CLEAR Scientific Computing And Optimization Tools Guide
Introduction
The CLEAR computing environment provides a variety of scientific computing, statistical analysis, and optimization tools to support coursework, research, and software development. This guide explains how to access, configure, and use applications such as Ruby, RStudio, Gurobi, and IBM ILOG CPLEX Optimization Studio on the CLEAR systems.
Whether you are performing statistical analysis, developing scientific applications, or solving optimization problems, this guide provides the information needed to configure your environment and begin using these tools on CLEAR.
Ruby
Ruby 2.0.0 is available as a parallel installation to the Ruby tools supplied with the operating system.
Starting a Bash Shell Session
To start a Bash shell with the Ruby 2.0.0 environment enabled, run:
exec scl enable ruby200 'bash'
Once the environment is enabled, you can use commands including:
erb gem irb rake rdoc ri ruby testrb
This Ruby version is provided as an alternate environment and does not replace the operating system's default Ruby installation.
RStudio
The CLEAR systems provide web-based access to RStudio.
Sign in using your Rice NetID and password.
If you receive an error indicating that you do not have a CLEAR home directory, submit an OIT Help Desk ticket requesting one. Include "need clear home directory" in the subject line.
Gurobi
The CLEAR systems have Gurobi installed and available for mathematical optimization and related coursework and research.
Getting Started
The simplest way to start Gurobi is to run:
gurobi.sh
The gurobi.sh wrapper script performs the required environment setup automatically.
You can also pass command-line options to the script. For example:
gurobi.sh --help
Advanced Usage
The current Gurobi installation is available through the CLEAR application environment.
To determine your login shell, run:
env | grep SHELL
Then load the appropriate Gurobi environment for your shell.
Bash or Sh
source /clear/apps/gurobi/gurobiEnv.sh
Verify the command and version with:
which gurobi_cl gurobi_cl --version
Csh or Tcsh
source /clear/apps/gurobi/gurobiEnv.csh
Verify the command and version with:
which gurobi_cl gurobi_cl --version
You must load the appropriate environment script for each new login session unless you configure your shell to load it automatically.
Automatic Environment Setup
If you regularly use Gurobi, you can configure your shell to load the appropriate environment automatically.
- Bash users: Add
source /clear/apps/gurobi/gurobiEnv.shto your~/.bashrcfile. - Csh users: Add
source /clear/apps/gurobi/gurobiEnv.cshto your~/.cshrcfile.
For most users, loading the Gurobi environment only when needed is recommended. This helps prevent environment settings from affecting other applications or coursework.
Available Gurobi Installations
To view Gurobi installations available under the CLEAR application directory, run:
ls -d /clear/apps/gurobi*
Additional documentation is available from the Gurobi website.
For additional assistance, contact the TS&S Service Desk.
IBM ILOG CPLEX Optimization Studio
IBM ILOG CPLEX Optimization Studio provides tools for mathematical optimization, planning, scheduling, and decision modeling.
Documentation
For information about using IBM ILOG CPLEX Optimization Studio, see the IBM ILOG CPLEX Optimization Studio 22.1.1 documentation.
IDE integration on CLEAR is currently a work in progress.