CLEAR Systems Reference Guide

A Python-enabled Vim installation is available on CLEAR for users who need Vim features that depend on Python support.

Quick Start

To use the CLEAR Vim 8.2 installation for the current terminal session, run:

export PATH=/clear/apps/vim-8.2/bin:${PATH}

Verify Python Support

To view the features compiled into this Vim installation, run:

/clear/apps/vim-8.2/bin/vim --version | grep python

The output should indicate whether Python and Python 3 support are available.

To display the complete Vim feature list, run:

/clear/apps/vim-8.2/bin/vim --version

Per Session or Terminal

After establishing an SSH session to CLEAR, run:

export PATH=/clear/apps/vim-8.2/bin:${PATH}

This change applies only to the current terminal session. If you open another SSH session or log out and reconnect, you must run the command again.

Permanent Configuration

For most users, enabling an alternate application only when needed is recommended. This helps prevent environment settings from affecting other courses or applications.

To determine your current shell, run:

echo $SHELL

Common shell initialization files include:

For Bourne-compatible shells, add the following line to the appropriate initialization file:

export PATH=/clear/apps/vim-8.2/bin:${PATH}

Log out and log back in after modifying your shell configuration.

If you need to change your default shell, see Modify Your Default Linux Shell below.

This section provides a basic introduction to navigating your CLEAR home directory and shared course directories.

Connect to CLEAR

Connect using SSH:

ssh <NetID>@ssh.clear.rice.edu

Replace <NetID> with your Rice NetID and complete the required authentication process.

On your first connection from a particular computer, your SSH client may ask you to confirm the identity of the remote host. Verify that you are connecting to the intended CLEAR host before accepting a new host key.

Your CLEAR Home Directory

After logging in, you should normally begin in your CLEAR home directory.

Display your current directory with:

pwd

List files and directories with:

ls -la

Return to your home directory at any time with:

cd

Course Directories

Shared course directories are generally located under:

/clear/courses

To view available course directories:

cd /clear/courses
ls -la

To enter a specific course directory:

cd /clear/courses/<course-name>

Replace <course-name> with the appropriate directory provided by your instructor.

Copying Files

To copy a file from your current directory to a course directory, use:

cp <file> /clear/courses/<course-name>/<destination>

Make sure you have permission to write to the destination directory before copying files.

File Permissions

Warning: Be careful when using commands such as chmod and chgrp on files or directories in your CLEAR home environment. Incorrect permission changes can prevent you or others from accessing files as expected.

If you are unsure about a permission change, contact the TS&S Service Desk before making broad recursive changes.

CLEAR supports several commonly used Linux shells, including:

• bash
• sh
• tcsh
• csh
• zsh

Your default Linux shell is associated with your Rice account and may be used by other systems that rely on the same directory information.

Change Your Default Shell

Use the Rice self-service account portal at whooru.rice.edu.

Open your profile settings, locate the Unix Shell setting, select the desired shell, and submit the change.

The change may not take effect immediately. Directory information can require time to propagate before the new default shell appears on all systems.

Systems Affected

The shell preference is stored in the campus directory service. Systems that obtain account information from that service may use the selected shell as your default login shell.

CLEAR, the Curricular Linux Environment At Rice, is a shared Linux computing environment designed primarily to support academic coursework and instructional computing.

Server vs. Desktop Computing

When you use your local Windows, macOS, or Linux computer, applications normally run directly on that computer.

When you use CLEAR, programs run on remote Linux systems. You typically interact with CLEAR using an SSH terminal session. Applications that require a graphical interface may also require X11 forwarding, VNC, a web interface, or another remote graphical-access method.

Before You Begin

You should have:

• A valid Rice NetID.
• Access to the required Rice authentication services.
• A CLEAR home directory.
• An SSH client on your local computer.

If you can authenticate to CLEAR but do not have a working home directory, submit an TS&S Service Desk ticket requesting a CLEAR home directory. Include "need clear home directory" in the subject line.

Quick Start

Connect to the general CLEAR SSH endpoint:

ssh <NetID>@ssh.clear.rice.edu

Complete the required authentication prompts.

Once connected, you can determine which system you are using with:

hostname

The general ssh.clear.rice.edu name directs users to an available CLEAR login system. Users may also connect to a specific CLEAR server when required for a class or application.

Graphical Applications

Some applications require graphical remote access. Depending on the application and your local operating system, you may use:

• X11 forwarding
• VNC
• A web browser
• Visual Studio Code Remote SSH

For Visual Studio Code and other remote development workflows, refer to the appropriate CLEAR IDE documentation.

