• current HDD is /dev/sda, it has a GPT (with bios_grub being /dev/sda1), separate /boot partition (/dev/sda2), and a physical LVM volume (/dev/sda3), where LVM holds all the remaining partitions (root, /home, /srv, …); LVM is properly configured, and system reboots with no problems
• your new drive is /dev/sdb, it is identical to /dev/sda, and it comes empty from the manufacturer (this is important! wipe the drive if it is not empty, especially if it used to be a part of another RAID)
• your system is Debian or Debian-based; in this exact example I’ve been using Ubuntu Server 10.04
• your LVM volume group is named vg0
• make sure you understand what each command does before executing it
• you do have an external backup of all your important data, and you do understand that the following operations are potentially dangerous to your data integrity

Inspired by: Debian Etch RAID guide, serverfault question.

1. Create the GPT on the new drive:
   parted /dev/sdb mklabel gpt
2. Get the list of partitions on /dev/sda:
   parted -m /dev/sda print
3. Create /dev/sdb partitions similarly to what you have on /dev/sda (my example numbers follow, use your numbers here):
   parted /dev/sdb mkpart bios_grub 1049kB 2097kB
   parted /dev/sdb mkpart boot 2097kB 258MB
   parted /dev/sdb mkpart lvm 258MB 2000GB
4. Set proper flags on partitions:
   parted /dev/sdb set 1 bios_grub on (GPT doesn’t have MBR, so you create a 1-MB partition instead to hold grub2′s boot code)
   (possibly optional) parted /dev/sdb set 2 raid on
   (possibly optional) parted /dev/sdb set 3 raid on
5. (possibly optional) To make sure /dev/sdb1 (the bios_grub) indeed contains grub’s boot code, I did dd if=/dev/sda1 of=/dev/sdb1
6. apt-get install mdadm
7. Note: at this point, older tutorials suggest adding a bunch of raid* kernel modules to /etc/modules and to grub’s list of modules to load. I’m not sure this is really necessary, but do see the tutorials mentioned at the top for more information. If you do modify the lists of modules – don’t forget to run update-initramfs -u.
8. Create two initially-degraded RAID1 devices (one for /boot, another for LVM):
   mdadm ––create /dev/md0 ––level=1 ––raid-devices=2 /dev/sdb2 missing
   mdadm ––create /dev/md1 ––level=1 ––raid-devices=2 /dev/sdb3 missing
9. Store the configuration of your RAID1 to the mdadm.conf file (important! this is not done automatically!)
   mdadm -Es >> /etc/mdadm/mdadm.conf
10. Verify the contents of your mdadm.conf:
    cat /etc/mdadm/mdadm.conf
    dpkg-reconfigure mdadm, and enable booting in degraded mode
11. Copy your current /boot (/dev/sda2) to the new /dev/md0 /boot partition:
    (one can use dd here as well, but for some reason my attempt at dd failed writing 1 last byte of data)
    mkdir /mnt/md0
    mount /dev/md0 /mnt/md0
    cp -a /boot/* /mnt/md0/
    umount /dev/md0
    rmdir /mnt/md0
12. Now extend your existing volume group to include the newly-created /dev/md1:
    pvcreate /dev/md1
    vgextend vg0 /dev/md1
13. Verify the list of logical volumes you curently have: enter lvm shell, and type lvs. Here’s what I had:
    LV VG Attr LSize Origin Snap% Move Log Copy% Convert
    home vg0 -wi-ao 1.70t
    logs vg0 -wi-ao 4.66g
    root vg0 -wi-ao 10.24g
    srv vg0 -wc-ao 100.00g
    swap vg0 -wi-ao 1.86g
    tmp vg0 -wi-ao 4.66g
14. Now, you can move all the logical volumes to new physical volume in one command: pvmove /dev/sda3 /dev/md1. Personally, remembering the problem I had with dd from /dev/sda2 to /dev/md0, I decided to move all logical volumes one-by-one; as this takes time, you may consider joining these operations with ; or &&, and putting the /tmp last (as the easiest one to re-create if it fails to move):
    pvmove ––name home /dev/sda3 /dev/md1
    pvmove ––name srv /dev/sda3 /dev/md1
    pvmove ––name logs /dev/sda3 /dev/md1
    pvmove ––name swap /dev/sda3 /dev/md1
    pvmove ––name root /dev/sda3 /dev/md1
    pvmove ––name tmp /dev/sda3 /dev/md1
15. To be safer, I ran FS check on a few volumes I could umount:
    umount /dev/mapper/vg0-srv
    fsck -f /dev/mapper/vg0-srv
    mount /dev/mapper/vg0-srv
    umount /dev/mapper/vg0-tmp
    fsck -f /dev/mapper/vg0-tmp
    mount /dev/mapper/vg0-tmp
16. Remove /dev/sda3 from the physical space available to your volume group:
    vgreduce vg0 /dev/sda3
17. Install grub2 to both drives, so as to make them both bootable in case of failure:
    grub-install ‘(hd0)’
    grub-install ‘(hd1)’
18. Edit /etc/fstab, pointing /boot to /dev/md0. You may use UUIDs here, but please do not use UUIDs from mdadm.conf – those are different from FS-UUIDs, instead do ls -l /dev/disk/by-uuid to find the UUID of /dev/md0. Personally, I had no problems just using /dev/md0.
19. Now is the time to add your original /dev/sda to the RAID1; be absolutely sure you have moved all the data off that drive, because these commands will destroy it:
    mdadm ––manage ––add /dev/md0 /dev/sda2
    mdadm ––manage ––add /dev/md1 /dev/sda3
    Re-syncing array will take some time.
20. To be on the safe side, you may want to run again update-initramfs -u and update-grub; I have also edited /etc/grub.d/40_custom, adding there 2 more boot options: from /dev/sda2 and /dev/sdb2 (/boot on both drives) – have no idea if that will work, but having more boot options didn’t hurt
21. Reboot into your new system. Actually, at this point reboot is only necessary to verify that your system is bootable – you may delay this reboot as long as you want to.
22. Many tutorials also suggest testing your RAID1 by manually “degrading” it, trying to boot, and then rebuilding it back. I haven’t done that, but you may want to.

