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Linux at CLASSE

Please see Linux Introduction for a brief introduction for newcomers to Linux.

See CLASSE Linux Overview for a presentation on Linux at CLASSE.

Introduction
Logging in
Software
- Desktop productivity
- Other notes
File Systems
- Home disk
- Central storage
Compute Farm
Policies
More Documentation

Introduction

Here at CLASSE, we use Linux for desktop computing, the CLASSE Compute Farm, and our core infrastructure (file servers, web servers, etc.). Almost all of these Linux systems are networked together, and they are configured to be virtually identical. This means that you can login to any Linux system at CLASSE (some restrictions apply) and experience the same computing environment as on any other Linux system here. And from any CLASSE Linux system, you can, in general, access the same file systems and programs because they are all hosted in a central location, not on your local Linux system.

In other words, you should think of any Linux system at CLASSE simply as a gateway to our central services. All of your files are stored by default on central storage, not your local disks. Any programs that you launch on your local desktop are read from a central repository of programs, although the programs will run on your local CPU. For applications that require more resources than you have available locally, we recommend the CLASSE Compute Farm.

Logging in

Most Linux computers at CLASSE can be reached using the instructions below. We also provide a general purpose login node lnx201.classe.cornell.edu, which should be used only for brief interactive jobs. (For intensive computation, please use the CLASSE Compute Farm.)

From a CLASSE Linux system: To log into a CLASSE Linux desktop system, enter your CLASSE ID and password on the login screen.
From a CLASSE Windows system: See ConnectingToALinuxMachineFromWindows.
From a non-CLASSE system: For remote access to our Linux resources, please see RemoteLinux.

Software

Desktop productivity

When logged into a Linux desktop system, we recommend the following programs for your daily desktop activities. You can launch these programs via the Xfce Desktop Environment interface or via the command line interface.

To open the command line interface from the Xfce, right-click on the desktop and select "Open in Terminal" (or "Terminal Emulator"). For other programs, click on the icon in the lower-left corner for a menu.

As we move to Scientific Linux 7 (SL7), please see the following for information about configuring your SL7 Xfce Desktop Environment:

These are our recommendations for your daily desktop activities.

Task	Program	Command
Desktop Environment	Xfce	`startx` (or, log in graphically)
Web browsing	Firefox Vivaldi	`firefox` `vivaldi`
Email	Launch Firefox or Vivaldi to browse to http://outlook.cornell.edu
Text editing (basic)	gedit, Pluma on SL7	`gedit`, `pluma` (for SL7)
Text editing (full)	Emacs, Visual Studio Code	`emacsª`, `code`
Text editing (hard-core)	Vi or Vim	`vim` (or type `vi`)
Word processing Spreadsheet Presentations	OpenOffice	`ooffice`
LaTeX (GUI)	Texmaker (GUI)	`/nfs/opt/texmaker/bin/texmaker` (GUI)
LaTeX (command line)	See LaTeX
PDF reader	Okular	`okular`
MultipleSessions remote desktop	Xfce
File Manager	Thunar	`thunar`

ª SL7 users may need use X2Go compatible version:

/nfs/opt/emacs-26.3-lucid.sl7/bin/emacs

Other notes

Whenever possible, we use software packages and versions that are supported by our distribution to ensure the integrity, stability, and security of our systems. To achieve this goal and maintain uniformity across all of CLASSE's linux systems, any installation of software on the local system (using rpm, yum, etc.) must be done by the computer group through a ServiceRequest.

In addition to the standard software distributed with the Linux operating system, the CLASSE IT group maintains its own software distribution in /nfs/opt, please see our CLASSE Linux Software Documentation. Examples of such software are Matlab, Mathematica, and various Fortran compilers.

Finally, most Linux programs and libraries can be built or installed in an NFS file system by a regular user. For example, as mentioned above CHESS users can install software in /nfs/chess/sw . Please submit a ServiceRequest for help determining the best way to install, configure, and support any program you may need. Please see LinuxSupport for more information.

