DESY Linux 5 at Zeuthen  


Status and Availability

DL5 is no longer supported

From 2004, to March 2005, DL5 was the default and recommended Linux version at DESY Zeuthen. It was replaced by Scientific Linux 3.

We no longer deploy DESY Linux 5, neither on new systems nor on existing ones with a broken hard drive (installation on recent hardware is not even possible unless we'd invest much time into it).

Support for DL5 was finally terminated in December 2005.

DL5 End of Life

Being based on SuSE 8.2, DL5 had good patch support until June 2005. Now, patches (and audits!) for SuSE 9.0, which is very similar, help keeping DL5 alive and secure. Where using the patches for 9.0 is not possible or would cause too much work, insecure software has to be removed from DL5 systems. The same happened to some software that is not essential and that can easily be used on any SL3 system, even if working on DL5.

Despite the help from SuSE 9.0, the problems not easily fixed or worked around keeps mounting. Hennce:

All systems allowing interactive access - including and particularly desktops - will become unusable December 1st, 2005. This has been announced to the group admins of the three remaining groups still running a few DL5 desktops in October 2005.

News and Changes to this Page

November 10, 2005
September 23, 2005
August 20, 2005
August 8, 2005
June 9, 2005
April 5, 2005
December 10, 2004
March 3
February 26
February 20
February 16
January 30
January 21
January 19
January 14
January 12
January 9
  • added information about windows/exceed font issues
    January 8
    • provided a fixed version of the du command that works correctly in the top level directory of AFS volumes
  • added information about the gcc3 preprocessor
  • updated the Status and Availability section

    Previous News are archived here.

    Why a new DESY Linux ?

    DESY Linux 4 - based on SuSE Linux Professional 7.2 - is about two years old now. There are several good reasons for replacing it with a DL5 based on a more recent distribution:
    • SuSE provides security patches for about two years only, and terminated support for 7.2 on October 1. From now on, keeping DL4 systems secure will place considerable additional demands on our time.

    • The system C library (glibc) coming with 7.2 is version 2.2.2. More and more software requires more recent glibc versions (typically at least 2.2.5) in order to be usable at all. One example for this is the GNU compiler: At least the C++ compiler of 3.3 (with considerable improvements over previous versions) will NOT work correctly on DL4. Other examples include recent mozilla versions and the latest intel compilers. Replacing DL4's glibc is not an option, since this could introduce subtle incompatibilities consuming the time of users and admins alike.

    • Contemporary hardware is supported better by a recent distribution. This is true in particular for graphics cards and everything related to USB. In addition - while we have no DESY Linux for notebooks yet - it's an advantage to run similar base distributions on notebooks and conventional systems. For example, ALL additional software DESY provides for DL5 will be available for notebooks as well. But SuSE 7.2 is way too old for installing it on current notebook hardware.

    Having your host(s) upgraded

    Upgrades of running systems will be handled the same way as the upgrade to DL4: After negotiating with the user or group admin, the installation will be prepared remotely and then triggered by a simple reboot. 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 desktop PCs with a root filesystem of less than 3 GB.

    Installation is possible on as little as 2 GB, but some bulky software packages like OpenOffice or LaTeX will be missing. This should not be a problem on any desktop PC foreseen to run another year. If in doubt, check with df -m /

    Once the upgrade is prepared, we have to disable all maintenance mechanisms for this host until it is performed. For this reason, we require the user to reboot and let the host upgrade itself the same day. Otherwise, we will reboot early next morning.

    Installation takes 20 minutes on latest generation desktops, to one hour on very old PCs.

    The monitor should be turned on during the upgrade because it's queried for its capabilities and a reasonable graphics setup is chosen accordingly. This works very well in most cases, but if you're not satisfied with the result, we change the settings (resolution, refresh rate) on short notice.

    Farm upgrade

    The upgrade of the common batch farm (ice, cube, husky machines) is being staged. As of February 20, some 60% of the nodes are running DL5, and this ratio will increase slowly and steadily.

