Linux systems

Linux is the Unix clone for PCs, and is the most common Unix-like operating system available, so hopefully most users don't need detailed guidance on how to use it. At present, we use Scientific Linux CERN 6 (SLC6) on our standard desktops. Some laptop users no doubt use other versions, but for most purposes the differences are minor. Some notes on installation of a Linux PC into the HEP environment are available, but are mainly aimed at administrators, and the operations discussed require their intervention, so the average user should not need to be concerned about them.

Linux systems are generally named pcxx.hep.phy.cam.ac.uk. The naming scheme we use is discussed elsewhere.

Logging on

You can login to a Linux PC either at the main screen, or from Windows systems. The latter provide a NX Client for X-windows or a PuTTY terminal login using ssh. See the Windows page for more details. Your home directory is on the NFS-served disk /usera  (see below for more details) whichever Linux system you use. In the past, the user environment was set up so that users could login to either Linux or DIGITAL UNIX without having to change things. This not relevant now as DIGITAL UNIX is no longer used, but you may still find relics of this in the login scripts. Be careful if modifying the execution path in particular - add your own paths to the end of the PATH variable (else you may mask system commands unintentionally). Also remember that experiments may have their own setup scripts which could affect your private setups in unexpected ways.

We use NIS to provide global authentication across all the Linux systems. To change your password, use passwd. This may take a few minutes to propagate your password to all Linux systems. Note that we now synchronise passwords between Linux and Windows systems, so a password change on one platform will propagate to the other. This also means that the stricter rules for Windows passwords apply: at least eight characters, and at least three out of the four categories uppercase, lowercase, numeric and special characters

Rebooting

If it is necessary to reboot your machine, please follow the procedure below. Do not simply switch off your machine. Not only does it take longer to reboot, but you may also trash the local disk. You are recommended to check with the local administrators if at all possible before rebooting. If rebooting is required frequently, you should definitely talk to the local administrators, as it may indicate something that needs investigation.

  • Check the system box for a label indicating that the PC serves a special function. If the PC does have such a label, you must contact a local administrator before rebooting (or be prepared for ritual disembowelling by the other users).
  • Please remember that our Linux PCs run batch jobs, so don't reboot just to fix some trivial problem if you know that your PC has a batch job running.
  • Switch to console mode (Ctrl-Alt-F1). Then type Ctrl-Alt-Del to reboot.
  • Alternatively, if the Gnome or KDE display manager is  running, you can also reboot from the login window. 

Ctrl-Alt-F7 will reverse the effect of Ctrl-Alt-F1 (i.e. get you back to graphics mode).

Mounting CDROMs, floppies or memory sticks.

With SLC6, mounting of removable media is usually automatic. Hence users should not need to do anything to be able to see the contents of floppies, CDs or memory sticks.

As an alternative for an MSDOS floppy, the mcopy, mdir etc. family of commands can be used, but the floppy must not be mounted in this case.

Use the umount command to unmount whichever device your have mounted - do not try to remove the device without unmounting first, or you may corrupt the file system on the stick.

Printers

We use CUPS as the printing package on Linux. There is a web interface at http://pclf.hep.phy.cam.ac.uk:631/, where the user documentation is available. The web page at http://pclf.hep.phy.cam.ac.uk:631/printers/ will display the various printer queues - there is also a description of the printers available on this page. You may print to the queues using the lpr command, or via a GUI dialogue box using the command kprinter <filename>. Apart from the web page mentioned above, lpstat -p will list the currently defined print queues. The lpoptions command can be used to set user defaults (e.g. lpoptions -d HPBWUP will set the user's default printer to be the HP B&W printer upstairs). lpq or lpc status will give the current status of the specified print queue.

