Scientific Linux DESY 3 at Zeuthen  

Updated: 2007-06-25

SL3 is our legacy platform, and being replaced by Scientific Linux 5


What Scientific Linux DESY 3 is

It is the current standard Linux at DESY Zeuthen. In many respects, it's a continuation of DESY Linux 5 rather than a successor, since the versions of the most important software (system and applications) are at least very close, often identical, to those on DL5.

SL3 is available in a 64bit version for AMD64/EM64T systems as well.

The major difference with respect to DL5 is its much longer lifetime and enhanced compatibility with most other HEP sites because it's based on Scientific Linux, an effort started and kindly made available by our colleagues from FNAL and meanwhile joined by those from CERN. It has been and still is being adopted by many labs and university departments, although some chose to purchase subscriptions for RedHat Enterprise Linux (which should not make any difference from the users' point of view).

Presentations about Scientific Linux at DESY were given in the DESY Linux User Meeting April 21st, 2004 and August 25th, 2004.
There also was a presentation to the CUC on August 2nd, 2004.
A presentation introducing Scientific Linux (DESY) in more detail was given in the Zeuthen Technical Seminar September 14th, 2004.
Knut Woller presented the Scientific Linux Roadmap for DESY in the computing seminar November 1st, 2004.
The introduction of SL3 at Zeuthen in Spring 2005 was accompanied by a presentation in the Zeuthen Technical Seminar April 19, 2005.
See also the SLD pages by -IT- in Hamburg .

Status and Availability

Since April 2005, SL3 was the default and recommended Linux at DESY Zeuthen. Since May 2007, its successor Scientific Linux 5 is available. While SL3 can still be installed and is supported, it is now also frozen (will not have new features added) and is foreseen to be replaced as the platform for user computing by the end of 2007.

It is in use on

As of October 2005, SL3 has essentially replaced DL5. Migration is complete except for very few servers, typically fileservers with uptimes of many months.

A public login 64bit system is available as well.

SL3 had been available to early adopters since January 7, 2005, and a public preview system ( had been provided since July 30, 2004. Any serious problems reported by users have been sorted out. As of June 8, 2005, the public preview was no longer available since it's no longer needed.

The last DL5 system accessible to users vanished December 29, 2005.

News and Changes to this Page

June 25, 2007
- added info about problems after latest KDE update to theknown problems section
- updated the Status: SL3 is slowly becoming obsolete
December 19, 2006
- Openoffice 2.1.0 is available
- new versions of addons for Mathematica FeynCalc version 5beta3-1 and FeynArts version 3.2a-1
- update of cernlib installation: now providing all include files
December 11, 2006
- Maple is updated to Version 10s Release 6.
- ROOT version 5.12.00 is being installed (32- and 64-bit), see the status page for this software
August 1, 2006
- firefox update to tonight (urgent security fixes)
July 3, 2006
- new versions of Openoffice and Subversion
- mozilla has been removed for security reasons
Feburary 6, 2006
- added to the list of reported bugs we cannot reproduce or don't understand
Feburary 1, 2006
- started a list of reported bugs we cannot reproduce or don't understand in the known problems section
January 30, 2006
- dcache client software (dccp, lib[p] is being updated to version 1.2.39
- ROOT version 5.08.00b is being installed (32- and 64-bit), see the status page for this software
- both changes should have become effective on all clients by tomorrow moring
January 7, 2006
- asian font packs for the linux version of Adobe Reader 7 are finally available, and now installed on all interactive systems
December 29, 2005
- Java updates: 1.4.2 to Update 10, 1.5.0 to Update 6
- removed the last DL5 system accessible to users
December 16, 2005
- added info about dvips/dvipdf workaround to Known Problems section
October 28, 2005
- added mathematica4 font issue (not new at all, but users keep finding it)
- updated DL5 status and EOL
September 24, 2005
- firefox is being updated to version 1.0.7
- ini fixed for gcc333, gcc343 and (32-bit only) gcc2
September 23, 2005
- mozilla is being updated to version 1.7.12
- version 9.0 of the intel compilers was installed recently. For the first time, this includes a 64-bit compiler on the amd64 platform.
- most systems have been upgraded to SL 3.0.5, the few remaining 3.0.4 systems will follow soon
September 22, 2005
- started a list of known, unfixed bugs in the upstream enterprise distribution
August 26, 2005
- we're at 85% SL3 now
- added information about missing asian fonts to Adobe Reader info
- added info and troubleshooting hints to USB Memory Sticks info
- 32-bit mysql shared libraries are now installed on all 64-bit systems
August 20, 2005
- updated Matlab 6 status - it now works
- added info about the hack we used to get it going to the glibc info
August 8, 2005
- some general updates, long overdue
- added information about to the software section
- Maple 10 is now available (native 64-bit executable on amd64 systems)
- added information about Maple to the software section
- added information about Matlab to the software section
- added information about Subversion to the software section
- updated Acrobat Reader status (version 5 was removed today)
- updated the Status and Availability section
June 15, 2005
- gks is now available for those still using it (32-bit only)
- rfio client software is now installed, mainly for backward compatibility
- Atrans (and afscp) are now available on 64bit systems as well
- implemented a workaround for an "xemacs unable to find italic font face" problem
June 10, 2005
- gcc 3.4.3, as coming with SL4, is now available
- all public login systems are SL3 now
June 9, 2005
- Fixed a minor problem with LaTeX's kpathsea not reusing user-generated fonts.
June 8, 2005
- GSL (GNU Scientific Library) was added to the package selection.
- the former preview system now serves as a legacy login host:
June 4, 2005
- Adobe Reader 7.0 is now available on all SL3 systems.
May 4, 2005
- updated the Status and Availability section - SL3 is our Standard Linux now
- added links to two more presentations
- enhanced the NPTL information
- updated firefox information
- added a hint how to make your choice of window manager permanent
- added information about removable media and their mount points
- added details and additional information about the upgrade procedure
- cleaned up the Known Problems section
March 7, 2005
- openoffice 1.1.3 english/german is now available on SL3.
  (the default is english, but can be changed with   ini ooo_de)
- firefox 1.0.1 is now available
- several updates to the Changes w.r.t. DL5 and Known Problems sections
January 7, 2005
- SL3 is now generally available to early adopters
- xdm logins are available
- we have not dumped HEPiX11 nor fvwm2
December 10, 2004
- the selection is close to final now
- automatic mechanisms for maintaining the set of installed packages on a running system are in place
- so are mechanisms for automatic package updates
- the reference system has been updated accordingly
- hostname on the reference system now returns the fully qualified name
- the AMD64 version generally has caught up with the 32bit version
- EM64T systems have been tested successfully, including a desktop class system
- automatic installation infrastructure is close to final
October 2, 2004
- the missing gv package was added to the selection
- added info about the glibc __ctype issue with the PGI compiler, and probably more 3rd party products
September 21, 2004
- updated links, added link to Zeuthen presentation
- added info about the hostname issue
August 26, 2004
- added links to several presentations and IT's SLD pages
- added info about nonavailability of libc5
- updated known problems w.r.t. AMD64
July 30, 2004
first version