Improvement suggestions, criticism and thank-you are welcome in the comments.

There are a few highly-popular patches, which haven’t yet made it into the Squeeze’s rtorrent version 0.8.6.

Note: ArchLinux already has an rtorrent-extended package, so you may want to look at that one (instead of my Debian package below). I might use Arch’s patchset next time to generate a truly extended rtorrent package.

I’ve incorporated 3 of such patches (#239 ipfilter, #2064 GeoIP support, and #2171 colours/eyecandy), and built a squeeze amd64 rtorrent-enhanced package.

A few excerpts to explain how these extra features are to be configured and used (all come from the above-mentioned trac tickets, some were edited/extended).

ipfilter

ipfilter allows to selectively blacklist/whitelist peers – based on IP address range files (so-called ipfilter files). The ipfilter files may, for example, come from bluetack.co.uk. Each line of the file contains a record in this format: range_description:start_IP-end_IP, where start_IP should be less than or equal to end_IP. Multiple files can be used. Overlapping ranges are merged automatically. Both incoming and outgoing connections are checked against the filter. Exclusions are not supported, so connection to/from IPs in all the loaded ranges will be disallowed and dropped.

Include “ip_filter=” directive in .rtorrent.rc. For example (paths are specified relative to user’s home directory):
ip_filter=ipfilter/level1,ipfilter/level2

It is probably a good idea to reload ipfilter files once in a while, so you can also include “reload_ip_filter” directive on schedule to refresh the filter. The same files named in “ip_filter” will be reloaded.

schedule = filter,18:30:00,24:00:00,reload_ip_filter=

To support the feature you may want to setup cron job to reload and unzip files from bluetack. Examples here and here.

GeoIP

In the Peers view of each torrent a new column – CC, country code – is added, which shows peer’s country code. When examining each peer, you will see more data from the GeoIP database (if you have the relevant files installed): AS num and city. At the very least, you need to have geoip-database installed. You can get free “lite” versions of city/AS-databases, rename them (removing “lite”) and put into an appropriate location to make rtorrent+geoip use them as well. Geop-isp data support isn’t integrated into this rtorrent package.

Colours

This patch somewhat changes the way rtorrent shows torrents. Seeding torrents have bold titles, there are no half-displayed torrents at the top/bottom when scrolling, and you can configure colours for active/done torrents (ticket libtorrent.rakshasa.no/ticket/1382, which seems to be gone now). Source code and testing hint at these configurable colours: done_fg_color, done_bg_color, active_fg_color, active_bg_color, and at these possible values: 1 (red), 2 (green), 3 (yellow).

