Atlantic Linux Blog

Java on Debian tip

The default Java environment installed by Debian is the GNU Compiler for Java, while GNU have made remarkable progress with this – anyone doing mainstream Java development will probably prefer to install the latest Sun Java environment on their system – even free software projects like Hadoop are primarily tested in this environment.

Most Linux distributions provide packages for Sun’s Java as well as GCJ and probably OpenJDK. When you install more than one package which provides similarly named commands, Debian’s Alternatives System comes into play – allowing you to select one command or another. When you install a different Java, you can of course manually update each Java command (java, javac, javadoc, jconsole, jmap,jps and so on) using the update-alternatives command, but if you want a quicker way, try the update-java-alternatives command from the java-common package.  It will automatically update the paths to all provided Java commands in one go once you tell it which installed Java environment you wish to use, for example,

update-java-alternatives -s java-6-sun

Tags: Debian 5.0, java, linux, sun java

Debian 5.0 (Lenny) install on Software RAID

As mentioned in previous posts, I’m a big fan of Linux Software RAID. Most of the Ubuntu servers I install these days are configured with two disks in a RAID1 configuration. Contrary to recommendations you’ll find elsewhere, I put all partitions on RAID1, not some (that includes swap, /boot and / – in fact I don’t normally create a separate /boot partition, leaving it on the same partition as /). I guess if you’re using RAID1, I think you should get the advantage of it for all of your data, not just the really, really important stuff on a single RAIDed partition.

When installing Ubuntu (certainly recent releases including 8.10 and 9.04) you can configure all of this through the standard installation process – creating your partitions first, flagged for use in RAID and then configuring software RAID and creating a number of software RAID volumes.

I was recently installing a Debian 5.0 server and wanted to go with a similar config to the following,

When I followed a standard install of Debian using the above configuration, when it came to installing GRUB, it failed with an error. The error seemed to be related to the use of Software RAID. Searching the web for possible solutions mostly turned up suggestions to create a non-RAIDed /boot partition but since this works on Ubuntu I figured it should also work on Debian (from which Ubuntu is largely derived).

First, a little background to GRUB and Linux Software RAID. It seems that GRUB cannot read Linux software RAID devices (which it needs to do to start the boot process). What it can do, is read standard Linux partitions. Given that Linux software RAID1 places a standard copy of a Linux partition on each RAID device, you can simply configure GRUB against the Linux partition and, at a GRUB level, ignore the software RAID volume. This seems to be how the Ubuntu GRUB installer works. A GRUB configuration stanza like the following should thus work without problems,

title           Debian GNU/Linux, kernel 2.6.26-2-amd64
root            (hd0,1)
kernel          /boot/vmlinuz-2.6.26-2-amd64 root=/dev/md1 ro
initrd          /boot/initrd.img-2.6.26-2-amd64

When I tried a configuration like this on my first install of Debian on the new server, it failed with the aforementioned error. Comparing a similarly configured Ubuntu server with the newly installed Debian server, the only obvious difference I could see is that the partition table on the Ubuntu server uses the old msdos format while the partition table on the Debian server seems to be in GPT format. I can’t find any documentation on when this change was made in Debian (or indeed whether it was something in my configuration that specifically triggered the use of GPT) but it seems like this was the source of the problems for GRUB.

To circumvent the creation of a GPT partition table on both disks, I restarted the Debian installer in Expert mode and installed the optional parted partitioning module when prompted. Before proceeding to the partitioning disks stage of the Debian installation, I moved to a second virtual console (Alt-F2) and started parted against each disk and ran the mklabel command to create a new partition table. When prompted for the partition table type, I input msdos.

I then returned to the Debian installer (Alt-F1) and continued the installation in the normal way – the partitioner picks up that the disks already have an partition table and uses that rather than recreating it.

This time, when it came to the GRUB bootloader installation step, it proceeded without any errors and I completed the installation of a fully RAIDed system.