Changes Relevant to Users with respect to DL5

SL3 users should be aware of the following:

Known Problems

We're aware of the following problems in SL3:

Having Your Host(s) Upgraded

This is historic information Upgrades of running systems are handled the same way as the upgrade to DL4/5 before: After negotiating with the user or group admin, the installation will be prepared remotely and then triggered by a simple reboot, typically by the user herself. No physical access to the host is required, and the installation need not be attended.

The content of /usr1 will be preserved except for hosts with very small disks:

The full set of software can not be installed on systems with a root filesystem of less than 3 GB.

Such systems will lack development tools and libraries, TeX, and some other Software. This should not affect any desktop system in use any more.

The Procedure:

  1. The "owner" or group admin contacts by e-mail, requesting the upgrade to SL3 and providing the following data:
    • the DNS name of the system
    • the date/time when the installation should happen
    • whether the system will be rebooted by the user or this should be done by - DV -
    • whether the /usr1 directory should be preserved (default) or cleaned up on the occasion
  2. - DV - prepares the upgrade on the requested date.

    For the curious: This involves changing the host entry in our configuration database, creating an installation profile (using live information from the system about it's partitioning if necessary), and running a script on the system to install to create an additional, default entry for the boot loader which will then start the installation process.

    Even after the preparation, it is possible to reboot into the old operating system in an emergency (say, if your desktop PC crashes during the afternoon, and you really just want to boot and not wait for the installation to finish before you can continue your work): Simply choose the second entry instead of "SL3-Upgrade" when booting. This will however undo the preparation, so please let us know.

  3. The user must make sure that for the installation
    • the monitor is switched on, to allow automatic configuration of an appropriate video mode
    • no USB devices are connected, except of course for the mouse if the system is equipped with a USB mouse
  4. The system is the rebooted the same day, by the user or - DV -, as negotiated before. It is perfectly ok and recommended to reboot in the evening and then go home. No need to stay around.
  5. If the user is unhappy with the result of the automatic video mode configuration, she contacts uco and asks for a change.

    While for TFT screen there's one and just one correct mode, CRTs allow for some variation. The automatic procedure aims for a reasonable compromise between a high refresh rate, a high total number of pixels, and a dpi resolution that's no too high to make it necessary to change all font sizes from their default (typically: 1152x864 on 17 inch CRTs, 1280x1024 on 19 inch, and 1400x1050 on 21 inch screens - at either 75 or 85 Hz depending on the monitor's capabilities). It generally yields a result that's at least acceptable - and won't damage the hardware - but users may have different preferences.

How long will it take ?

SL3 installation is significantly slower than DL5 installation for several reasons; Here are some ballpark figures (for SL3.0.3 in March 05 ~ worst case):
Stephan Wiesand