Geek’s cellar
A related (though not used in any way for the preparation of the package) resource is rtorrent mods page.

Relatively schematically, applying patches and building the package was performed in these steps (starting within some newly-created directory):

1. sudo aptitude install cdbs devscripts [and whatever else you find you're missing]
2. apt-get source rtorrent
3. dpkg-source -x rtorrent_0.8.6-1.dsc
4. cd rtorrent-0.8.6
5. cdbs-edit-patch 01-ipfilter.patch
6. patch -p1 < /path/to/patch/239
7. exit 0
8. cdbs-edit-patch 02-geoip.patch
9. patch -p1 < /path/to/patch/2064-after-ipfilter
10. exit 0
11. cdbs-edit-patch 03-eyecandy.patch
12. patch -p1 < /path/to/patch/2171-mod-with-canvas
13. exit 0 [you could do all 3 patches together, but I prefer cleaner and manageable approaches]
14. [some weird operation to be explained below]
15. dpkg-buildpackage

Weird operation: I didn’t know how to make dpkg-buildpackage run autorun.sh (which is required for one of the patches I’ve used) before configure (could someone enlighten me how to do that?), so I started a new patch with cdbs-edit-patch, then ran one by one `autoreconf -if`, `./autorun.sh`, `./configure`, exited with zero status and was done with that problem. The resulting “patch” was 2MB large

• if you don’t have the python-stdeb package: sudo aptitude install python-stdeb
• pypi-install pycassa

That’s it.

Refer to stdeb readme for more information. You will need that if there are dependencies – which might not be resolved automatically by stdeb.

Before stdeb, it wasn’t exactly trivial to make a .deb from python module.

That’s my first encounter of Shapado, so it was interesting to read Shapado authors’ justification and a related question on meta.SO.

Debian has a number of packages enabling remote (over the network) backup: backupPC, backupninja, backup-manager, dirvish, duplicity, luckybackup, rdiff-backup, and some others.

In my setup I wanted backups to be initiated by the external backup server (as opposed to internal, production server initiated backup). Also, I was going to backup linux server to another linux box. Thus, it would be preferable to have support for rsync on both boxes and hardlinks on the backup box. I needed backup to be run regularly, I didn’t need any kind of GUI, and I would prefer to keep a bunch of older backups around (in case the most recent backup is of a compromised system, for example). Also, having an incremental backup of SQL databases was yet another requirement.

A few tools more or less matched my requirements: backupPC, duplicity, rdiff-backup, and dirvish.

backupPC, judging from its description and a few tutorial articles, is a cool piece of software. I think I might use it next time. But this time I really had no need for over-SMB backups (intended for Windows boxes), and no need for a nice administrative web-interface to backupPC. If not these extra features (which I don’t currently need) I’d go for backupPC. Here’s a guide for Ubuntu.

Duplicity claims to still be in beta, thus I haven’t given it a try. rdiff-backup seemed a bit too simple (and with no ready templates to get working regular backups faster), so I skipped that one as well.

Dirvish really caught my attention, partially thanks to a good and relatively short quick-start tutorial. That tutorial also mentions automysqlbackup – a nice, almost no-configuration tool to take regular dumps of MySQL databases. In combination, these two now regularly backup up my whole server to another linux box.

I would definitely recommend using dirvish+automysqlbackup for remote/off-site backup needs. However, other solutions might be as good or better for your use case.

1. Back up important data from partition just in case
2. Find out size of ‘$Bad’ attribute in $Badclus using ntfsinfo -i 8 partition (partition is for example /dev/sda1). It will be the “Allocated size” value in the “Dumping attribute $DATA (0x80)” (there will be two 0x80 attributes. Only one has an “Allocated size” line). Let us write down (remember) this size as ntfs_size.
3. Use ntfstruncate partition 8 0x80 ‘$Bad’ 0 to set $Bad’s attribute length to zero.
4. Use ntfstruncate partition 8 0x80 ‘$Bad’ ntfs_size to set $Bad’s attribute length back to proper value ntfs_size which was recorded in step 2.
5. Boot into Windows and run chkdsk -f diskname. It will find errors and should fix them.

However, Debian’s ntfsprogs package does not have the ntfstruncate binary.

