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Drinking from the Firehose

For a complete list of all installed software, see NodePackageList

Most Commonly Used Software

OpenMPI

Version 1.4.3

Scilab

Version 5.4.0

R

Version 3.0.3

Modules

We provide a small number of R modules installed by default, these are generally modules that are needed by more than one person.

Installing your own modules

To install your own module, login to Beocat and start R interactively

R

Then install the package using

install.packages("PACKAGENAME")

Follow the prompts. Note that there is a CRAN mirror at KU - it will be listed as "USA (KS)".

After installing you can test before leaving interactive mode by issuing the command

library("PACKAGENAME")

Running R Jobs

You cannot submit an R script directly. 'qsub myscript.R' will result in an error. Instead, you need to make a bash script that will call R appropriately. Here is a minimal example. We'll save this as submit-R.qsub

#!/bin/bash
# First, lets tell the qsub command which resources we need
# lets start with memory (in this case I ask for 1 gigabyte).
# For help on these, see SGEBasics

#$ -l mem=1G
# Now we tell qsub how long we expect our work to take: 15 minutes (H:MM:SS)

#$ -l h_rt=0:15:00

# Lets output a little useful information This will put something like "Starting the job at: Thu Jan 26 10:43:26 CST 2012" in your output file
echo -n "Starting the job at: "
date

# Now lets do some actual work. A lot of our users use R, so we'll go over that
# This starts R and loads the file myscript.R
R --no-save -q < myscript.R

# like before, this is just useful information
echo -n "Ending the job at: "
date

Now, to submit your R job, you would type

qsub submit-R.qsub

Java

Versions 1.6 and 1.7

We support 4 versions of the Java VM on Beocat. IcedTea 6 and 7 (based on OpenJDK), Sun JDK 1.6 (Java 6), and Oracle JDK 1.7 (Java 7).

We allow each user to select his or her Java version individually. If you do not select one, we default to Sun JDK 1.7.

Selecting your Java version

First, lets list the available versions. This can be done with the command eselect java-vm list

% eselect java-vm list
Available Java Virtual Machines:
  [1]   icedtea-bin-6
  [2]   icedtea-bin-7
  [3]   oracle-jdk-bin-1.7  system-vm
  [4]   sun-jdk-1.6

If you'll note, oracle-jdk-bin-1.7 (marked "system-vm") is the default for all users. If you have a custom version set, it will be marked with "user-vm". Now if you wanted to use icedtea-6, you could run the following:

eselect java-vm set user 1

Now, we see the difference when running the above command

% eselect java-vm list
Available Java Virtual Machines:
  [1]   icedtea-bin-6  user-vm
  [2]   icedtea-bin-7
  [3]   oracle-jdk-bin-1.7  system-vm
  [4]   sun-jdk-1.6

To verify you are seeing the correct java, you can run java -version

% java -version
java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.7) (Gentoo build 1.6.0_27-b27)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)