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Chemistry Linux Workstation FAQ

 

What password do I use and how to change it?

All the machines use your Admitto password for authentication. Some machines are locked down so only members of certain research groups can access them. If this is the case you will get an error message saying 'only members of group whatever may log in' if you are not in the appropriate group.

You can change your Admitto password from a web browser at https://apps.ch.cam.ac.uk/ssms/changepassword.

How do you print?

The workstation should be set up to print to the nearest black and white printer. To print from the command line use the lpr command, but be careful as you cannot print all file types from the command line. Postscript, PDF, and plain text are fine. For other file types open them in the program you used to create them and select File>Print.

If you want to print to a different printer then you can use lpr -P printername. See this question for more help on printing.

How do you read email?

There are three main options: thunderbird, alpine, or webmail. For webmail go to https://webmail.hermes.cam.ac.uk/. The other two can be found on the desktop menus or by typing thunderbird or alpine on the command line. Thunderbird is graphical and alpine is text based. They are preconfigured to read mail from Hermes, the University of Cambridge mail server, but can be reconfigured to point at other servers.

How do you change printer options or install new printers?

Point your web browser at http://localhost:631/ to edit the printer settings on your machine or add new queues.

How do you customize the desktop?

Go to the Dash icon on the launcher bar. This is the icon in the top lefthand corner of the screen. Click on it and a search box will appear. Type 'settings' in this box to show the available applications for changing settings. The two to start with are 'System Settings' and 'Compiz Configuration'.

What desktops/window managers are available?

Unity is the default desktop on the Ubuntu 16.04 image. It has been configured so that a terminal and web browser are readily available. GNOME, KDE, and Fvwm are also available but not supported by the computer office. This means you're welcome to use them but we can't help fix them if you encounter problems. If you wish you may install your own window manager and use a .xsession file to launch it.

How do you run large compute jobs?

Really large compute jobs should be run on one of the compute servers. However smaller ones can be run on the workstations. It is usually a good idea to start these using the "at" command. This means that if you log out or lose your network connection your job won't be killed.

How do you view/print PDF files?

The viewers installed on the system are Foxit and evince. You can print PDFs by going to File>Print within evince, or using the command line pdf2ps command to turn the PDF file into Postscript (which is the language printers speak).

If a PDF will not print one way, try another method or a different model of printer. Some PDFs are buggy. Some printers are buggy. Consequently some combinations just do not work.

Some PDFs will not print in duplex on the duplex queues no matter what you do. If you capture and examine the Postscript being sent to the printer, you will see that it contains commands to turn off duplexing. This comes from the original PDF document and there's not a lot we can do about it. If it bothers you, you can pdf2ps the document and edit the Postscript before printing to save a bit of paper.

How do you access pen/usb drives?

Plug it in and wait a few seconds. The Nautilus file manager will show an icon for the disk if you look in it, but you can also see it under /media/$USER/disk or /media/$USER/usbdisk or similar. To safely remove it you either right-click on the Nautilus icon and select "Umount volume".

If you have put a Unix filesystem on your disk Linux will mount it in read-write mode but you may still find you can't read or write your files. This is because the Unix user accounts on the disk do not match up with those on your workstation. In this case you will need to make the files world-writable on the machine where you first put the Unix filesystem on the disk.

How do you log in remotely?

See the section on ssh access in this document.

How do backups work?

Some of the workstations are backed up. Others are not. It depends on whether the sector/group that owns the workstation made arrangements for backups. At the moment the Theory and CMI workstations are definitely supposed to be backed up. For workstations in those groups, we backup data in /home, but anything under /scratch is not backed up. We usually aim to:

  • have a few backups taken over the last 24 hours
  • then, about one backup per day for the previous week
  • then, about one backup per week for the previous month
  • then, about one backup per month for the previous few months

but this is reliant on a number of factors, such as: how rapidly your data changes, your computer being switched on when a backup is scheduled to run, whether you have a large number of small files (which take longer to backup than one large file), as well as other factors. Thus, we cannot guarantee to have all of the backups listed above for a particular workstation.

For managed Linux workstations in other parts of the Department, check with your group computer rep or the Computer Officers. Another good way to check is to look at the system monitor records for your machine. These can be found at http://hobbit.ch.cam.ac.uk/hobbit/ (Raven-protected). If you click on the 'administration' menu on that website you can search for your machine.

