TableOfContents

About Scientific Linux 5 at DESY, Zeuthen

Status and Availability

• Scientific Linux 5 for the i386 platform was released May 7, 2007.
• As of May 8, 2008, SL5 is available for early adopters at DESY Zeuthen. Requests to update systems to 32-bit SL5 are welcome.

  • Notice SL5 is quite young. Early users will undoubtedly discover problems not yet known.

    Betas and release candidates have been in use on more than a dozen systems for months though, and we believe SL5 is very usable. Several colleagues in the computing centre are using it in their desktops.
• The x86_64 flavour will be made available as soon as the final release is on scientificlinux.org.
• Public Login systems for both platforms are available (see below). Problem reports for both are welcome.
• A special SL5 queue on the batch farm is being prepared.

Public Preview Systems

Two DNS aliases have been set up:

• sl5.ifh.de (x86)

• sl5-64.ifh.de (x86_64)

They point to (virtual) systems suitable for getting familiar with SL5, finding remaining problems with it to report to uco, and to test or port user software. These systems are not for production use.

General Points

AFS Sysname List

The AFS sysname list (the output of the fs sysname command) in Zeuthen is:

Login Shells

We made a serious effort to make bash a supported login shell, but it's impossible.

There is no way to reliably give bash users a working environment identical to that of zsh and tcsh users, due to bash's limited functionality w.r.t. startup files processing.

We recommend using zsh, zsh or zsh as the login shell. Tcsh is available for those who insist. Bash is not, sorry.

Notice this does not prevent users from writing or using bash scripts in any way.

Language Support, UTF8

It was initially planned to introduce use of UTF8 as the default with SL4. Alas, it was found that it's causing too much trouble, and makes things too incompatible to the rest of our environment. This hasn't changed with SL5. Also notice that a lot of software still has bugs when used under a UTF8 locale.

Hence the default for the LANG environment variable on SL5 systems is C, as on Sl4, SL3 and DL5 before. Early SL4 systems had a default of en_US, because it makes certain GNOME applications behave more sensible (in particular gnome-terminal), but it was found to cause other problems (among them, changes in the date format and sorting order).

Any user may change the personal default by creating a file ~/.i18n:

# recommended and default:
#LANG=C

# alternative:
#LANG=en_US

# I want to suffer
LANG=en_US.UTF-8

We do not install language support packages for other languages than US-english, with the sole exception of dictionaries for spellchecking. Languages other than english for the user interface are not supported.

Removable Media and Hotplug Storage Devices

• Mount points are now in /media. They are created at mount time, not after plugging the device. No fstab entries are used, that's why you cannot use the usual mount and umount commands. The names of the mount points are taken from the file system's volume label if applicable. They are removed when the device is removed.

• Manual Mounting If the automatic mounting of devices by GNOME/KDE is not used, gnome-mount can be called manually like this, using the appropriate device file:

  gnome-mount -d /dev/sda1
  gnome-umount -d /dev/sda1

• Hotplug should work better than on SL3 or SL4, thanks to the more modern kernel and hotplug scripts. It is known to not work perfectly in all cases though.

  • Multiple partitions on USB storage devices should work now, at least if all partitions have a supported filesystem, and the partition table format is legal.

  • The new hotplug system does not assign ownership of the device to the user. Hence you can't partition the device or create filesystems, unlike on SL3.

  • The new hotplug system will clean up properly if a mounted device if removed, and it no longer causes problems to log out while a hotplug device is mounted.

    It is still recommended to always umount all filesystems on a hotplug device before removing it physically, and before logging off from the console.

    Notice the GNOME desktop will automount filesystems on hotplug devices when they are

    connected. This feature can be turned off under System->Preferences->Removable Storage:BRattachment:g-v-p.png

• Notice there is no firewire support

Printing

• Print Service has been changed from LPRng to [:Printing_with_Cups: Cups] because LPRng is obsolete and Cups is better integrated in KDE, Gnome, OpenOffice and other tools.

Backward Compatibility

Binaries

SL5 should be binary backward compatible with SL4. This means that executables built on and for SL4 should work on SL5. It does not mean that any executable that works on SL4 will work on SL5 as well: If it worked only due to legacy support before, it may no longer work on SL5.

In particular, binaries that depend on setting the environment variable $LD_ASSUME_KERNEL to a value lower than 2.6.9 won't work on SL5.