    If your jobs can execute on both DL4 and DL5,
    there's nothing special you have to do.
    If your jobs can execute on DL4 only,
    you must submit your jobs with qsub -l farm=ice
    (and should make them work on DL5 since the fraction of the farm available to your jobs will become smaller and smaller).
    If your jobs should execute on DL5 only,
    you must submit your jobs with qsub -l farm=iceDL5

    Jobs can find out in which environment they are running by examining the ouput of the command livesys (NOT sys) which is i386_linux24 on DL4 and i586_linux24 on DL5.

    An elegant way to make use of the different sysnames is to employ AFS' ability to substitute a path component of @sys by this value.
    For example:

    • put your DL4 executable into /afs/
    • put your DL5 executable into /afs/
    • from your job script, call /afs/

    Base distribution

    The base distribution for DESY Linux 5 was chosen to be SuSE Linux Professional 8.2 because it has two years of supply with compatible bug fixes and security patches by the distributor and is reasonably up to date. The contenders (debian woody and RedHat 9 Professional) both fail to meet one of these criteria.

    The glibc version of SuSE 8.2 is 2.3.2 - the same as on RedHat 9, chosen to be the next Linux version at many HEP labs.

    Changes Relevant to Users

    • AFS sysname

      The AFS sysname of DL5 is i586_linux24

      A common trap is that ~/bin is a symbolic link pointing to ~/.@sys/bin. You may want to ln -s .i386_linux24 .i586_linux24.

    • Backspace/Delete issues

      For users with the default setting RUBOUT=BackSpace, this seems to be worse than on previous DESY linux versions. RUBOUT=Delete generally works much better. You get this by touching a file ~/.Delete (and making sure ~/.BackSpace does not exist). Xemacs users may want to set the variable delete-key-deletes-forward to a non-nil value to restore the usual behaviour.

    • The default and recommended desktop environment is KDE now.

      The fvwm2 environment is still available and supported, but users are encouraged to give KDE a try, which is now also the default option set on the login screen. Fvwm addicts may want to move their ~/.wmrc to a place where kdm can read it so the default will be set to the last session type chosen. To do this, execute

      mv .wmrc public
      ln -s public/.wmrc .wmrc
    • KDE 3.1.1

      With many enhancements and new features. You may want to save ~/.kde/, ~/.kderc, ~/Desktop before using it the first time. Another option is to replace them by links into @sys (i386_linux24 for DL4, i586_linux24 for DL5) which should allow switching back and forth smoothly.

    • Font issues for Windows users

      KDE seems to use some fonts not yet available on our font server. These issues are resolved quickly once reported. As a workaround, all KDE applications allow changing the fonts used easily, but please report these problems anyway.

    • Desktop PCs

      • The mount point for the floppy drive is /media/floppy
      • The mount point for CD/DVD Readers is /media/cdrom
      • The mount point for CD writers is /media/cdrecorder
      • The mount point for USB memory sticks is /media/sda1

      • USB support is enabled by default

      • While scdrecord for writing CDs is still available and supported, we recommend you also give the KDE application k3b a try.

      As announced in the past, the /usr1/data directory will be renamed to /usr1/scratch. If this breaks software installed there, we set a compatibility link on request, for a limited time. Remember that local disks may break and are not backed up.

    • Compilers: GCC

      The C++ ABI has changed with gcc version 3.2. This means that C++ code compiled by earlier versions can NOT be linked with C++ code compiled by recent gcc versions, and vice versa.

      The default compiler on DL5 is gcc version 3.3.2. This is a deviation from both SuSE 8.2 (coming with a prerelease of 3.3) and RedHat 9 (coming with the relased 3.3). Versions 3.3.1 and 3.3.2 are mainly bugfix releases of 3.3, but updated runtime libraries are needed at least for C++ in order to run software compiled with the new compiler on a DL5 system. For SuSE 8.2, the rpm packages needed to make a normal installation compatible will be provided.

      Version 3.3.3 is available since March 5 and will become the default soon.

      The vanilla gcc 3.3 is also provided. Note that even C++ code compiled with this version will NOT work with the shared libraries provided by SuSE 8.2 by default.