If you need something restored from a backup please send email to support@ch.cam.ac.uk . On some of the machines read-only copies of the backups may also be available as an NFS mount under /rsnapshots on the machine itself, but not all of the backup servers can provide this functionality. 

How do you write CDs?

There is a user-friendly GUI program called Brasero for this. You can find it on the menus or type brasero on a command line.

How do you open a Word/Excel/other Microsoft proprietary document?

OpenOffice or LibreOffice will open many of the Microsoft Office document formats.

Why is /home so small?

If /home is small then it is probably because your workstation is one of those that is backed up by the sector it belongs to. Providing two weeks worth of nightly backups for a large collection of workstations takes a lot of disk space. All the machines have an unbacked up /scratch filesystem in which you have much more space and you can put large temporary files, your (legal) music collection, and so on. Please note that not all the workstations are backed up! Check with the Computer Officers or your group computer rep if you are not sure, or look at the Hobbit system monitor which records backup status.

How do you install software?

The 'main user' of the machine should find they have rights to run the package manager to install packaged software. Here's an example:

 

$ aptitude search frozen-bubble # search for a package
p   frozen-bubble                   - Pop out the bubbles!                      
p   frozen-bubble-data              - Data files for Frozen-Bubble 
$ sudo aptitude install frozen-bubble # install it

Most non-packaged software can be installed in your home directory by using appropriate configuration options. The UCS run an excellent course on how to build software on Unix with a lot of emphasis on installing in /home, the notes for which can be found here.

If you think a package is likely to be useful to several people in the sector please mention it to the Computer Officers. If we have time we may install it on the image so everyone can use it. Mentioning the URL for the package is helpful.

If the Linux distribution that the standard image is based on contains a pre-packaged version of the software you want then just ask the Computer Officers to install the package for you. However the package has to come from the exact version of the distribution that we are using. We will also not install 3rd party RPMs or debs for this reason. If you aren't sure, by all means ask the Computer Officers.

Much software is already available on the image. There is a complete list here.

Where are the compilers/Schrodinger/some other thing we definitely have a licence for?

Check the modules system as you probably need to load a module. Shorter version: type 'module avail' to see the options, and then 'module load whatever' to load the one you want.

Long explanation: The workstations have lots of different software packages installed. Some are only available to research groups who have paid for licences; others are available to all. Some come in multiple versions and different groups like to use different versions. There are so many options that we use the modules system to manage a lot of the application software; a default set of modules is usually loaded on a new user account but no default set can please everyone. If you don't seem to have the package you want (or any copy of your package at all) in your environment, read the modules documentation to see how to list and load the available software packages.

Where is the root password?

The root password is kept by the Computer Officers. We do not give out root passwords to managed workstations because they rapidly become unmanageable when someone else can change their configuration without telling us.

Having said that, on the Ubuntu image the 'main user' of the machine should have sudo rights to run the package manager. This depends on the machine being configured with the right 'main user' in our database, so if you think you should have sudo rights and don't just let support@ch.cam.ac.uk know. Here's how to use the package manager:

$ aptitude search frozen-bubble # search for a package
p   frozen-bubble                   - Pop out the bubbles!                      
p   frozen-bubble-data              - Data files for Frozen-Bubble 
$ sudo aptitude install frozen-bubble # install it

Flash doesn't work on some websites?

This generally happens on 64-bit machines and is because of bugs in the wrapper that allows the 64-bit workstations to run the 32-bit Flash plugin. We've yet to encounter the problem on Precise or Trusty so this is probably now fixed.

How do I get a newer version of a LaTeX package?

There are many ways of accomplishing this. You can get a much newer version of texlive by upgrading to Ubuntu 16.04. Another way, if you just want a few packages is to add this to your local texmf tree.

CTAN has a number of up to date packages. Simply download and extract one of them in a temporary directory, run latex on the .ins file, then copy the files to your local texmf directory (e.g /home/spqr/texmf/tex/latex/chemcompounds/chemcompounds.sty). You can then verify which file will be used by running kpsewhich (e.g "kpsewhich chemcompounds.sty" would give "/home/spqr/texmf/tex/latex/chemcompounds/chemcompounds.sty").

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