Patching NetCDF

1. download a copy of the NetCDF 4.2 source. The package that we built the patch against was build on Oct 24, 2011 The NetCDF Java download website is here: http://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp

An ftp link for the package we used for the patch can be found here: ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v4.2/ncSrc-4.2.zip

We downloaded the zip file with this command

wget ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v4.2/ncSrc-4.2.zip

and we downloaded that file into this directory

/install/netcdf42

2. unzip your zip file. Our command looked like this

   unzip ncSrc-4.2.zip

3. download the NetCDF patch from github a) install git. On Ubuntu this command does the trick

   sudo apt-get install git

b) configure git via these two commands

git config --global user.name "Joe Smith"
git config --global user.email "[email protected]"

c) create a directory to hold the source code. Ours is at /hub/SciHadoop

d) cd into that directory

e) run git init

f) add the remote repository like so (we named the remote repo scihadoop)

git remote add hub/scihadoop git://github.com/four2five/SciHadoop.git

git fetch hub/scihadoop

git checkout -b scihadoop hub/scihadoop/master

g) copy the NetCDF patch into the NetCDF source directory, in our case that is /install/netcdf42

cp netcdf_path/netcdf42.diff /install/netcdf42/

h) install ant. On Ubuntu, this command will do that

sudo apt-get install ant

i) cd into the cdm directory and run this command

ant makeMainComplete

j) within the cdm directory, there should now be a directory named target. Within target, there is a jar file named netcdfAll-4.2.jar. This is the NetCDF library that SciHadoop will use.

k) add the NetCDF library to your CLASSPATH and HADOOP_CLASSPATH environment variables. In your ~/.bashrc file, add this line (assuming you build the NetCDF library in /install/netcdf):

CLASSPATH=$CLASSPATH:/install/netcdf/cdm/target/netcdfAll-4.2.jar

and then, in the conf/hadoop-env.sh file located in your hadoop installation (our Hadoop installation is at /install/hadoop-0.20.203.0 ), add this line

export HADOOP_CLASSPATH=/install/netcdf/cdm/target/netcdfAll-4.2.jar