetcdf-dev netcdf-bin bc libcurl4-gnutls-dev curl udunits-bin libudunits2-dev libgmp-dev python-dev libgdal1-dev libproj-dev expect

# install packages needed for ED2
apt-get -y install openmpi-bin libopenmpi-dev

# install requirements for DALEC
apt-get -y install libgsl0-dev

# install packages for webserver
apt-get -y install apache2 libapache2-mod-php5 php5

# install packages to compile docs
apt-get -y install texinfo texlive-latex-base texlive-latex-extra texlive-fonts-recommended

# install devtools
echo 'install.packages("devtools")' | R --vanilla

# done as root
exit

23.5.1.2 Install Postgres

Documentation: http://trac.osgeo.org/postgis/wiki/UsersWikiPostGIS21UbuntuPGSQL93Apt

sudo -s

# point to latest PostgreSQL
echo "deb http://apt.postgresql.org/pub/repos/apt `lsb_release -s -c`-pgdg main" > /etc/apt/sources.list.d/pgdg.list
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -

# update package list
apt-get -y update

# install packages for postgresql (using a newer version than default)
apt-get -y install libdbd-pgsql postgresql postgresql-client libpq-dev postgresql-9.4-postgis-2.1 postgresql-9.4-postgis-2.1-scripts

# install following if you want to run pecan through the web
apt-get -y install php5-pgsql

# enable bety user to login with trust by adding the following lines after
# the ability of postgres user to login in /etc/postgresql/9.4/main/pg_hba.conf
local   all             bety                                    trust
host    all             bety            127.0.0.1/32            trust
host    all             bety            ::1/128                 trust

# Once done restart postgresql
/etc/init.d/postgresql restart

exit

To install the BETYdb database ..

23.5.1.3 Apache Configuration PEcAn

# become root
sudo -s

# get index page
rm /var/www/html/index.html
ln -s ${HOME}/pecan/documentation/index_vm.html /var/www/html/index.html

# setup a redirect
cat > /etc/apache2/conf-available/pecan.conf << EOF
Alias /pecan ${HOME}/pecan/web
<Directory ${HOME}/pecan/web>
  DirectoryIndex index.php
  Options +ExecCGI
  Require all granted
</Directory>
EOF
a2enconf pecan
/etc/init.d/apache2 restart

# done as root
exit

23.5.1.4 Apache Configuration BETY

sudo -s

# install all ruby related packages
apt-get -y install ruby2.0 ruby2.0-dev libapache2-mod-passenger 

# link static content
ln -s ${HOME}/bety/public /var/www/html/bety

# setup a redirect
cat > /etc/apache2/conf-available/bety.conf << EOF
RailsEnv production
RailsBaseURI /bety
PassengerRuby /usr/bin/ruby2.0
<Directory /var/www/html/bety>
  Options +FollowSymLinks
  Require all granted
</Directory>
EOF
a2enconf bety
/etc/init.d/apache2 restart

23.5.1.5 Rstudio-server

NOTE This will allow anybody to login to the machine through the rstudio interface and run any arbitrary code. The login used however is the same as the system login/password.

wget http://download2.rstudio.org/rstudio-server-0.98.1103-amd64.deb

# bceome root
sudo -s

# install required packages
apt-get -y install libapparmor1 apparmor-utils libssl0.9.8

# install rstudio
dpkg -i rstudio-server-*
rm rstudio-server-*
echo "www-address=127.0.0.1" >> /etc/rstudio/rserver.conf
echo "r-libs-user=~/R/library" >> /etc/rstudio/rsession.conf
rstudio-server restart

# setup rstudio forwarding in apache
a2enmod proxy_http
cat > /etc/apache2/conf-available/rstudio.conf << EOF
ProxyPass        /rstudio/ http://localhost:8787/
ProxyPassReverse /rstudio/ http://localhost:8787/
RedirectMatch permanent ^/rstudio$ /rstudio/
EOF
a2enconf rstudio
/etc/init.d/apache2 restart

# all done, exit root
exit

23.5.1.6 Additional packages

HDF5 Tools, netcdf, GDB and emacs

sudo apt-get -y install hdf5-tools cdo nco netcdf-bin ncview gdb emacs ess nedit

23.5.2 CentOS/RedHat

These are specific notes for installing PEcAn on CentOS (7) and will be referenced from the main installing PEcAn page. You will at least need to install the build environment and Postgres sections. If you want to access the database/PEcAn using a web browser you will need to install Apache. To access the database using the BETY interface, you will need to have Ruby installed.

