39 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.

39.1 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", repos="http://cran.rstudio.com/")' | R --vanilla

# done as root

39.2 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              trust
host    all             bety            ::1/128                 trust

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


To install the BETYdb database .. ## 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
a2enconf pecan
/etc/init.d/apache2 restart

# done as root

39.3 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
a2enconf bety
/etc/init.d/apache2 restart

39.4 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.

Based on version of ubuntu 32/64 use either of the following

32bit only

wget http://download2.rstudio.org/rstudio-server-0.98.1103-i386.deb

64bit only

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=" >> /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/
a2enconf rstudio
/etc/init.d/apache2 restart

# all done, exit root

39.5 Additional packages

HDF5 Tools, netcdf, GDB and emacs

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

39.6 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.

39.7 Install instructions

39.7.1 ED2 ED2.2 r46 (used in PEcAn manuscript)

# ----------------------------------------------------------------------
# Get version r46 with a few patches for ubuntu
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
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

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

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

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`
make OPT=VM
sudo cp ../ed_2.1-VM /usr/local/bin/ed2.git

39.7.2 SIPNET Sipnet Installation

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
sudo cp sipnet /usr/local/bin/sipnet.runk SIPNET testrun

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

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

39.7.4 Linkages Installation

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

39.7.5 DALEC Installation

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

39.7.6 LINKAGES Installation

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

39.7.7 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):


Next you are ready to go to the run directory:


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:


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.

39.7.8 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


    wget https://github.com/metomi/fcm/archive/2015.05.0.tar.gz
  1. edit makefile ```bash 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 ```

  1. 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

39.7.9 MAESPA

Navigate to a directory you would like store MAESPA and run the following:

git clone https://bitbucket.org/remkoduursma/maespa.git

cd maespa


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


39.7.10 GDAY

Navigate to a directory you would like to store GDAY and run the following:

git clone https://github.com/mdekauwe/GDAY.git


cd src


gday is your executable.

39.7.11 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