PPUNIX FAQ

This applies to pplxint8 and 9 running Scientific Linux 6

General

General Notes on the Unix System

The general purpose Linux login servers are pplxint8 and pplxint9 - referred to as as the interactive machines. All these will be kept running for as much time as possible.

In case of problems software or hardware the system may have to be taken down at short notice.

Access to all UNIX systems (except pplxintn) from outside of the .physics.ox.ac.uk domain is disabled. When you are away and wish to connect, login to pplxint8 or 9, then on to the others if needed. You should use ssh where ever possible so that passwords do not pass in the clear over the Ethernet. This avoids hackers "sniffing" them. So for example you should type:

ssh -l username pplxint8.physics.ox.ac.uk

Long jobs on the interactive machines should be run niced. Jobs that are left running using large amounts of CPU
may have the priority lowered without notice. This helps keep interactive response acceptable.

Please read the notes on Best Practice for Interactive Usage

I'm confused by all the options for places to log in, user names and passwords

You will have a "PPUNIX" account name that you can use to log in to pplxint8-10. This document refers to the resources provided to you by virtue of you having this account. You will have a PHYSICS account that you use for email, logging in to Windows and linux DESKTOP computers and Windows terminal servers. This technology is shared with the rest of the physics department. For the purposes of this document these desktop machines are barely referred to except in reference to their use as a gateway to the Linux systems. You can also use your physics account to log in to pplxint8/9 but only after we have added you to the system by creating the unix account.

You may also have an Oxford (SSO) account, something like abcd1234, which you can ignore for the purposes of this document.

What version of the Operating System are pplxint5 and 6 and pplxint8 and 9 running

pplxint8 and 9 are running Scientific Linux 6
plxint10 is running CentOS 7

How do I change my password?

The majority of users now use the physics password system. To change the password please refer to the following webpage: How to change your physics department password.

The unix systems operate with a second, common username and password which is served by pplxusers2. This will go away in due course as it is insecure and should you wish to get in touch with us we will remove your unix password early if you wish.

How can I set my prompt in tcsh

set prompt = "%/% " gives directory followed by %
set prompt = "%~% " uses the ~ notation if possible
set prompt = "%B%~> %b" gives current dir with ~ notation in bold followed by >
set prompt = "%B%m:%~ > %b" gives hostname : before the path in bold followed by > e.g. pplxint9:~/linux/NEWSYSTEM >
set prompt = "%B`id -nu`@%m:%~> %b" gives username@hostname before the path in bold followed by > e.g. gronbech@pplxint9:~/linux/NEWSYSTEM >

What should be in my startup files? (.cshrc and .login)

The following instructions are valid on the unix nodes.

A copy of the latest recommendations for your .bashrc, .cshrc and .login are in /etc/skel on pplxint8

This includes the PATH environment variable that ensures all the programs and commands are available to you.

Backspace key in Exceed not working

For some time now there have been some problems with certain combinations of Gnome versions and certain versions of Exceed. The problem is that the BackSpace key (just above the return key) is usually used to delete the character to the left of the cursor. Under some combinations of gnome and exceed it does not work.

If you have this problem try the following

  • Run Xconfig, select keyboard Input,
  • In the Keyboard mapping section you will usually have primary: oxdec.kbf select edit and click on the backspace key
  • Select Edit, Mapping
  • Set Unshifted to BackSpace (it is probably on delete)
  • Save as oxdec2.kbf

Select this as your primary and click ok.
A reset of exceed and then try your favourite linux node and see if works.

File Systems

How do I use AFS

NOTE: From 2017 AFS at CERN is being decommissioned. Overtime access to the AFS servers there will be removed, please find alternative ways to access the data you need there. Experimental software may well be accessable via CVMFS.

AFS client software is loaded on pplxn. It is available under the /afs tree eg: cd /afs/cern.ch

In order to authorize yourself you will have to use kinit. By default we are part of the cern domain so if you want to access files at desy:
klog -cell desy.de
after you have finished you can relinquish your key with the
unlog
command.

How can I see the unix disks from MS Windows

The unix disks are to be found on managed windows PCs at Y:/LinuxUsers/pplinux

For other systems, use WinSCP for preference. It should be installed on all recently set-up
desktops as Programs->WinSCP3 & PuTTY->WinSCP. If it's not already installed it can
just be dowloaded directly from <http://winscp.net/eng/download.php> and put it somewhere convenient (possibly just straight on the desktop). This can be used to provide a graphical method to click and drag files between the two systems using scp as a backend.