This document also contains information on how to install the Rstudio server edition as well as any other packages that can be helpful.

23.5.2.1 Install build environment

sudo -s

# install packages needed for PEcAn
yum -y groupinstall 'Development Tools' 
yum -y install git netcdf-fortran-openmpi-devel R bc curl libxml2-devel openssl-devel ed  udunits2 udunits2-devel netcdf netcdf-devel gmp-devel python-devel gdal-devel proj-devel proj-epsg expect

# jags
yum -y install http://download.opensuse.org/repositories/home:/cornell_vrdc/CentOS_7/x86_64/jags3-3.4.0-54.1.x86_64.rpm
yum -y install http://download.opensuse.org/repositories/home:/cornell_vrdc/CentOS_7/x86_64/jags3-devel-3.4.0-54.1.x86_64.rpm

# fix include folder for udunits2
ln -s /usr/include/udunits2/* /usr/include/

# install packages needed for ED2
yum -y install environment-modules openmpi-bin libopenmpi-dev

# install requirements for DALEC
yum -y install gsl-devel

# install packages for webserver
yum -y install httpd php
systemctl enable httpd
systemctl start httpd
firewall-cmd --zone=public --add-port=80/tcp --permanent
firewall-cmd --reload

# install packages to compile docs
#apt-get -y install texinfo texlive-latex-base texlive-latex-extra texlive-fonts-recommended

# install devtools
echo 'install.packages("devtools")' | R --vanilla

# done as root
exit

echo "module load mpi" >> ~/.bashrc
module load mpi

23.5.2.2 Install and configure PostgreSQL, udunits2, NetCDF

sudo -s

# point to latest PostgreSQL
yum install -y epel-release 
yum -y install http://yum.postgresql.org/9.4/redhat/rhel-7-x86_64/pgdg-centos94-9.4-1.noarch.rpm

# install packages for postgresql (using a newer version than default)
yum -y install postgresql94-server postgresql94-contrib postgis2_94 postgresql94-devel udunits2 netcdf

# install following if you want to run pecan through the web
yum -y install php-pgsql

# enable bety user to login with trust by adding the following lines after
# the ability of postgres user to login in /var/lib/pgsql/9.4/data/pg_hba.conf
local   all             bety                                    trust
host    all             bety            127.0.0.1/32            trust
host    all             bety            ::1/128                 trust

# Create database
/usr/pgsql-9.4/bin/postgresql94-setup initdb

# Enable postgres
systemctl enable postgresql-9.4
systemctl start postgresql-9.4

exit

23.5.2.3 Apache Configuration PEcAn

Install and Start Apache

yum -y install httpd
systemctl enable httpd
systemctl start httpd

# become root
sudo -s

# get index page
rm /var/www/html/index.html
ln -s /home/carya/pecan/documentation/index_vm.html /var/www/html/index.html

# fix selinux context (does this need to be done after PEcAn is installed?)
chcon -R -t httpd_sys_content_t /home/carya/pecan /home/carya/output

# setup a redirect
cat > /etc/httpd/conf.d/pecan.conf << EOF
Alias /pecan /home/carya/pecan/web
<Directory /home/carya/pecan/web>
  DirectoryIndex index.php
  Options +ExecCGI
  Require all granted
</Directory>
EOF
a2enconf pecan
/etc/init.d/apache2 restart