File Systems

We provide petabytes of storage that are accessible from any CLASSE computer (any operating system). Please see:

NetworkedFilesystems for general Linux instructions.
DataStewardship for the locations of the file systems available for your use.

Home disk

When you login to a CLASSE Linux box using your CLASSE username, either remotely via ssh or locally, you start out in /home/username. This is known as your home directory, and is where environment setup scripts, programs files, etc. reside. Your home directory is not local to each computer; it is a networked filesystem and is therefore accessible from all CLASSE Linux systems and is backed up on a regular basis. For more information, please see HomeDisk.

Central storage

To maximize the resources available to you while ensuring the security and availability of your files (in the event of a disk failure, etc.), all of your data should be stored in NFS directories. These are centrally maintained file maintained served from a cluster of servers using enterprise-class redundant hardware that is available from Linux using NFS and from Windows, OS X, and Linux using Samba. Most (but not all) NFS file systems are backed-up nightly. The only local directories you can write to are /tmp and /var/tmp (please see TemDisk for more information). Your supervisor and colleagues should be consulted for advice on where to store your data. Please submit a ServiceRequest if you have any questions, or would like a file system created or expanded.

Most NFS file systems are accessed from CLASSE Linux systems in /nfs/. For example, /nfs/user/username is the CLASSE UserDisk (\\samba\user\username from Windows or OS X), CHESS users can save data in /nfs/chess/aux and install software in /nfs/chess/opt, etc. Please see NetworkedFilesystems and DataStewardship for more information. Backup policies for networked filesystems can be seen at BackupSchedule.

Compute Farm

For compute-intensive or parallel-processing tasks, you can submit interactive, batch, GPU, or parallel jobs to the CLASSE Compute Farm.

Policies

We try to standardize and maintain uniformity among all of our Linux systems in order to maximize the resources available to you, secure your data, and minimize support overhead. For example, before deploying any new system-level packages, we thoroughly test them, manage their installation with our configuration management system, and eventually push them to all CLASSE linux systems.

Software installation

With few exceptions, CLASSE Linux systems run 64-bit Scientific Linux 6, a distribution put together (primarily) by Fermilab and CERN with the goal of providing a stable common install base while reducing duplicated efforts across the scientific community. Scientific Linux is built from (and binary compatible with) RedHat Enterprise Linux, inheriting the stability and security from RedHat's Quality Assurance. Any software that has not been validated by RedHat and the Scientific Linux community can compromise the integrity of the operating system. Moreover, once the CLASSE IT Group installs any additional software, we monitor that software for security exploits, updates, and potential conflicts with the base operating system.

In order to support the number of systems installed in our lab, we rely on the packages provided from RH and SL wherever possible. Conversely, we do not install individual packages on individual systems.

Before installing any additional software on our systems, we must establish a legitimate need that cannot be met with software already installed or available from RH or SL. If you are developing software that will run on CLASSE Linux systems, the software must be developed on CLASSE Linux systems.

In many cases where there is a localized need for a particular piece of software, it is possible for users or groups to install the software themselves using either the binary or source distribution of the software. Software installed in user space can be maintained by users and avoids many of the above-mentioned risks to system security and stability. However, the CLASSE IT Group will not be able to provide any support for software installed in this manner.

Software updates

As an enterprise-class distribution focusing on stability and security, Scientific Linux provides security updates which are applied on a nightly basis. For a list of updated packages, please see the appropriate errata pages.

SSH Key based authentication

For heightened security, users can use ssh-keygen to create authentication keys for use on our Linix systems. However, users must also use a passphrase when generating this key, so that even if somebody gets a copy of your private key, you will reduce the risk of having them gain access to your account. For more information, please see the US-CERT (Computer Emergency Response Team) warning for SSH Key-based Attacks on Linux-based services.