How can I see the MS windows disks from unix

(Note: AT 2017 this service is currently broken)

On pplxint8 and 9 the files are directly available from /physics/Users/Particle. You will have to type kinit @PHYSICS.OX.AC.UK to authenticate to the central physics systems first.

The Microsoft Windows userdisks can be accessed from any of pplxint8/9 using sshfs. E.g. on pplxint8:

mkdir ~/mountpoint sshfs @winssh.physics.ox.ac.uk:/home/ ~/mountpoint</p></strong>

You may have to add the following lines into your $HOME/.ssh/config file for this to work.

host winssh.physics.ox.ac.uk winssh GSSAPIAuthentication no

For self-managed systems, you can also use sshfs or sftp to winfe.

You can also mount the disks directly from the kde graphical environemnt using SMB. See here for details.

Printing

How do I print something on the unix nodes?

lpr -PDWBSharpL6 filename

As the default printer is already set you can actually just use:

lpr filename

For duplex printing use:
lpr -o Duplex=DuplexNoTumble filename

How do I check the print queues on unix?

DWBSharpL6 is the queue for the main photocopier/printer on level6.

The best way to check a queue is with the command:lpq -Pqueuename
lpq -PDWBSharpL6

How do I print from a web-browser (firefox) on unix?

The following instructions are valid when running netscape on the unix nodes.

  • Select the File menu
  • Select the Print option
  • In the print dialog box select the format for the printed document... choose Postscript
  • Now complete the print command: lpr -PDWBSharpL6 for level 6

What Colour printers are available?

The new Sharp Photocopier/Printer has colour.DWBSharpL6.

This needs to be tested to see how to get colour out as by default it prints in Black and White

How can I print out a man page?

If you know the command you need, type man . Some do not have man pages, but you can often get help with commandname --help

Email

What email clients are available

Web browsers can be setup to read mail via the Web interface to Exchange or via IMAP.

You can access the exchange interface from the link: https://mail.physics.ox.ac.uk/owa.

Another option is to use thunderbird. Instructions are here: http://www.physics.ox.ac.uk/IT/email/exchange/2010/ThunderbirdSetup.htm

alpine is available on pplxint. It can be used to read email as an IMAP client to access the exchange server. To set it up to access the exchange server edit your .pinerc file as detailed here.

Note, the use of pine and alpine is heavily discouraged as the emails are stored in plain text. Auto-login passwords are also stored in plain text.

How do I print from pine or alpine

Note, the use of pine is heavily discouraged as the emails are stored in plain text. Auto-login passwords are also stored in plain text. Below instructions rely on the .pinerc config file being correctly configured.

  • In pine select M for main menu
  • S for setup
  • P for printer
  • use the arrow keys to select "personally selected printer command"
  • press return and enter a print command

How do I get a unix system to forward mail to another system

If for example you get your email on the exchange server and want any email sent directly to your unix account to be forwarded. You should create a .forwardp file in your home directory and send the mail to your unique physics address eg pete.gronbech@physics.ox.ac.uk and that will route it on to your prefered location to receive mail.

Make sure this is not the unix account as you will then have created an email loop.

So for example the .forward file would contain just the one line: pete.gronbech@physics.ox.ac.uk

Misc

How do I run Mathematica on the Linux systems?

We use a network licence which is served by mathematica.physics.ox.ac.uk. This means users may run on any of the systems where it is installed.

Please exit the program when you are finished to free up the licence for other users.

Start it by typing (works on pplxint8 and 9 only):

/network/software/linux-x86_64/arc/mathematica/9.0.1/Executables/mathematica

How Can I browse the World Wide Web?

Use firefox

How do I include Postscript pictures in TeX/LaTeX?

What editors are available on the systems?

The following instructions are valid on the unix nodes.

There are many editors available on the Digital Unix systems, first the basic unix ones: [b]ed[/d] - Basic line mode editor. Do not use unless mad!

vi - A Full screen unix text editor often used by system managers. On linux this is replaced by vim an improved vi . type vimtutor to learn the basics.

The following public domain editors are available:

  • emacs - The most popular "Do Everything editor/environment"
  • xemacs - formally known as lemacs, as above but with nice motif menus
  • kate - Part of the kde suite of programs a simple to use X windows editor
  • gedit - Part of the gnome suite of programs a simple to useX windows editor

How can I access PC applications from a unix system?