# done as root
exit

23.5.2.4 Apache Configuration BETY

sudo -s

# install all ruby related packages
sudo curl --fail -sSLo /etc/yum.repos.d/passenger.repo https://oss-binaries.phusionpassenger.com/yum/definitions/el-passenger.repo
yum -y install ruby ruby-devel mod_passenger

# link static content
ln -s /home/carya/bety/public /var/www/html/bety

# fix GemFile
echo 'gem "test-unit"' >> bety/Gemlile

# fix selinux context (does this need to be done after bety is installed?)
chcon -R -t httpd_sys_content_t /home/carya/bety

# setup a redirect
cat > /etc/httpd/conf.d/bety.conf << EOF
RailsEnv production
RailsBaseURI /bety
PassengerRuby /usr/bin/ruby
<Directory /var/www/html/bety>
  Options +FollowSymLinks
  Require all granted
</Directory>
EOF
systemctl restart httpd

23.5.2.5 Rstudio-server

NEED FIXING

NOTE This will allow anybody to login to the machine through the rstudio interface and run any arbitrary code. The login used however is the same as the system login/password.

wget http://download2.rstudio.org/rstudio-server-0.98.1103-amd64.deb

# bceome root
sudo -s

# install required packages
apt-get -y install libapparmor1 apparmor-utils libssl0.9.8

# install rstudio
dpkg -i rstudio-server-*
rm rstudio-server-*
echo "www-address=127.0.0.1" >> /etc/rstudio/rserver.conf
echo "r-libs-user=~/R/library" >> /etc/rstudio/rsession.conf
rstudio-server restart

# setup rstudio forwarding in apache
a2enmod proxy_http
cat > /etc/apache2/conf-available/rstudio.conf << EOF
ProxyPass        /rstudio/ http://localhost:8787/
ProxyPassReverse /rstudio/ http://localhost:8787/
RedirectMatch permanent ^/rstudio$ /rstudio/
EOF
a2enconf rstudio
/etc/init.d/apache2 restart

# all done, exit root
exit

Alternative Rstudio instructions

23.5.2.5.1 Install and configure Rstudio-server

Install RStudio Server by following the official documentation for your platform. Then, proceed with the following:

add PATH=$PATH:/usr/sbin:/sbin to /etc/profile

   cat "PATH=$PATH:/usr/sbin:/sbin; export PATH" >> /etc/profile

add rstudio.conf to /etc/httpd/conf.d/

   wget https://gist.github.com/dlebauer/6921889/raw/d1e0f945228e5519afa6223d6f49d6e0617262bd/rstudio.conf
   sudo mv rstudio.conf /httpd/conf.d/

restart the Apache server: sudo httpd restart
now you should be able to access http://<server>/rstudio

23.5.2.6 Install ruby-netcdf gem

cd $RUBY_APPLICATION_HOME
export $NETCDF_URL=http://www.gfd-dennou.org/arch/ruby/products/ruby-netcdf/release/ruby-netcdf-0.6.6.tar.gz
export $NETCDF_DIR=/usr/local/netcdf
gem install narray
export NARRAY_DIR="$(ls $GEM_HOME/gems | grep 'narray-')"
export NARRAY_PATH="$GEM_HOME/gems/$NARRAY_DIR"
cd $MY_RUBY_HOME/bin
wget $NETCDF_URL -O ruby-netcdf.tgz
tar zxf ruby-netcdf.tgz && cd ruby-netcdf-0.6.6/
ruby -rubygems extconf.rb --with-narray-include=$NARRAY_PATH --with-netcdf-dir=/usr/local/netcdf-4.3.0
sed -i 's|rb/$|rb|' Makefile
make
make install
cd ../ && sudo rm -rf ruby-netcdf*

cd $RUBY_APPLICATION
bundle install --without development

23.5.2.7 Additional packages

NEED FIXING

HDF5 Tools, netcdf, GDB and emacs

sudo apt-get -y install hdf5-tools cdo nco netcdf-bin ncview gdb emacs ess nedit

23.5.3 Mac OSX

These are specific notes for installing PEcAn on Mac OSX and will be referenced from the main installing PEcAn page. You will at least need to install the build environment and Postgres sections. If you want to access the database/PEcAn using a web browser you will need to install Apache. To access the database using the BETY interface, you will need to have Ruby installed.

