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Installing simform

Getting simform running the first time can be très-annoying! On ubuntu, with CDH3 on EC2, it's actually pretty painless -- see the demo directory.
But no one who puts up real clusters seems to use Ubuntu.

Requirements

All nodes

  • A recent branch of python2, say 2.6
  • numpy
  • pynetcdf or python-netcdf (Scientific.IO.NetCDF)
  • Hadoop -- tested with CDH3, earlier prototypes tested with Hadoop 0.21
  • python-hadoop package

Only the head node, or job submission node

  • make -- nothing special here, any version should do
  • dumbo
  • dumbo-feathers -- this requires compiling some Java against the current version of Hadoop
  • A version of the JDK to compile dumbo-feathers
  • mrjob

Recommended for all nodes

Recommended for the head node

  • git

Required environment variables

One of the most common problems is forgetting to set the HADOOP_HOME environment variable. This should be set to whereever your hadoop installation lives, e.g. /usr/lib/hadoop

Ubuntu install with CDH3

See the demo directory.

Ubuntu 10.04 (Lucid)

All nodes

sudo apt-get install python-dev python-numpy \
    python-setuptools python-netcdf \
    libatlast3gf-base
    
sudo easy_install -z typedbytes 
sudo easy_install ctypedbytes

Head node

Install the easy stuff

sudo apt-get install git-core
sudo easy_install -z dumbo

Install MRJob

mkdir ~/devextern
cd ~/devextern
git clone https://github.com/dgleich/mrjob.git
cd mrjob
sudo python setup.py install

Install python-hadoop locally

cd ~/devextern
git clone https://github.com/hyysun/Hadoop.git
cd Hadoop/python-hadoop
python setup.py sdist
sudo easy_install dist/Hadoop-0.20.tar.gz

You must install the same Hadoop-0.20.tar.gz file via easy_install on all nodes -- see below. We may be able to turn this into an egg distribution in the future.

Install feathers

You must install feathers into a subdirectory of the current simform distribution. Here's an example:

cd simform/src # THIS ONLY WORKS AFTER YOU INSTALL SIMFORM!
cd model
git clone https://github.com/klbostee/feathers.git
cd feathers
sh build.sh
cp feathers.jar ..

All nodes again

<copy Hadoop-0.20.tar.gz from head>
sudo easy_install Hadoop-0.20.tar.gz

For these last steps, here is what I did on a test cluster for EC2:

for node in 10.34.86.56 10.76.213.246 10.116.190.35 10.35.94.101 10.113.42.21; do
  scp -o "UserKnownHostsFile /dev/null" -o StrictHostKeyChecking=no  dist/Hadoop-0.2.tar.gz $node:~
  ssh -o "UserKnownHostsFile /dev/null" -o StrictHostKeyChecking=no $node sudo easy_install Hadoop-0.2.tar.gz
done

Redhat install with CDH3

These were written for a different purpose, but do contain all of the install instructions. If you think it's easier to follow the ubuntu instructions, you can follow them for any of the install except for the apt-get pieces, which, obviously, don't work on Redhat.

Here are some install instructions you can reference to meet the requirements:

On all nodes (hadoop namenode and datanodes), we should install the following packages:

# install numpy
wget "http://sourceforge.net/projects/numpy/files/NumPy/1.6.1/numpy-1.6.1.tar.gz/download"
tar xfz numpy-1.6.1.tar.gz
cd numpy-1.6.1
python setup.py install
cd ..

# install ctypedbytes
git clone https://github.com/klbostee/ctypedbytes.git
cd ctypedbytes
python setup.py install
cd ..

# install netcdf
wget "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz" 
tar xfz netcdf-4.1.3.tar.gz 
cd netcdf-4.1.3 
./configure --with-pic --disable-dap --disable-netcdf-4 
make 
make install 
make check
cd ..

# install pynetcdf
wget "http://downloads.sourceforge.net/project/pylab/PyNetCDF/0.7/pynetcdf-0.7.tar.gz"
tar xfz pynetcdf-0.7.tar.gz 
cd pynetcdf-0.7 
python setup.py install 
cd ..

# install hyy-python-hadoop
git clone https://github.com/hyysun/Hadoop.git
cd Hadoop
cd pyhton-hadoop
python setup.py install
cd ..
cd ..

If you have some problems about netcdf, try:

  1. Place usr-local.conf in /etc/ld.so.conf.d on all nodes. (see icme-hadoop1 /etc/ld.so.conf.d/ for the template)
  2. Run ldconfig -v as root on all nodes.

We need to install the following packages on the Hadoop namenode:

# install mrjob
git clone https://github.com/dgleich/mrjob.git
cd mrjob
python setup.py install
cd ..

# install dumbo
git clone https://github.com/klbostee/dumbo
cd dumbo
python setup.py install
cd ..
  1. To get dumbo feathers, run following: git clone https://github.com/klbostee/feathers.git cd feathers bash build.sh

After that, move feathers.jar into your java classpath or just copy feathers.jar to src/model.