The rdp client rdesktop is available. To connect, run the following command, subsitituting in your windows username and preferred geometry after the "-g".

rdesktop termserv.physics.ox.ac.uk -u -D PHYSICS -g workarea

Disks

How do I find out how much disk space is available to me?

The following instructions are valid on the unix nodes.

All users have a home directory on a userdisk. Disk quota's are enabled on the user disks. You can check your quota with the quota command.

Other than atlas and lhcb, There are data disks for particular groups such as /data/sno, /data/zeus, /data/delphi for use by the SNO, ZEUS and Delphi groups. Use the df command to see what disks are mounted and how much
space is available on them. Use df -k to get the size in kb's.

Users can check who is using the space with the commands; for example

cd /data/snoplus du -sk *

It is up to users within a particular group to fight (negotiate) disk usage!!

Extremely large data disks are available for atlas and lhcb which use the gluster technology. The df command does not work, and the du command will take about a week so should not be run. Hourly quota usage statistics are recorded in /data/{atlas,lhcb}/usage.txt.

How can I save disk space/See what I'm using?

The following instructions are valid on the unix nodes.

Check what files /directories are taking up a lot of space by typing:

  • cd to get to your login directory
  • du -sk *|sort -nr|more to list the largest files/dir's first

Then look at the largest files and directories and see if you can delete anything. If you are not using some files you can compress them with gzip e.g. gzip *.ps *.eps to compress all Postscript and Encapsulated Postscript images.

If you have a whole directory that you are not using why not create a compressed tar file of it. e.g. tar cf bigdir.tar ./big ; gzip bigdir.tar Where ./big is the directory that has loads of old files you want tared. Once you have the compressed tar file you can delete the directory

rm -r ./big or \rm -r ./big if you don't want to be prompted.

Which disks are backed up and when?

Incremental backups of the /home directories are performed every weekday evening. The policy has been not to backup data disks as we do not have the capacity to back every thing up, but we do now backup some of the smaller ones to the OUCS HFS.

Some data disks are still backed up to the OUCS HFS (Oxford University Computing Service Hierarchical File Store) using the IBM ADSM software. This provides an ability to restore a disk if it is lost but does not provide any history. So if you modify a file and later want the original version there is no way of getting it. If you delete a file and wish to get it back provided you ask for it within a week or two it should be retrievable.

If users have important data they are strongly recommended to take their own personal backups and store them somewhere other than the Unix systems. Do NOT store your thesis on a group data disk!! If you need more space on your home ask pp_unix_adminATphysics.ox.ac.uk for it.

What about PC backups?

Non standard PC's are your personal responsibility.

You may have a Linux or a Windows PC.

Windows

Most new PC's will be installed as a standard Physics Windows clone and will be managed by Russell Allcock. Any files stored in the H: drive are backed up.

Linux Desktops

Any files stored under /physics/home/ are identical to the H: drive on Windows and are backed-up.
Unless your desktop is in the range pplxdt20-30 then your home directory is not backed up by default.

NOTE: For general PC questions see  John Harris or Russell Allcock or email itsupport@physics.ox.ac.uk

What happens to my data when I leave the department

Ensure that you make adequate arrangements to transfer your data to a safe place. World and group readable data becomes the property of your group and may be cleaned up to save disk space or re-used. Personal files are deleted after a short time.

Process Control

What jobs am I running?

Use the command:

  • ps x to list the processes you are running.
  • top can be used to the processes taking up the most CPU. You should not allow more than one of your processes to take up more than 50% CPU.

How do I kill off a job/process?

Use the command:
>kill to kill a process where pid is the process id given by the ps command.

Or use top and the [b]k[b] command. If the process is not killed, use kill -9

Graphics

How can I view graphics images?

  • Use xv
  • Use ghostview (or gv) for postscript images.
  • Use acroread for pdf files.

What graphics drawing packages are available?

xfig and gimp are available on this system

What plotting packages are available?

  • ROOT is the main package on this system.
  • matplotlib and numpy are becoming popular with python users accross other scientific disciplines
  • mathematica
  • gnuplot Simple plotting package from GNU.
  • NAG Graphics The NAG Graphics libraries are available to link to in /system/naglibs/mark9clibs/gcc/cll6a09dgl/lib/

Program Development

Using the grid
Web pages hosted by the unix systems
Particle Physics Linux Batch Farm

Categories: Linux | faq | ppunix