      For backward compatibility with DL4, gcc 2.95.3 is also provided (activated by ini gcc2), as well as several versions of root built by this compiler and - again - an rpm package with the shared libraries needed for running such code on plain SuSE 8.2. Note that most other libraries containing C++ code (in particular Qt and the KDE libs) are NOT available with the old ABI. Code compiled with gcc2 on DL5 may still work on DL4.

      The new compiler does not accept K & R C.

      The new compiler honours namespaces. You have to include using namespace std; in your code if you want to access items from the standard library without qualifying them with std::

      C Functions with variable arguments still using the long deprecated varargs.h must be rewritten to use stdarg.h instead.

      In many cases it is no longer possible to access symbols from errno.h without explicitly including this header file.

      The preprocessor of gcc3 has stricter syntax requirements - it was always meant to be used for processing C and C++ only. If you abused it for something else in the past, the flag -traditional-cpp may help.

    • Compilers: Intel

      • Version 6.0 no longer works
        since it cannot deal with the new glibc on DL5.

      • Version 7.0 does work
        and is available as ifc after an ini ic7.

      • Version 8.0 is installed as well as of January 12, 2004.
        The Fortran compiler, C++ compiler, and the debugger can be used without ini, the respective commands are ifort, icc, and idb.

        Whether or not DESY will purchase licenses for these products is still under review (and user feedback may play a role in that process). Meanwhile, users have to obtain a free, personal, non-commercial-use license before they can use them. Check the ouput of the command prpm -qi icc and/or prpm -qi ifort for instructions how to obtain the license key files and what to do with them. You should be able to get started within about 10 minutes. License keys obtained in the past for previous versions seem to work fine as well.

        Note that version 8 can not be used on DL4 since its glibc is too old.

    • HEP Software

      • Only versions 2002 and 2003 of cernlib are provided.

        As of January 12, 2004, new versions of both the 2002 and 2003 packages are installed. The changes are:

        • built with gcc2
        • libgeant built without optimization (like CERN IT do)
        • results of all test runs during build are available in the BuildInfo tarball
        • all available writeups and similar documentation was collected and is now part of the package

        The first two items should at least partially address the issue of reproducibility of numeric results mentioned below.

        The build procedure for patchy as it comes with the cernlib source (version 5?) seems to be broken. Patchy version 4.15 is available as a separate package.

      • cmz is available as a separate package. Since it is no longer maintained, the best we can do is to provide the last build available (from 2000) as is, without support: Since we don't have access to the source code, there's nothing we can do when it stops working.
      • Version 3.05.07 of root is provided for both gcc 3.3.x and 2.95.3.
      • The old workhorse version 3.02.07 of root is provided for gcc 2.95.3 only (it can't be built with 3.3).
      • Version 3.10.02 of root, recently promoted to the recommended version by the developers, is available as well
        (now including the latest User's Guide).
      • The new development version 4.00.00 of root was made available January 25.

    • Maple

      Versions 7, 8, 9 are available through /opt/products RPM packages and are independent of the license server. Version 6 is available through links into the old /products installation and does depend on the license server. All essential commands (maple, xmaple, mint, maple8, xmaple8, ...) are available without ini.

      Version 9 is actually 9.01, with the update to 9.03 coming soon.

      The default (=java) interface of xmaple in version 9 is unable to print. This is due to it leveraging the java printing API, and this can only print to a single printing system which is not in use at DESY. We're evaluating the option of replacing the JRE 1.4.0 coming with maple with version 1.4.2, which does allow printing at least on user's default printer. As a workaround, you can start maple with the old GUI by running maple -cw.

    • Mathematica

      Version 5 is available through /opt/products RPM packages (commands math, math5, mathematica , mathematica5, mcc, mcc5). Version 4 is available through links into the old /products installation (commands math4, mathematica4).