Here’s how you can easily build one yourself (you may need a few extra packages with build tools for that):

1. apt-get source ntfsprogs
2. cd linux-ntfs-2.0.0
3. ./configure && make extra
4. cd ntfsprogs && ./ntfstruncate

You can also install ntfstruncate system-wide, but I have no idea if that will interfere with the already-installed ntfsprogs package, so I just used this binary directly from linux-ntfs-2.0.0/ntfsprogs.

Bad clusters happen not only when cloning an NTFS partition between 2 physical hard disk drives. Once, after a brief blackout (with a turned on PC, and not on a UPS), the SMART status of my new HDD started showing 1 ‘Pending sector’. Correspondingly, all the SMART tests (performed with a smartctl utility) reported read errors. To help my HDD examine and fix the problem itself, I performed a write operation to that single unreadable sector, which restored it (and reset the ‘Pending sector’ counter back to zero). It was possible, because not the physical sector itself, but the hidden CRC field had errors after power failure; modern hard drives can detect and fix this kind of errors upon write operations (read operations only mark the sector as ‘pending’, because data read is not consistent with the stored CRC).

However, NTFS partition still had 4096 bytes in ‘bad clusters’. A little research revealed the presence of internal NTFS bad clusters counter, which can be reset following the procedures above.

The project does provide a 64-bit package for Ubuntu 8.10 “Intrepid Ibex”, but it has a dependency on python-zope-interface – which in Debian testing is a virtual package, currently provided by python-zope.interface. That single dependency made my aptitude complain all the time, so I edited the .deb-file, renaming depends/python-zope-interface to depends/python-zope.interface (following nice and simple instructions). After that – no more aptitude complaints, and Chandler works fine.

Download the modified Chandler 1.0.3 Debian testing amd64 package (md5: 239071715977bea2eb75f3bb54491a02).

Error in openPDF(vif) :
getOption(‘pdfviewer’) is ”; please use ‘options(pdfviewer=…)’

and you are tired of running this command every time:

> options(pdfviewer=”okular”)

then you should check if your system-wide Renviron file has proper PDF viewer set:

grep -i pdf /etc/R/Renviron

R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-’/usr/bin/pdflatex’}}
R_RD4PDF=${R_RD4PDF-’times,hyper’}
## Default PDF viewer
R_PDFVIEWER=${R_PDFVIEWER-”}

It wasn’t in my case.

To set one, either edit the system-wide Renviron (e.g. by editing the R_PDFVIEWER=${R_PDFVIEWER-”} line to look like R_PDFVIEWER=${R_PDFVIEWER-’/usr/bin/xdg-open’} – this will use MIME types to open your preferred PDF viewer), or one of the per-user/per-directory Renviron files to fix this minor annoyance (format is the same, e.g. R_PDFVIEWER=okular ).

At least two convenient utilities are available in Debian Lenny for non-X Samba browsing.

smbtree (part of smbclient package) will list all visible workgroups, their servers, and share names of those servers – including “hidden” shares like C$, IPC$, ADMIN$, print$. Very handy and greppable!

samba-commander (smbc package) is a ncurses samba browser with “find file” functionality.

First of all, sudo aptitude install mesa-utils. Then run in a Terminal/Konsole glxgears, and wait for ~15 seconds; if your FPS is ~400 or less, then you do have sluggish video performance (usually manifesting itself as slow scrolling in Firefox/Iceweasel, slow window switching/minimziing/maximizing etc).

After reading through several forums and bug reports and blog posts, I’ve ended with the following modifications to my /etc/X11/xorg.conf:

1. backup your current xorg.conf: sudo cp /etc/X11/xorg.conf /etc/X11/xorg.conf.before-exa
2. open your /etc/X11/xorg.conf with a favourite editor; I’ve added these lines to section “module”:
   

   Load “dbe”
   Load “xtrap”
   Load “record”
   Load “GLcore”

   These are not really performance-related and could be skipped; I’m giving them here, because they were suggested as default entries by dexconf or some other xorg.conf-generator utility. Again – they are not supposed to improve performance, so you can skip these.