This document also contains information on how to install the Rstudio server edition as well as any other packages that can be helpful.

23.5.3.1 Install build environment

# install R
# download from http://cran.r-project.org/bin/macosx/

# install gfortran 
# download from http://cran.r-project.org/bin/macosx/tools/

# install OpenMPI
curl -o openmpi-1.6.3.tar.gz http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.3.tar.gz
tar zxf openmpi-1.6.3.tar.gz
cd openmpi-1.6.3
./configure --prefix=/usr/local
make all
sudo make install
cd ..

# install szip
curl -o szip-2.1-MacOSX-intel.tar.gz ftp://ftp.hdfgroup.org/lib-external/szip/2.1/bin/szip-2.1-MacOSX-intel.tar.gz
tar zxf szip-2.1-MacOSX-intel.tar.gz
sudo mv szip-2.1-MacOSX-intel /usr/local/szip

# install HDF5

curl -o hdf5-1.8.11.tar.gz http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.11.tar.gz
tar zxf hdf5-1.8.11.tar.gz
cd hdf5-1.8.11
sed -i -e 's/-O3/-O0/g' config/gnu-flags 
./configure --prefix=/usr/local/hdf5 --enable-fortran --enable-cxx --with-szlib=/usr/local/szip
make
# make check
sudo make install
# sudo make check-install
cd ..

23.5.3.2 Install Postgres

For those on a Mac I use the following app for postgresql which has postgis already installed (http://postgresapp.com/)

To get postgis run the following commands in psql:

##### Enable PostGIS (includes raster)
CREATE EXTENSION postgis;
##### Enable Topology
CREATE EXTENSION postgis_topology;
##### fuzzy matching needed for Tiger
CREATE EXTENSION fuzzystrmatch;
##### Enable US Tiger Geocoder
CREATE EXTENSION postgis_tiger_geocoder;

To check your postgis run the following command again in psql: SELECT PostGIS_full_version();

23.5.3.3 Additional installs

23.5.3.3.1 Install JAGS

Download JAGS from http://sourceforge.net/projects/mcmc-jags/files/JAGS/3.x/Mac%20OS%20X/JAGS-Mavericks-3.4.0.dmg/download

23.5.3.3.2 Install udunits

Installing udunits-2 on MacOSX is done from source.

download most recent version of Udunits here
instructions for compiling from source

curl -o udunits-2.1.24.tar.gz ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.1.24.tar.gz
tar zxf udunits-2.1.24.tar.gz
cd udunits-2.1.24
./configure
make
sudo make install

23.5.3.4 Apache Configuration

Mac does not support pdo/postgresql by default. The easiest way to install is use: http://php-osx.liip.ch/

To enable pecan to run from your webserver.

cat > /etc/apache2/others/pecan.conf << EOF
Alias /pecan ${PWD}/pecan/web
<Directory ${PWD}/pecan/web>
  DirectoryIndex index.php
  Options +All
  Require all granted
</Directory>
EOF

23.5.3.5 Ruby

The default version of ruby should work. Or use JewelryBox.

23.5.3.6 Rstudio Server

For the mac you can download Rstudio Desktop.

23.5.4 Installing BETY

**************THIS PAGE IS DEPRECATED*************

Official Instructions for BETY are maintained here: https://pecan.gitbook.io/betydb-documentation

If you would like to install the Docker Version of BETY, please consult the PEcAn Docker section.