    • OpenOffice

      • must be started with the command OOo (that's three times the letter "O")

      • can only be installed on hosts which have a root filesystem of at least 3 GB. This is met by all public login hosts, but some older desktops may fail to meet this requirement, at least unless the disk is repartitioned. Use the command df -m / to check.>

    • Browsers

      • Netscape 4 is provided as a legacy fallback

      • Mozilla is the default browser on DL5, provided as an /opt/products package, with some DESY customization. This customization is per user and created automatically the first time mozilla is started, unless a user configuration already exists.

        It is recommended to move ~/.netscape, ~/.netscape6 and ~/.mozilla out of the way, then start mozilla, and afterwards reimport your bookmarks.html and reset other settings you do not like in the new default.
        If you don't want to do this and encounter problems with SSL certificates, try removing all certX.db files in your profile directory (typically: ~/.mozilla/default/xyz.slt). You have to reimport all certificates afterwards.

        Major differences from a plain mozilla installation are:

        • the disk cache is created in /tmp/ by default, hence does not waste space in your home directory or backup capacity
        • you should get a working, secure setup for email and news
        • mozilla will silently accept SSL certificates signed by the DESY or DFN since their CA certificates are already imported correctly
        • weak SSL encryption ciphers are turned off

        Plugins provided:

        • Java from the jdk in /opt/products/java.
        • Flash There are known issues with scripted flash animations on recent builds (using the new gcc). Most animations seem to work well though.
        • Acrobat reader from /opt/products/acroread.

          Since version 1.6, the latter one is no longer a plugin by default because some users don't like it this way and it's hard to get rid of. To have mozilla open the acroread plugin in it's own window instead of calling the external acroread program for PDF files, you can link /opt/products/acroread/5.0.8/Browsers/intellinux/ into the directory ~/.mozilla/plugins . A future release of the acroread package will provide a generic location for the plugin.

        • RealPlayer 8

    • Software Management

      Starting with DL5,

      • Software built by DESY is provided in /opt/products instead of /products

      • Executables show up in /opt/products/bin (and some still in /opt/products/scripts, but they will be moved into bin) instead of /usr/local/bin. For users who stay with the PATH variable provided, or only modify it, this change is transparent. Users setting their PATH from scratch (which is not recommended) have to add /opt/products/bin.

      • /usr/local is local to the host and almost empty

      • Headers and libraries show up in /opt/products/include and /opt/products/lib, but using these locations is highly deprecated. Instead, it is recommended to explicitly use the files found in /opt/products/name/version

      All software in /opt/products is from rpm packages, and hence can be installed on any SuSE 8.2 system. This should however NOT be done by simply installing the packages with normal rpm commands but a separate RPM database should be used (installing several versions of the same package in parallel is reasonable and legal, but will confuse tools like YOU). Detailed documentation on how to do this is in progress. Contact us if you feel you must do it before the documentation is ready.

    • Backup and Archiving Commands

      Since the new version of the NetWorker Software strictly requires a license (which is per client and expensive) in order to run any client command, the commands nwarchive and [nw]recover are only available on pub1.

      Since the commands also fail to detect their server correctly, the parameter -s jupiter always has to be given.

    Known Problems

    We're aware of the following problems in DL5:
    • mathematica 4 (called as mathematica) complains about the font installation.
      It basically works though. This is actually the same state as on DL4 and hence not a DL5 issue.

    • OpenOffice doesn't allow choosing the printer and will only print on your default printer.

    • xfig is missing some fonts. The reason is an incompatibility between xfig under recent X11 version with fonts found on our default font server. This will probably not be fixed for DL5. As a workaround, it helps to remove tcp/fontsrv:7100 from the font path.

    • There was a report of fortran code using GEANT3 producing different results on DL5 than on DL4. An investigation revealed that the GEANT code seems to be quite sensitive to the compiler and the optimization level used to produce the library. It also turned out that even the builds from CERN (done with no optimization at all) produce different results, depending on the RedHat version they were built on. This issue has been forwarded to DESY's scientific computing staff, and is not at all limited to DL5. Additional user input on this topic is very welcome.

    Some more information:
    January 28, 2006 Stephan Wiesand