Executables failing with *** glibc detected *** error messages

If your executable does not work, but instead fails like this

 ~ % voms-proxy-init
Cannot find file or dir: /afs/ifh.de/user/w/wiesand/.glite/vomses
Your identity: /O=GermanGrid/OU=DESY/CN=Stephan Wiesand
Enter GRID pass phrase:
Creating proxy ............................................................ Done
*** glibc detected *** voms-proxy-init: munmap_chunk(): invalid pointer: 0xbf97bd02 ***
======= Backtrace: =========
/lib/libc.so.6(cfree+0x1bb)[0x47c216db]

and so on, that's a bug in the application's memory management. Starting with SL3, glibc began detecting such bugs and warning about them. Since SL4, processes exhibiting such bugs are terminated by default. With SL5, glibc detects more of these problems, hence this may affect applications that worked on older releases.

As a workaround, you can set the environment variable MALLOC_CHECK_ to 1, to keep glibc from terminating such processes: {{{~ % MALLOC_CHECK_=1 voms-proxy-init malloc: using debugging hooks Cannot find file or dir: /afs/ifh.de/user/w/wiesand/.glite/vomses Your identity: /O=GermanGrid/OU=DESY/CN=Stephan Wiesand Enter GRID pass phrase: Creating proxy ................................................................................. Done *** glibc detected *** voms-proxy-init: free(): invalid pointer: 0xbf900d01 *** Your proxy is valid until Wed May 9 03:49:39 2007 }}}

Notice the 'malloc: using debugging hooks' message before each command. Since this also costs performance, do not add this environment variable to your profile.

Source Code

• GCC4 is much stricter than previous versions, some C and C++ code may need to be adapted.

  • GCC4 hints for fixing the typical new compiler errors: http://dev.gentoo.org/~vanquirius/gcc4-porting-guide.html

• The FORTRAN frontend of GCC4 is gfortran=, no longer g77, and some code may need to be adapted

Software

Browser

Firefox ist the recommended web browser. We provide the java, flash and realplayer plugins.

Mail Client

Pine is the recommended e-mail client. It will however soon be superseded by alpine, and you may wnt to give that a try instead.

Compilers

GCC

• The default compiler suite is GCC 4.1.1.
• The compatibility release 3.4.6 (default on SL4, available on SL3) is installed as well.

  • Invoke as gcc34, g++34, g77

  g77 is the FORTRAN frontend from the old compiler. The new frontend is gfortran .

Intel

Version 9.1 of the C, C++, and FORTRAN compilers are available. The 32-bit runtime environment is installed on 64-bit Systems as well.

• Invoke as icc, icpc, ifort

Portland Group

Version 7.0 of the PGI compiler is installed. The 32-bit runtime system is available on 64-bit hosts.

• Invoke as cc, CC, f77, f90 after ini pgi

Java

Version 1.5 is the default and installed locally. It's 32-bit even on 64-bit systems, to make the browser plugin work.

Versions 1.4.2 and 1.6 are available in /opt/products, as well as a 64-bit Version of 1.5.

ROOT

We provide version 5.14.00 built with GCC4. Older versions for older compilers could be provided on request.

As on SL3/4, the 64-bit build is installed in /opt/products/root64, the 32-bit one in /opt/products/root.

Known Problems

Software that will not be available on SL5

• Atrans/afscp

Software is not yet available, but will be eventually

• afs_admin

• ICA/Wincenter

PC Upgrades

Requirements

• A supported PC (najade class or newer), 128 MB RAM, 20 GB disk

• A root filesystem of at least 6 GB ( 8 GB for 64-bit)

  • example: this is sufficient for a 32-bit installation: {{{[host] ~ % df -H /

Filesystem Size Used Avail Use% Mounted on /dev/hda7 6.3G 4.9G 1.1G 82% / }}}

• If your / is too small, the disk has to be repartitioned. This should only affect a few of the oldest najade class Systems.

Procedure

1. The owner or group admin of the PC contacts uco by e-mail with a subject of SL5 upgrade, providing the following information:

   • the PC's hostname
   • whether or not the /usr1 partition should be preserved
   • date of the upgrade
   • whether the PC should be rebooted by DV or by the user
2. DV prepares the upgrade on the required date.

3. The next reboot starts the upgrade installation. This must happen the same day.

Checklist

To prepare the PC for the upgrade, please

• make sure the PC and the monitor are switched on

• unplug all USB devices (except a USB mouse)
• remove all CDs, DVDs, Floppies

Installation Times

Installing the 64bit flavour takes 10% longer.