23.5.4.1 Install Database + Data

note To install BETYdb without PEcAn, first download the load.bety.sh script

# install database (code assumes password is bety)
sudo -u postgres createuser -d -l -P -R -S bety
sudo -u postgres createdb -O bety bety
sudo -u postgres ./scripts/load.bety.sh -c YES -u YES -r 0
sudo -u postgres ./scripts/load.bety.sh -r 1
sudo -u postgres ./scripts/load.bety.sh -r 2

# configure for PEcAn web app (change password if needed)
cp web/config.example.php web/config.php 

# add models to database (VM only)
./scripts/add.models.sh

# add data to database
./scripts/add.data.sh

# create outputs folder
mkdir ~/output
chmod 777 ~/output

23.5.4.2 Installing BETYdb Web Application

There are two flavors of BETY, PHP and RUBY. The PHP version allows for a minimal interaction with the database while the RUBY version allows for full interaction with the database.

23.5.4.2.1 PHP version

The php version comes with PEcAn and is already configured.

23.5.4.2.2 RUBY version

The RUBY version requires a few extra packages to be installed first.

Next we install the web app.

# install bety
cd
git clone https://github.com/PecanProject/bety.git

# install gems
cd bety
sudo gem2.0 install bundler
bundle install --without development:test:javascript_testing:debug

and configure BETY

# create folders for upload folders
mkdir paperclip/files paperclip/file_names
chmod 777 paperclip/files paperclip/file_names

# create folder for log files
mkdir log
touch log/production.log
chmod 0666 log/production.log

# fix configuration for vm
cp config/additional_environment_vm.rb config/additional_environment.rb
chmod go+w public/javascripts/cache/

# setup bety database configuration
cat > config/database.yml << EOF
production:
  adapter: postgis
  encoding: utf-8
  reconnect: false
  database: bety
  pool: 5
  username: bety
  password: bety
EOF

# setup login tokens
cat > config/initializers/site_keys.rb << EOF
REST_AUTH_SITE_KEY         = 'thisisnotasecret'
REST_AUTH_DIGEST_STRETCHES = 10
EOF

23.5.5 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.

23.5.5.1 BioCro

# 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](https://github.com/dlebauer)

23.5.5.2 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

23.5.5.2.1 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.

23.5.5.3 DALEC

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

23.5.5.4 ED2

23.5.5.4.1 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

23.5.5.4.2 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

23.5.5.4.3 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

23.5.5.5 CLM-FATES

Prerequisites

sudo apt-get upgrade libnetcdf-dev
sudo apt-get install subversion
sudo apt-get install csh
sudo apt-get install cmake
sudo ln -s /usr/bin/make /usr/bin/gmake
sudo rm /bin/sh
sudo ln -s /bin/bash /bin/sh

wget https://github.com/Unidata/netcdf-fortran/archive/v4.4.4.tar.gz
cd netcdf-4.4.4
./configure
make
sudo make install

you might need to mess around with installing netcdf and netcdf-fortran to get a version FATES likes…

Get code from Github (currently private) and go to cime/scripts directory

git clone git@github.com:NGEET/ed-clm.git
cd ed-clm/cime/scripts/

Within CLM-FATES, to be able to build an executable we need to create a reference run. We’ll also use this reference run to grab defaults from, so we’ll be registering the location of both the reference case (location of executable, scripts, etc) and the reference inputs with the PEcAn database. To begin, copy reference run script from pecan

cp ~/pecan/models/fates/inst/create_1x1_ref_case.sh .

Edit reference case script to set NETCDF_HOME, CROOT (reference run case), DIN_LOC_ROOT (reference run inputs). Also, make sure DIN_LOC_ROOT exists as FATES will not create it itself. Then run the script

./create_1x1_ref_case.sh

Be aware that this script WILL ask you for your password on the NCAR server to download the reference case input data (the guest password may work, haven’t tried this). If it gives an error at the pio stage check the log, but the most likely error is it being unable to find a version of netcdf it likes.

Once FATES is installed, set the whole reference case directory as the Model path (leave filename blank) and set the whole inputs directory as an Input with format clm_defaults.

23.5.5.6 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.

