HPC:Manual Software Install

This page describes how software can be installed in a user's own home (or lab's project directory)

Other Pages

• HPC Main Page
• Connecting to the PMACS cluster
• User Guide
• Available Software
• PMACS Archive System

Manually Installing Software in home directories

Installing software in home directories is allowed. The following example shows how to install a program (from source) like R in a home directory.

Note 1: All the steps below must be done in an interactive session, not on the head node, consign.pmacs.upenn.edu! Else, the installation will fail.

Note 2: The example below describes how to install the software to $HOME/bin. If an alternative location is preferred, the configure/make install steps can be altered such that the program is installed the desired location.

Installation

First, from the head node, launch an interactive session:

$ bsub -Is bash

Then, download the source and untar it into a directory:

$ wget https://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz

$ tar zxvf R-3.2.2.tar.gz

Compile and install the program in the desired location:

$ cd R-3.2.2/

$ ./configure --prefix=$HOME/

$ make

$ make install

R is now installed in a directory called "bin" inside your home directory ($HOME/bin). If an alternate location is preferred, change either the "--prefx=$HOME/" to something different or run the "make install" step as "make install DESTDIR=<path_to_new_location"

Use

Once installed the program can either be run interactively or non-interactively, based on the application.

The above example installation will install the program under $HOME/bin. To run this program in an interactive session:

$ $HOME/bin/R --version

$ $HOME/bin/R 

To run an Rscript using this version of R, include "$HOME/bin/Rscript" (without quotes) in your job script.