Common Development Tools

Common tools available in the CLEAR environment include:

• Command-line text editors such as Vim, Emacs, and Nano
• Programming languages and compilers
• Scientific and optimization software
• Python and Conda environments
• Jupyter Notebook and JupyterLab
• Remote development tools

Refer to the dedicated CLEAR KB guides for detailed setup and usage instructions.

Additional Resources

• CLEAR SSH Access Guide
• CLEAR X11 Forwarding and Graphical Applications
• CLEAR Integrated Development Environments (IDE) Guide
• CLEAR File Storage and Data Management

Faculty Support

Faculty who need a Linux environment or CLEAR resources for a course should contact the appropriate Rice support team through the TS&S Service Desk.

CLEAR provides multiple programming languages, compilers, and development environments. Exact versions may change as the systems are updated.

GNU Compiler Tools

GNU compiler tools available on CLEAR may include:

gcc
g++
gfortran

Additional compiler toolsets may be available through wrapper scripts such as:

gcc-SCL
g++-SCL
gfortran-SCL

Use the dedicated CLEAR C/C++ Development Environment Guide for current compiler setup instructions.

Other Languages and Environments

Depending on the CLEAR system and installed software, available environments may include:

• Clang
• Rust
• Julia
• Python
• Perl
• R and RStudio
• Java
• MATLAB
• Gurobi
• IBM ILOG CPLEX Optimization Studio

Some user-managed environments, such as Miniconda and Jupyter, may be installed in individual CLEAR home directories.

Because software versions change over time, refer to the dedicated CLEAR application and development guides for current version-specific instructions.

CLEAR server names provide information about the operating-system generation associated with a system.

System Naming

Individual CLEAR systems generally follow this convention:

<system>.clear<version>.rice.edu

For example:

borax.clear8.rice.edu
agate.clear9.rice.edu

In these examples, clear8 and clear9 identify systems associated with the corresponding CLEAR operating-system environments.

Future generations may follow the same convention, such as:

<system>.clear10.rice.edu

General CLEAR Login Name

The general CLEAR login endpoint is:

ssh.clear.rice.edu

This provides a stable login name that can direct users to the current default CLEAR environment.

Version-Specific Cluster Names

Version-specific cluster aliases may follow the pattern:

ssh.clear<version>.rice.edu

Examples include:

ssh.clear8.rice.edu
ssh.clear9.rice.edu

The default environment behind ssh.clear.rice.edu may change as newer CLEAR generations become the primary platform.

Specific CLEAR Systems

Users should normally connect through ssh.clear.rice.edu unless a course, instructor, application, or troubleshooting procedure requires a specific CLEAR system.

CLEAR is a shared curricular computing environment. Resource limits help ensure that systems remain available and responsive for all users.

RHEL 9 Compute Node Resource Limits

The following limits were documented for the RHEL 9 CLEAR compute environment. Limits may be adjusted as system requirements change.

Users running long-running or resource-intensive workloads should ensure that their work is appropriate for the CLEAR curricular environment.

Shared-System Usage

CLEAR systems are shared by many students and courses. Users should avoid workloads that unnecessarily consume system resources or interfere with other users.

When possible:

• Stop applications and services that are no longer needed.
• Shut down unused Jupyter, VNC, and remote-development sessions.
• Monitor disk usage in your home directory.
• Use tmux when appropriate for terminal sessions that need to survive an SSH disconnect.

Use CLEAR for Its Intended Purpose

CLEAR is primarily intended to support curricular and instructional computing. Use the environment responsibly and avoid workloads that interfere with course activities or other users.

CLEAR Home Directory

If you can log in but do not have a working CLEAR home directory, submit an TS&S Service Desk ticket and include "need clear home directory" in the subject line.

Disk Quota

If you receive disk quota warnings, review your home directory for large or unnecessary files before requesting additional storage.

For additional guidance, see CLEAR File Storage and Data Management.

Understanding the Login Message

When you connect to CLEAR, the login message may provide important information about:

• Appropriate system usage
• Current system availability or load
• Operational announcements and system news

Review the login message when connecting because it may contain information about maintenance, outages, software changes, or other current CLEAR conditions.

Check Your Current System

To determine which CLEAR host you are currently using, run:

hostname

If troubleshooting requires a specific system, connect directly to the appropriate CLEAR hostname instead of using the general ssh.clear.rice.edu alias.

Need Help?

For additional information or assistance, contact the TS&S Service Desk.