Physics

The Particle Physics UNIX FAQ

Some info is obsolete or needs updating this is coloured in purple.

This applies to ppslgen and pplxgen running Linux

General


File Systems


Printing


Email


Misc


Disks


Tapes


Mathematica


Process Control


Graphics


Program Development


Using the GRID


Web pages hosted by the unix systems


Particle Physics Linux Batch Farm


General Notes on the UNIX system

The general purpose Linux login servers are pplxint5 and pplxint6. 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 pplxgen, 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 pplxint6.physics.ox.ac.uk

Long jobs 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


What version of the Operating System is pplxint1 2/5/6 running

pplxint1 and 2 are running Scientific Linux 4.

pplxint5 and 6 are running Scientific Linux 5


How do I change my password?

The unix systems operate with a common username and password which is served by pplxgen. This is running Network Information Services (NIS formerly yellow pages (yp)).  On the Linux nodes you must type yppasswd


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 > eg

pplxint5:~/linux/NEWSYSTEM >

set prompt = "%B`id -nu`@%m:%~> %b"

gives username@hostname:  before the path in bold followed by > eg

gronbech@pplxint5:~/linux/NEWSYSTEM >


Backspace key not working in Exceed

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.


How do I use AFS

AFS client software is loaded on pplxintn. It is available under the /afs tree eg

cd /afs/cern.ch

In order to authorize yourself you will have to use kinit followed by aklog.

kinit username@CERN.CH

aklog

 

after you have finished you can relinquish your key with the

unlog

command.


How can I see the unix disks from Windows

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

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.

An alternative for users with linux laptops is to use somthing like sshfs or fuse to mount the home area in an NFS like way but using ssh.

 


How can I see the MS windows disks from unix

The Microsoft Windows userdisks are mounted using NFS on both pplxgenng and ppslgen under the directory /windows. Use the df command to see. You may find that you do not have ownership of your files, if this is the case please ask Ian McArthur to match the unix uid with the windows user id.

 


How do I print something on the unix nodes?

lpr -PDWBSharpL6 filename

 


How do I check the print queues on unix?


DWBSharpL6 Postscript queue for the main photocopier/printer on level6
The best way to check a queue is with the command
lpq -Pqueuename
for example lpq -PDWBSharpL6
 


How do I print from WWW (Netscape/Mozilla)?

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 a man page?


 


What email clients are available?

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.

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


How do I print from pine

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
print5

This will output on the printer outside the graphics area called PS4.


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 .forward file in your home directory and send the mail to your unique physics address eg p.gronbech1@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:
p.gronbech1@physics.ox.ac.uk


How can I browse the World Wide Web?

Use firefox

There are several browsers available.


How Can I use the Oxford web proxy server?

The compulsory web cache has been discontinued.

Oxford University now imposes a compulsory Web cache. All web traffic will automatically be redirected through it so you do not have to make any changes to your web browser.

 


How do I include Postscript pictures in TeX/LaTeX?

Encapsulated PostScript files can be included into LaTeX/TeX by using the psfig macro. The psfig documentation in Postscript is readable and the source tex file is available.


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 pplxint5
This includes the PATH environment variable that ensures all the programs and commands are available to you.


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:
ed - 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
nedit - Part of the Fermitools suite of programs a simple to use X windows editor


How can I access PC applications from a unix system?

The rdp client rdesktop is  available.

Or use a web browser and use the JAVA applet as detailed on the following web page:

http://www.physics.ox.ac.uk/it/mswindows/terminalservers.htm


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

The following instructions are valid on the unix nodes.
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.
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.
There are several data disks, some are for general use, freedisk. Anybody can create a directory on /freedisk. Files will be deleted from here if they have not been modified for 90 days!!

There are data disks for particular groups such as /data/sno, /data/atlas, /data/zeus, /data/delphi for use by the SNO, ATLAS, ZEUS and Delphi groups.
Users can check who is using the space with the commands; for example
cd /lhc
du -sk *
It is up to users within a particular group to fight (negotiate) disk usage!!


How can I save disks 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 .eg
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?

The following instructions are valid on the unix nodes.
John Harris performs local backups, full backups are carried out every other Saturday and incremental backups 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 most to the OUCS HFS.

All userdisks and a few data disks are backed up locally to tape every week day night.

Most data disks are now 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.
A file in the top of each disk partition will indicate whether the disk is backed up but for the latest information contact John Harris or Pete Gronbech. eg /zeus/This_disk_IS_backed_up.txt or /zeusdata2/THIS_DISK_IS_NOT_BACKED_UP.txt


If users have important data they are strongly recommended to take their own personal backups. Do NOT store your thesis on a group data disk!! If you need more space on your userdisk ask
me for it.


What about PC backups?

Non standard PC's are your personal responsibility.
Most new PC's will be installed as a standard Physics NT clone and will be managed by John Harris, Chris Hunter or Ian McArthur. The Windows PC's here have the user area's automatically backed up on the NT server see John Harris or Russell Allcock for details.
NOTE: For general PC questions see  John Harris, Russell Allcock or Richard Smith.


How do I use tapes on the Linux Systems?

To save a directory full of files use the tar command eg
cd ~gronbech/important_data
tar cf /dev/nrst0 .
mt -f /dev/nrst0 rewoffl
/dev/nrst0 is the DLT drive on pplx2. Note: the n in front of rst0 is very important as it stands for no rewind. The . at the end of the tar command line means "all the files here". The mt command is used here to rewind and eject the tape. Use man mt to find out about other options for mt (such as fsf).
If the device is busy check with the command ps auxw for any jobs running that are using the tape. eg dump, rdump, dd, tar, mt etc. and ask the user if they are finished.
The Tape drive is usually used by the SNO group for reading data tapes. The drive is in the graphics area room 651 (access by swipe card) on the Left Hand side. pplx2 is in the next room the cable goes through the wall!


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.

The current version is 4.1 Start it by typing
math or math -raw
To start it using the X windows interface type
mathematica

Running mathematica via exceed

In order to allow exceed to display the mathematica fonts the following steps must be taken:

  1. Run Xconfig (from Startmenu, Programs, Network Applications, Exceed)
  2. Double Click Fonts
  3. Click Fonts Database
  4. Click Add, Browse
  5. Select Y:\Sharable\eXceed\FONT\math42  (Where y: is the dfs directory)
  6. Enter math42 in the File Name (*.fdb) box, click OK
  7. In The Font Database window click off Automatic Font Substitution, click OK
  8. In The Font Settings Window click close
  9. Now start an Exceed session to pplxgen and run mathematica

 


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.


How do I kill off a job/process?

Use the command
kill -9 pid to kill a process where pid is the process id given by the ps command.

Or use top and the k command.


How can I view graphics images?

Use xv
Use ghostview for postscript images.
Use acroread for pdf files.


What graphics drawing packages are available?

xfig is available on this system


What plotting packages are available?

PAW is the main package on this system.
mathematica
maple
histo Part of the Fermitools suite.
nplot Part of the Fermitools suite.
gnuplot Simple plotting package from GNU.
xmgr Simple plotting package.
NAG Graphics The NAG Graphics libraries are available to link to in /usr/local/naggl04d.
ROOT


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22 March 2013
PDG