Using the Hadoop cluster and Rhipe

Using the Hadoop cluster and Rhipe

The SCF's test Hadoop cluster is now offline due to limited use. Please see our page on Spark or contact us if you would like to try out Hadoop or Spark in cluster computing. The material below is now out of date, but preserved at the moment for historical purposes.

SCF Hadoop Cluster Information

The SCF has a small Hadoop test cluster that all SCF users can use to run Hadoop jobs, including R jobs that use the Rhipe package as a front end to Hadoop.

The Hadoop cluster has eight nodes, each with two cores, and a total of about 1 Tb of disk space set up with the Hadoop distributed file system. Note that the nodes are a set of our outdated compute servers and the amount of disk space is limited. The goal of the Hadoop cluster at this point is to serve as a testbed rather than for doing real analyses of large data. If you have need for more resources please contact us and we can discuss how you might use cloud resources such as Amazon's EC2.

Below is more detailed information about using the Hadoop cluster.

Basic Configuration So You Can Run Jobs

First, you must email us and let us know that you would like to use the cluster. We will create a directory on the Hadoop distributed file system (HDFS) for you to store your files. The directory will be /user/username, where username is your SCF username. Note that /user/username is on the HDFS and is not directly accessible on the Linux filesystem of the Hadoop nodes.

Second, add the line 'hadoop=1' to your .bashrc file in your SCF home directory. It should be added before the following lines, which should already exist in your .bashrc file:

if [ -f ~skel/std.bashrc ]; then
    source ~skel/std.bashrc

This sets up some environment variables that you need in order to use Hadoop.

Running Hadoop and Rhipe Jobs

All jobs must be run from one of the following compute servers:

badger, crow, dorothy, heffal, mole, rabbit, toad, witch

You can also find this list of servers by typing the following on any SCF machine:

sitehosts broadcomm

To check on the status of the cluster, go to the following URL using a browser running on any SCF machine (this could be a browser on an SCF machine that is ssh-tunneled to your local machine):


If you know how to interact with the HDFS directly or how to use Hadoop, you can do so from the command line of any of these machines.

To use Rhipe, start R, and load and initialize the Rhipe package:

rhinit(TRUE, TRUE) # the TRUEs are not necessary but give debugging information

How Interact with the HDFS

You can use UNIX-like syntax to interact with the HDFS.

To look at directories and files:

hadoop fs -ls /  # to see the root directory
hadoop fs -ls /user/username # to see the home directory of the user username

To see your disk usage on the HDFS:

hadoop fs -du /user/username

To get a list of various Hadoop filesystem commands:

hadoop fs

Some Tips on Using Rhipe

Any data that you want to write to the HDFS should be written to /user/username. It's also possible to write to /tmp but we ask that you not do this.

In some cases, to fully exploit all 16 cores on the cluster, you may need to explicitly specify the number of map tasks and reduce tasks for your MapReduce job. These can be specified in the mapred argument passed into the rhmr() function. Hadoop documentation suggests that the number of map tasks be 10 times the number of slaves and the number of reduce tasks be two times the number of slaves, so in R, you would specify

z <- rhmr(..., mapred = list( = 10*8, mapred.reduce.tasks = 2.8), ...)

where the ... indicate the various other arguments you are passing in. These can also be set via rhoptions().

The Rhipe package website has some example code. Per the above comment, you'll need to change any HDFS file paths to point to your user directory on the HDFS. Also, note that the code has some bugs in it and the syntax is not fully up to date with Rhipe v. 0.71, which is the version we are currently using. Please email for more information and updated code.

After you have created the MapReduce job using rhmr(), you can run it and monitor its status as follows:

r <- rhwatch(z)

You can also see some information about the Hadoop processes by going to the URL printed out by rhwatch(). As above, you need to enter that URL in a browser running on an SCF machine.

Note that debugging may be difficult because the R code is run across multiple nodes, the data are distributed across multiple nodes, and Hadoop jobs are based on Java, so you may get error messages from Java. You can email for assistance.