3. my “Device” section is now:
   

   Section “Device”
   Identifier “Intel Corporation 82915G/GV/910GL Integrated Graphics Controller”
   BoardName “82915G/GV/910GL Integrated Graphics Controller”
   Vendorname “Intel Corporation”
   #Driver “i810″
   Driver “intel”
   BusID “PCI:0:2:0″
   Option “DRI” “true”
   Option “AccelMethod” “exa”
   Option “MigrationHeuristic” “greedy”
   Option “ExaNoComposite” “false”
   EndSection

   Driver i810 (xserver-xorg-video-i810 package) was about 10-20 FPS slower than Driver intel (xserver-xorg-video-intel package) for me. The most important lines here are Option AccelMethod exa (which enables EXA acceleration instead of the older XAA; if you run 2.6.28 or later kernel, you can try UXA instead of EXA) and Option MigrationHeuristic greedy. Option ExaNoComposite false doesn’t make a difference for me, and Option DRI true might be redundant (didn’t bother trying to remove it).

4. at the end of xorg.conf I have two more sections:
   

   Section “DRI”
   Mode 0666
   EndSection

   Section “Extensions”
   Option “Composite” “enable”
   Option “MIT-SHM” “Yes”
   EndSection

5. sudo nano /etc/environment, and add one line: INTEL_BATCH=1 (if you have graphics stability issues or screen corruption – try removing this change first)
6. you can test if your xorg.conf is syntactically correct by running X -config /etc/X11/xorg.conf (provided that you edited this exact file)

This is it. Before these modifications, my FPS in glxgears was around 430; after these modifications it is ~915.

As time permits, I might try the XAA configuration, suggested at foolcontrol.

Update: with compiz enabled, XAA configuration recommended at foolcontrol is definitely faster in 2D.

Improvements, suggestions, corrections are welcome.

(…)
it is a very useful tool for performing installations if you’ve got something like a LiveCD which supports your hardware.
(…)

Installing new Debian systems with debootstrap, and also as a debootstrap PDF (with comments).

Two most common reasons (and fixes) for the MySQL server has gone away (error 2006) are:

1. Server timed out and closed the connection. How to fix: check that wait_timeout variable in your mysqld’s my.cnf configuration file is large enough. On Debian: sudo nano /etc/mysql/my.cnf, set wait_timeout = 600 seconds (you can tweak/decrease this value when error 2006 is gone), then sudo /etc/init.d/mysql restart. I didn’t check, but the default value for wait_timeout might be around 28800 seconds (8 hours).
2. Server dropped an incorrect or too large packet. If mysqld gets a packet that is too large or incorrect, it assumes that something has gone wrong with the client and closes the connection. You can increase the maximal packet size limit by increasing the value of max_allowed_packet in my.cnf file. On Debian: sudo nano /etc/mysql/my.cnf, set max_allowed_packet = 64M (you can tweak/decrease this value when error 2006 is gone), then sudo /etc/init.d/mysql restart.

If you get MySQL server has gone away (error 2006) when using MySQL ODBC driver – give this hint a try.

Though I prefer ‘testing’ (which is currently codenamed Lenny) over ‘stable’ (aka Etch).

For the case of ATI (and ATI Mobility) Radeon series, the easiest procedure would be (doing all as root, or prepending sudo to all commands):

1. aptitude update, to ensure you’ve got the list of latest packages
2. aptitude install fglrx-driver fglrx-control fglrx-kernel-src, for the actual driver; I also installed fglrx-atieventsd and fglrx-glx (these are driver-recommended packages)
3. aptitude install module-assistant, required for building the kernel module
4. module-assistant prepare, to verify that you have everything needed for the module build procedure
5. module-assistant update
6. module-assistant auto-install fglrx, to build and install the fglrx kernel module
7. depmod -a
8. modprobe fglrx, to load the fglrx kernel module
9. aticonfig ––initial, to configure ATI’s device section in /etc/X11/xorg.conf (for more options, see aticonfig ––help)
10. reboot

That should make your ATI hardware work as expected, and make fgl_glxgears show gears again.

If everything went fine, then your movies will play smoother , and the output of fglrxinfo will look similar to

display: :0.0 screen: 0
OpenGL vendor string: ATI Technologies Inc.
OpenGL renderer string: ATI MOBILITY RADEON X600
OpenGL version string: 2.1.7769 Release

This procedure should be also possible for the latest ATI-provided installer-generated Debian packages (as described elsewhere), but I decided to stick to the repository version – this requires no extra tweaking.

For much more information, see the ATI Debian Installation Guide.