23.5.5.7 JULES

INSTALL STEPS: 1) Download JULES and FCM JULES: Model requires registration to download. Not to be put on PEcAn VM Getting Started documentation: https://jules.jchmr.org/content/getting-started Registration: http://jules-lsm.github.io/access_req/JULES_access.html

FCM:

    https://github.com/metomi/fcm/
    wget https://github.com/metomi/fcm/archive/2015.05.0.tar.gz

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

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

23.5.5.8 LINKAGES

23.5.5.8.1 R Installation

# Public
echo 'devtools::install_github("araiho/linkages_package")' | R --vanilla

23.5.5.8.2 FORTRAN VERSION

#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

23.5.5.9 LPJ-GUESS

Instructions to download source code

Go to LPJ-GUESS website for instructions to access code.

23.5.5.10 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:

23.5.5.10.1 Solution 1

### From the Command Line
sudo apt-get install r-cran-rgl

then from within R

install.packages("Maeswrap")

23.5.5.10.2 Solution 2

### From the Command line 
sudo apt-get install libglu1-mesa-dev

then from within R

install.packages("Maeswrap")

23.5.5.11 SIPNET {inst-sipnet}

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

23.5.5.11.1 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

23.5.6 Installing data for PEcAn

PEcAn assumes some of the data to be installed on the machine. This page will describe how to install this data.

23.5.6.1 Site Information

These are large-ish files that contain data used with ED2 and SIPNET

rm -rf sites
curl -o sites.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/sites.tgz
tar zxf sites.tgz
sed -i -e "s#/home/kooper/Projects/EBI#${PWD}#" sites/*/ED_MET_DRIVER_HEADER
rm sites.tgz

rm -rf inputs
curl -o inputs.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/inputs.tgz
tar zxf inputs.tgz
rm inputs.tgz

23.5.6.2 FIA database

FIA database is large and will add an extra 10GB to the installation.

# download and install database
curl -o fia5data.psql.gz http://isda.ncsa.illinois.edu/~kooper/EBI/fia5data.psql.gz
dropdb --if-exists fia5data
createdb -O bety fia5data
gunzip fia5data.psql.gz
psql -U bety -d fia5data < fia5data.psql
rm fia5data.psql

23.5.6.3 Flux Camp

Following will install the data for flux camp (as well as the demo script for PEcAn).

cd
curl -o plot.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/plot.tgz
tar zxf plot.tgz
rm plot.tgz

23.5.6.4 Harvard for ED tutorial

Add datasets and runs

curl -o Santarem_Km83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/Santarem_Km83.zip
unzip -d sites Santarem_Km83.zip
sed -i -e "s#/home/pecan#${HOME}#" sites/Santarem_Km83/ED_MET_DRIVER_HEADER
rm Santarem_Km83.zip

curl -o testrun.s83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.s83.zip
unzip testrun.s83.zip
sed -i -e "s#/home/pecan#${HOME}#" testrun.s83/ED2IN
rm testrun.s83.zip

curl -o ed2ws.harvard.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/ed2ws.harvard.tgz
tar zxf ed2ws.harvard.tgz
mkdir ed2ws.harvard/analy ed2ws.harvard/histo
sed -i -e "s#/home/pecan#${HOME}#g" ed2ws.harvard/input_harvard/met_driver/HF_MET_HEADER ed2ws.harvard/ED2IN ed2ws.harvard/*.r
rm ed2ws.harvard.tgz

curl -o testrun.PDG.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.PDG.zip
unzip testrun.PDG.zip
sed -i -e "s#/home/pecan#${HOME}#" testrun.PDG/Met/PDG_MET_DRIVER testrun.PDG/Template/ED2IN
sed -i -e 's#/n/scratch2/moorcroft_lab/kzhang/PDG/WFire_Pecan/##' testrun.PDG/Template/ED2IN
rm testrun.PDG.zip

curl -o create_met_driver.tar.gz http://isda.ncsa.illinois.edu/~kooper/EBI/create_met_driver.tar.gz
tar zxf create_met_driver.tar.gz
rm create_met_driver.tar.gz