Note: This document provided for informational purposes

We recommend that users download the PEcAn (pecan.ova) or ED (ed.ova) VM instead of creating from one from scratch.
Then install VirtualBox or VMware and follow instructions on the page Using VM's.

VM Creation

Create Virtual Machine

First create virtual machine

# ----------------------------------------------------------------------
# CREATE VM USING FOLLOWING:
# - CPU      = 1
# - MEMORY   = 1GB 
# - DISK     = 50GB
# - PACKAGE  = openssh
# ----------------------------------------------------------------------

Make sure machine is up to date.

# ----------------------------------------------------------------------
# Update VM
sudo apt-get update
sudo apt-get dist-upgrade
reboot

Install compiler and other packages needed.

# ----------------------------------------------------------------------
# install build environment
sudo apt-get -y install build-essential

Install tools for virtual environment, either VMWare or VirtualBox

# ----------------------------------------------------------------------
# install vmware tools (if running in VMWare)
sudo apt-get -y install --no-install-recommends open-vm-dkms open-vm-tools

# ----------------------------------------------------------------------
# install virtual box tools (if running in virtual box)
#sudo apt-get --no-install-recommends -y install virtualbox-ose-dkms virtualbox-ose-guest-utils
sudo mount /dev/cdrom /mnt
sudo /mnt/VBoxLinuxAdditions.run
sudo umount /mnt
sudo addgroup pecan vboxsf

Make sure machine has SSH keys (rc.local)

sudo wget -O /etc/rc.local http://isda.ncsa.illinois.edu/~kooper/EBI/rc.local

related issues

Install ED

# ----------------------------------------------------------------------
# install build environment
sudo apt-get -y install dkms build-essential bzr gfortran openmpi-bin libhdf5-openmpi-dev

Pull code for ED from ebi-cluster

# ----------------------------------------------------------------------
# Get latest code from David
#bzr branch  sftp://kooper@ebi-forecast.igb.uiuc.edu/home/kooper/src/EDBRAMS
# PECAN 1.0
wget http://isda.ncsa.illinois.edu/~kooper/EBI/EDBRAMS.tgz
tar zxf EDBRAMS.tgz
rm EDBRAMS.tgz

Following fixes have been checked into this version of ED:

# ----------------------------------------------------------------------
# fix some compile errors
vi +118 EDBRAMS/ED/src/utils/rsys.F90
   real                  :: etime

vi +37 EDBRAMS/ED/src/io/h5_output.F90
 ,globdims,plist_id

Create configuration file for ubuntu (this is already in bazaar, include.mk.opt.ubuntu)

Update paths.mk file to point to install location of the source code and create symlink.

# ----------------------------------------------------------------------
# configure and compile ed
cd EDBRAMS/ED/build/bin

# set path in paths.mk
sed -i -e "s#^ED_ROOT.*#ED_ROOT=${HOME}/EDBRAMS/ED#" paths.mk 

ln -s include.mk.opt.ubuntu include.mk.opt

Can now compile ED and install the binary as ed2 in /usr/local/bin

# compile ed and install as ed2 in /usr/local/bin
bash ./install.sh
sudo cp ../ed_2.1-opt /usr/local/bin/ed2
cd

ED Testrun

# ----------------------------------------------------------------------
# Get data

wget http://isda.ncsa.illinois.edu/~kooper/EBI/sites.tgz
tar zxf sites.tgz
rm sites.tgz
wget http://isda.ncsa.illinois.edu/~kooper/EBI/inputs.tgz
tar zxf inputs.tgz
rm inputs.tgz

# fix metdata
sed -i -e "s#/home/kooper/projects/EBI#${HOME}#" sites/*/ED_MET_DRIVER_HEADER

# ----------------------------------------------------------------------
# Create sample run
mkdir testrun.ed
cd testrun.ed
Create the ED2IN file and config.xml files by downloading the following two attachments: 
wget -O ED2IN http://isda.ncsa.illinois.edu/~kooper/EBI/ED2IN
sed -i -e "s#\$HOME#$HOME#" ED2IN
wget -O config.xml  http://isda.ncsa.illinois.edu/~kooper/EBI/config.xml
  1. execute test run
    time ed2
  1. after about 4 minutes it should be finished

PEcAn Installation

Check out PEcAn and add alias to help build pecan

cd

# check out pecan
# latest
#bzr branch sftp://kooper@ebi-forecast.igb.uiuc.edu/home/kooper/src/pecan
# PECAN 1.0
wget http://isda.ncsa.illinois.edu/~kooper/EBI/pecan.tgz
tar zxf pecan.tgz
rm pecan.tgz

# add build alias
if ! grep buildpecan ~/.bashrc > /dev/null
then
    echo "alias buildpecan='sudo /home/$USER/pecan/bash/pecanbuild.sh'" >> ~/.bashrc
fi
alias buildpecan='sudo /home/$USER/pecan/bash/pecanbuild.sh'

Install R

# add Michael Rutter's deb repository of R packages 
sudo apt-get install -y python-software-properties
sudo add-apt-repository ppa:marutter/rrutter
sudo apt-get update

# install minimal R
sudo apt-get --no-install-recommends -y install r-base-core

# install other R packages
sudo apt-get install -y default-jre libdbd-mysql libmysqlclient16-dev mysql-server mysql-client jags r-cran-rjags r-cran-xml r-cran-hdf5 r-cran-mass r-cran-rmysql liblapack-dev

# have R install rest of dependencies
sudo R --vanilla < ~/pecan/rscripts/install.dependencies.R

Compile PEcAn and install

sudo ~/pecan/bash/pecanbuild.sh

PEcAn Testrun

Create folders

mkdir testrun.pecan
cd testrun.pecan

Create BETY database

# needs to be done only once
mysql -u root -p -e "grant all on bety.* to bety@localhost identified by 'bety';" 

# download and update/install database
wget http://isda.ncsa.illinois.edu/~kooper/EBI/bety.sql
mysql -u bety -p"bety" -e 'drop database if exists bety; create database bety;'
mysql -u bety -p"bety" bety < bety.sql
rm bety.sql

Create the files needed for a single run: 
wget -O template.pavi http://isda.ncsa.uiuc.edu/~kooper/EBI/template.pavi
wget -O pecan.xml http://isda.ncsa.uiuc.edu/~kooper/EBI/pecan.xml
wget -O runall.sh http://isda.ncsa.uiuc.edu/~kooper/EBI/runall.sh

chmod 755 runall.sh

To run the full PEcAn workflow you can simple execute:

./runall.sh

Helper Scripts

Script to create a SSH key (sshkey.sh)
Script to clean the VM and remove as much as possible history (cleanvm.sh)

wget -O ~/sshkey.sh http://isda.ncsa.uiuc.edu/~kooper/EBI/sshkey.sh
wget -O ~/cleanvm.sh http://isda.ncsa.uiuc.edu/~kooper/EBI/cleanvm.sh
chmod 755 ~/sshkey.sh ~/cleanvm.sh