This post is based on the iwanabeguru’s response at Linux Forums.

• SysCP
• Domain Technologie Control, DTC
• Virtualmin (also Webmin, Usermin)
• ISPConfig
• RavenCore (no longer developed)
• GNUPanel

SysCP: looks good to me (though demo isn’t functional), has customer billing module. Unsure as to where it is used, but most probably sponsors are also the users of SysCP. Majority of support forums are in German.

DTC: has no demo, only some screenshots. Has a set of packages for Debian lenny (which is a huge plus for maintenance and future upgrades). DTC is being developed by GPLHost, and is also used by GPLHost – so this is a live (used) distribution. Seems quite feature-rich.

Virtualmin claims to be the “world’s most powerful and flexible web server control panel”. Virtualmin offers 4 means to control it: Web, mobile device, command line, and remote API. There are both screenshots and demo. Has both GPL and Professional versions. GPL version has a number of limitations, comparing to Pro version. From what I’ve read about Webmin (all three – Virtualmin, Webmin, Usermin – are just different “layers” of server control), it is a framework with a number of “interface scripts”, which allow to control various services. As such, it is easily extendible, but is not monolithic – in the sense of module inter-dependencies and action triggers.

RavenCore was a promising CP.

GNUPanel is a year-old control panel, but has a news item on the front page (dated August, 17) promising new, completely rewritten release somewhere in October. By the feature list, looks promising. However, I need the panel right now, and even in October, that will be quite a rough release, not really used/tested anywhere, so not a good option as well. But GNUPanel is a panel to check in half a year for progress.

As the final choice, I had ISPConfig (which seems to be the best by people’s comments), and which is also quite widely used, and is easy to install onto Debian (at least the Perfect setup: Debian Etch says so), and DTC. I discarded Virtualmin (for the poor functionality of the GPLed version), RavenCore (for the lack of current descriptions and non-functioning demo), GNUPanel (which just isn’t ready yet), and SysCP (because ISPConfig seems better ).

As DTC has Debian packages (and will be easier to maintain/upgrade), I decided to try it first. I already have it installed (that’s easy, esp. if you first read the DTC Debian Express Setup). Later I might post my impressions from using DTC.

Update: DTC is indeed easy and pleasant to use. I had problems allowing FTP and SSH access using MySQL authorization, but at least FTP was an easy one to fix (SSH access with MySQL authorization is still unconfigured, but that’s a low priority for me). There is a minor concern about the files and directory permissions setup, but thanks to chrooted environment that is only minor concern. Use of a single Apache installation for hosting admin and serving user sites might be a sub-optimal decision, but it works. Traffic and disk space accounting are plain superb! Server memory use for the dtc-toaster installation is troublesome, but for a powerful RAM-my server that is not a problem (I now have about 800-900MiB RAM occupied, but that includes the XCache’s cache, quite big MySQL cache, and loads of Apache and PHP modules).

But I’m still willing to try other control panels. As I expected, GNUPanel hasn’t released anything yet; Ravencore‘s online demo is still unfunctional; ISPConfig has recently released RC (and their demo is working as it should and as it used to); SysCP is also up and running fast. If my little hosting service starts pouring in some cash, then I’ll try SysCP on my second server – to compare it with DTC, and choose one of them for further support/extension/localization.

develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

Check this project out – you might find that the software you need is already available as Debian package.

This post was stimulated by Steffen’s comment.

I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

This yet has to be fixed somehow.

If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:

- first, install all the necessary packages:
aptitude install build-essential libxml2 libxml2-dev python-dev

- then configure, make and install libsbml:
./configure ––with-python (execute from the directory where the downloaded libsbml archive was extracted to)
make
make install
ldconfig

- then check if installation was successful:
python
and when the python prompt >>> appears, run from libsbml import * – if there are no warnings/errors, then you are done!

What is on offer (mirrors):

• backports.org
• cygwin
• deb.opera.com
• debian – stable, testing, sid
• debian-archive (starting from 1.1!)
• debian-multimedia
• installation media (CDs/DVDs)
• debian-security
• even debian-volatile is here!

All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

Gone editing /etc/apt/sources.list

P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

Update: some time after publishing this post, debian.org.ua was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec . I found that ftp2.debian.org.ua mirror is faster at the moment.

Also as a PDF: Debian how-to: CPU frequency scaling and power management.