PPUNIX FAQ
This applies to pplxint12 and 13 running AlmaLinux 9
General Notes on the Unix System
The general purpose Linux login servers are pplxint12 and pplxint13 - 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 pplxint12 or 13, 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:
[b]ssh –XJ login@bastion.physics.ox.ac.uk login@pplxint12.physics.ox.ac.uk[b]
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 Physics account name that you can use to log in to pplxint12/13. 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 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 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 pplxintn running
plxint12 and 13 are running AlmaLinux 9 AKA EL9
How do I change my password?
To change the password please refer to the following webpage: How to change your physics department password.
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. pplxint12:~/linux/NEWSYSTEM >
set prompt = "%B`id -nu`@%m:%~> %b" gives username@hostname before the path in bold followed by > e.g. gronbech@pplxint12:~/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 pplxintn
This includes the PATH environment variable that ensures all the programs and commands are available to you.
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File Systems
How can I see the unix disks from MS 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 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.
Printing
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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 firefox on the Linux 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
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How Can I browse the World Wide Web?
What editors are available on the systems?
There are many editors available on the Linux 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
How can I access PC applications from a unix system?
rdesktop termserv4.nat.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/snoplus, /data/atlas, /data/lhcb for use by the SNO, Atlas and LHCb 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
It is up to users within a particular group to negotiate disk usage!!
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. They are backed up to the OU IT Services HFS (Oxford University IT Services Hierarchical File Store) using the IBM Tivoli software. This provides an ability to restore files if it is deleted. 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 advised 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.
NOTE: For general PC questions see John Harris or Russ 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. Please ensure any data that will be of use to your group or supervisor is placed in a group area. 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
