Module

Multiple versions of various software packages are available on luria.mit.edu Versions are managed using module.

module commands

• List available applications on the system:

module avail

• Load an application so it can be used:

module add

• Specify version number of an application, e.g.

module add tophat/2.0.12

We recommend you always module add the version number so that you know which version of the software is used. Otherwise, a running application may generate different results or break when the software is upgraded in the future.

Note: some packages are available only after you load the python (for python packages) or jre (for java packages) modules. For example, compare the output of the following:

module avail

with

module add jre/1.6.0-29
module add python/2.7.2
module avail

• R and R packages - Various versions of R are installed on luria. Each one has a collection of associated packages. Execute the following commands taking note of the comment lines:

# Load an R version
module add r/2.15.3
# Start R
R

• Once inside R, check out the available R packages

#List R packages and direct the list into an object called "a"
a<-installed.packages()
#Display the dimensions of the object "a"
dim(a)
#List the parts of object "a" that have package name and package version
a[,c(1,3)]

• NOTE: Those package version numbers may not be consistent from month to month and can change without warning.

• When working with R, capture your session info with the command below so you can reproduce the environment if needed:

sessionInfo()

• quit R

q(save="yes")
#enter y at prompt

• Once back in the shell, view the R data that remains

ls -lat | head
cat .Rhistory

• List loaded applications:

module list

• Unload an application:

module del

• Print module help:

module help