File system

All of the disk space provided for Linux users is served from the Linux systems. Data backup is done on one (Linux) system. The discussion of disk space accessible to users is on a dedicated page, but there is a summary below of the main features. The local disks on the Linux systems are usually split into several partitions (ignoring the extra complication of dual boot setups on several PCs). / and /var contain the PC-specific system files and is backed-up very rarely (usually when we have a suspicion about the local disk and want to take a copy to make recovery easier). A directory /var/work exists on each Linux box and is intended for volatile local user files. /afs-cache provides the local cacheing area for AFS. Another partition (typically twice the size of the memory in the PC) is set aside for swap space. Most of the file space a user will be interested is served by NFS from file servers. We use the automounter to mount and dismount filesystems as required. Typical file systems available to users are:

  • Home directory: This is at /usera/<user> and served from pciv. Typically 100GB is permitted for each user before we start to discuss disk usage with you, though we try to be sympathetic to specific needs. The disk is archived daily.
  • Experiment directories: (/atlas, /lhcb etc.) These are intended for experiment-specific files that require regular backups - for example code distributions and databases. They are not designed for large data files. We try to tailor the disk size to correspond to what is required - let us know if you feel that we've got it wrong! These disks are archived once a week.
  • Scratch areas: These include /work, which is a central scratch area, and /var/work on each of the Linux systems' local disks. The latter areas are all automounted on the local /var/work of the PC you are currently on - the one for host pcxx is available at /var/work/pcxx. These areas have open access for all users. None of these areas are backed-up. They are meant for volatile files and could be deleted at any time if the space is urgently needed. Users should make clear the ownership of the files by creating an appropriately-named directory for them on these areas.
  • Data disks: These are currently /r01, /r02, /r03-/r04 and /r11-/r16 and are meant for large datasets (raw data, Monte Carlo generation, N-tuples, etc.). These will only be archived on request - it is up to users to ensure that anything they want archiving is put on tape (though the management will do the actual archiving for you). Write access to these disks is by request and usually controlled at the per-experiment level.

The frequencies of the different disk backups are mentioned above - there is a page which discusses general backup policies and mechanics, which you should look at if you want to know more detail than is necessary.

Tapes

We have a LTO5 (1.5TB native) autoloader, with a 8-tape capacity, for handling tapes. This is used mainly for archives nowadays - it is relatively rare to use tapes for data transfer to other sites with the modern, fast networking we have available.  It also has hardware compression, which can typically give a gain of 2:1 in capacity (for data files this is usually not true as they are already typically in a compressed format.

CD/DVD Writing

We have DVD writers on most of our Linux systems. xcdroast is available to do the writing. You should discuss with the management if you have a need to write Linux DVDs and don't understand how to do it.

Applications and tools

ssh

Secure shell (ssh) is available and should be used for all interactive logins. For X sessions it has the benefit that the redirection works automatically without the user having to set the DISPLAY variable (though remember to use the "-X" option). scp and sftp are also available for file transfers.

Remote X sessions

For X sessions from remote locations, NX 3.5.0 is available. It is lighter on resources than VNC which is also available.

Window manager

The management have no intention of getting in the middle of a flame war on this - Gnome and KDE are the normally-available window managers with Redhat Linux, but if you have another favourite we are willing to listen to requests. FVWM2 is an older and lighter window manager which might work on our systems - you will be provided with a default ~/.fvwm2rc file when your account is created, which you can tailor to your needs. Be warned that if you have a ~/.xesssion file, this will detemine the window manager you get.

Editing

emacs 23.1.1 is installed as part of SLC6, though xemacs is no longer available. A default ~/.emacs file is provided. The vim (version 7.2) and joe (version 3.7) editors are also available.

Mail

Thunderbird and Alpine are available for dealing with e-mail. We recommend the use of secure IMAP to access your mail on our server. There is a separate page dedicated to this topic - users should check there for more details.

Web browsers

Firefox 24 and Opera 12.15 are available.

Document preparation

Latex, dvips etc. are available for document preparation. If there are any missing fonts, please let us know. xdvi, ghostscript, gv are available to view your document.

We also have LibreOffice 4.0.4 installed if you prefer something closer to MicroSoft Office for your document preparation.

Compilers

f95 (a.k.a. gfortran) is available for FORTRAN compilations.

For C/C++, gcc/g++ is provided - we have the 4.4.7 version installed.

Batch working

We currently use Condor 7.8.8.  See the separate page for a more detailed discussion.

AFS

OpenAFS client is installed on all Linux systems. The default cell is cern.ch. Typically 2GB of the local disk is set aside as an AFS cache.


Steve Wotton and John Hill Last update 29 February 2016.