Tags: Debian, Debian 5.0, grub, linux, Linux software raid, partitioning, Ubuntu, ubuntu 8.10, ubuntu 9.04

BIOS flash upgrades on Linux

To upgrade your system BIOS you normally need to run a piece of software from the system manufacturer which loads an updated copy of the BIOS into the EPROM chip on your system motherboard – a process known as flashing your BIOS. Most system manufacturers supply BIOS upgrades in a form that will run under DOS or, occasionally, Windows. It is rare to find a BIOS upgrade program that runs under Linux (I’d love to hear about one). Recognising that not all of their customers are necessarily running a 28 year old, 16-bit operating system – some system manufacturers supply their BIOS upgrades in the form of an image which you can burn to a CDROM and boot from (making the question of what OS you are running irrelevant).

I recently had to upgrade the BIOS on one of our Supermicro systems (an X7DVL-E system). Supermicro provide their BIOS upgrades as a ZIP file containing the actual BIOS and a DOS flash program. They also seem to provide some software which you can run on Windows to create a BIOS flash floppy disk (for the younger readers in the audience, that’s another wonderful technology from the 80s, and I’m talking about the super-modern 3.5″ floppy there). I’m not singling out Supermicro for particular criticism here, a lot of the system manufacturers seem to work on the assumption we’re still running PCs with Windows and a floppy drive (to be fair, if you have the optional IPMI management card installed, you can normally upload your firmware through that, but we don’t) – but for those of us running Linux servers, upgrading the BIOS can be a painful process.

There is a work-around for this problem. Thanks to the Linux boot-loader, GRUB – you can boot from a DOS disk image containing your BIOS upgrade program and run the program from within that booted image without ever actually installing DOS or a floppy drive in your system. The following procedure worked well for me on an Ubuntu 9.04 system (with thanks to this OpenSUSE page and and this Ubuntu forums posting for some assistance along the way) and the same approach should work on other distributions.

WARNING: Upgrading your system BIOS is an inherently risky process – with the primary risk being that if things go wrong you can brick your system. Things that can go wrong include flashing your system with a BIOS upgrade for a different system or the power getting interrupted while you are in the middle of a BIOS upgrade. In some cases, you may be able to reflash the BIOS using some emergency procedure but with most systems, you may be looking at a motherboard replacement. So proceed with caution and only upgrade your BIOS if you have a specific problem which the upgrade fixes.

1. Download a bootable DOS disk image from the FreeDOS distribution site (FreeDOS is an excellent open source version of DOS. It is widely used by hobbyists and companies including Dell, HP and Seagate).

   wget http://www.fdos.org/bootdisks/autogen/FDOEM.144.gz

2. Download your system manufacturers BIOS upgrade

   wget http://www.example.com/bios/version2.zip

3. Place the downloaded BIOS upgrade program and files into the downloaded bootable DOS image.

   gunzip FDOEM.144.gz
   sudo mount -o loop FDOEM.144 /mnt
   sudo mkdir /mnt/bios
   cd /mnt/bios
   unzip <path to download BIOS upgrade file>/version2.zip
   umount /mnt

4. Add the bootable DOS image (with the bios upgrade software) to your Linux bootloader (this requires a file from the syslinux package),

   sudo aptitude install syslinux
   sudo mkdir /boot/dos
   sudo cp /usr/lib/syslinux/memdisk /boot/dos
   sudo cp FDOEM.144 /boot/dos
   sudo vi /boot/grub/menu.lst

   and add the following section to the end of the file

   title DOS BIOS upgrade
   kernel /boot/dos/memdisk
   initrd /boot/dos/FDOEM.144

5. Reboot your system and choose the DOS BIOS upgrade boot option. If the boot is successful you should shortly be presented with the A:\ DOS boot prompt. At this point you can run the BIOS upgrade software, for example,

   A:\CD BIOS
   A:\FLASH V2BIOS.ROM

6. Once the upgrade finishes, reboot and enjoy your upgraded system.

Tags: BIOS, Boot loaders, Flash, FreeDOS, grub, linux, Linux startup process, syslinux, Ubuntu, ubuntu 9.04