Math Phys cluster changes: an update

Quite a lot of changes have been made to the Math Physics cluster in recent months, aimed at both improving the facilities for the section's users and to bring the systems more in line with the rest of the Maths department's Unix/Linux systems, making it easier to add more facilities in the future. Here's a summary of what has been done, the problems that cluster users may encounter following these changes and what remains to be done.

User home directory changes

The user filesystem was reorganised on March 30th and is now in /home/h/ instead of /home/ as before. (You can find a detailed description of the filesystem changes here.) This means any scripts that explicitly refer to your old home directory path must be changed to reflect the new path, /home/h/. Also, some programs such as Netscape will no longer find your bookmarks and other settings such as email mailboxes, etc as it will expect them to be under /home/ instead of /home/h/.

Those of you who have used the environment variable $HOME in your scripts instead of "hard-coded" paths will not be affected by these changes as $HOME picks up the current home directory path from the NIS passwd file. Some users have put links in their ~/bin/alpha directories pointing to various private progrmas in their user space. If these use an absolute reference, with the full home directory path, then these will fail as the path no longer exists. Eg:

~/bloggs> ls -l bin/alpha
total 1
lrwxrwxrwx	1 bloggs   mathphys 	22 Mar  20 15:42 bind -> /home/bloggs/bin/named

will fail miserably but this one won't:

~/bloggs> ls -l bin/alpha
total 1
lrwxrwxrwx	1 bloggs   mathphys 	12 Mar  20 15:42 bind -> ../bind/named

as it's a relative link.

To fix Netscape problems related to the home directory changes, do the following:

  1. change to the /home/h/(username)/.netscape directory, where username is your own username

  2. now look for a file called preferences.js; if it is missing, then you can skip the rest of these steps as you don't yet have a Netscape preferences file and it will be created the next time you use Netscape. You also don't have any problems with Netscape not recognising home directory paths!.

  3. make sure Netscape isn't running and edit the preferences.js file with your favourite text editor and change every occurrence of /home to /home/h.

  4. save the file and then run Netscape - it will now find your personal settings, bookmarks, etc.

Shared applications

For legacy reasons, the Maths Phys cluster has supported two only-partially compatible versions of Digital Unix (DU 4.0E and OSF/1) running on Alpha hardware of varying vintages - plus an even older flavour of Unix called Ultrix and running on MIPS hardware. This means as many as three different versions of some shared applications need to be installed on the servers h and tera, and the arrangements for ensuring the correct version of software is served to the correct type of workstation hardware is something of a nightmare.

To make this easier to manage and upgrade, late last year all the shared applications for modern Digital Unix 4 systems were moved out of tera (itself an older OSF/1 system) to a new /usr/local disk on h. tera now only serves older Alphas running OSF/1 and MIPS systems running Ultrix. With all the modern applications on h and unconstrained by historical considerations, work will commence soon on upgrading these applications, and adding more.

Paths on older Alpha OSF/1 machines

The recent disabling of telnet, rlogin, rsh and rexec daemons in favour of ssh has uncovered a can of worms on the older systems - there have always been problems with the tcsh shell which was installed locally long ago. Basically, it tends to ignore defined paths and even when a program or command appears to be in a user's path, it won't execute unless the user types the full path to the command.

This appears to have a lot to do with the myriad of different user .cshrc and .login files in use and is being actively investigated. The problem is most evident when trying to run one of the ssh clients, which reside in /usr/local/bin. You may need to give the full path to the command - /usr/local/bin/ssh1 .. or /usr/local/bin/ssh2 ... as appropriate.

Accessing your cluster home directories on Maths open access machines

The Linux systems in room 6m29 now mount home directories from the Math Phys cluster as well as the usual set from the main departmental server, geometry. When you log into one of these systems, your default home directory will be that from the geometry server and your home directory will usually be:


Your Math Phys cluster home directory will be found in:


This is been made possible by the cluster file system changes as described above.

The new Linux machines in 6m36

Three new Linux systems have joined the cluster in 6m36 - these are high performance Transtec systems based on the AMD Athlon 1.2 GHz processor, with 40 GB of disk space, 256 MB of memory and a graphics card that will drive two monitors. They have a rather higher performance than the Alpha XP1000 workstations.

Although they are installed and ready for use, they are not yet fully integrated into the Digital Unix-dominated Maths Phys environment. In particular, the standard user login scripts used in Math Phys try to execute various commands peculiar only to Digital Unix and you will see a screenful of error messgess if you log into one of these SuSE Linux systems with unmodified login scripts. These error messages may be safely ignored - new 'standard' .cshrc and .login scripts are being written which will support Linux as well as the three Unix versions in use in Math Phys.

There are also problems due to the differing way in which Linux and Digital Unix/Ultrix handle X-windows start-up scripts and this prevents many (but not all) Maths Phys users from logging into a graphical login screen. It all depends on exactly what's in your login scripts and this is being looked into but for the time being, there is a workaround for this:

  1. At the graphical login screen, type in your useranem or select your pictorial icon.

  2. Near the bottom left of the login screen you will see a dropdown menu labelled Session Type - select failsafe.

  3. Now enter your password and either hit return or click on the Go! button.

  4. You will then be logged into a very basic X-Windows session with no window manager or desktop, and you will see a plain xterm window in the bottom right of the screen. If you see a lot of error messages here, these are due to your login scripts trying to run Digital Unix commands. Ignore them.

  5. Now type in the name of the desktop (kde2, kde) or window manager (twm, fvwm2, etc) you'd like to use and hit return.

  6. Your chosen desktop or window manager will now come up on the screen.

  7. If you want to use twm as seems to be popular on the Alphas, please note it will look a little different. Pressing the mouse buttons will bring up pop-up menus as usual but there will be little clutter on the screen at other times. This is because the Alphas have a twm desktop customised for Math Phys, which the Linux systems currently lack, as they have a standard twm build. (If there is demand for it, the Math Phys look & feel could be implemented on the Linux systems too).

  8. Logging out: when you have finished your session and want to log out, logout from the xterm window that first appeared when you first logged in.

Andy Thomas

Unix/network sys admin,
Department of Mathematics

last updated: 3.4.2001