Managment of Software Packages with module

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Multiple Versions of Various Software Packages are Available on rous.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

and

module add jre/1.6.0-29
module avail
  • R and R packages - Various versions of R are installed on rous. 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
#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 that those package version numbers may not be consistent from month to month. when using R you
#should capture session info with the command:
sessionInfo()
#quit R
q(save="yes")
#enter y at prompt
#view R data that remains
ls -lat|head
cat .Rhistory
  • List loaded applications:
module list
  • Unload an application:
module del
  • Print module help:
module help
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