• 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.

Here's a sample script (call it e.g. git-truncate and put into your ~/bin or whichever location you have in PATH).

Invocation: cd to your repository, then git-truncate refspec, where refspec is either a commit's SHA1 hash-id, or a tag.

Expected result: a git repository starting with "Truncated history" initial commit, and continuing to the tip of the branch you were on when calling the script.

If you truncate repositories often, then consider adding an optional 2nd argument (truncate-commit message) and also some safeguards against improper use - currently, even if refspec is wrong, the script will not abort after a failed checkout.

Thanks for posting any improvements you may have.

Source: Tekkub's post on github discussions.
See also: how to remove a single file from all of git's commits.

• 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.

ENSRNOG00000018677 1368832_at 25233
ENSRNOG00000002079 1369102_at 25272
ENSRNOG00000043451 25353
ENSRNOG00000001527 1388013_at 25408
ENSRNOG00000007390 1389538_at 25493

In the example above I need '25353', which does not have corresponding affy_probeset_id in the 2nd column.

It is clear how to do that:

This outputs a column of required IDs (EntrezGene in this example):

116720
679845
309295
364867
298220
298221
25353

However, I need these IDs as a comma-separated list, not as newline-separated list.

There are several ways to achieve the desired result (only the last pipe commands differ):

These solutions differ in efficiency and (slightly) in output. sed will read all the input into its buffer to replace newlines with other separators, so it might not be best for large files. tr might be the most efficient, but I haven't tested that. paste will re-use delimiters, so you cannot really get comma-space ", " separation with it.

Sources: linuxquestions 1 (explains used sed commands), linuxquestions 2, nixcraft.

Step-by-step:

1. Identify current swap UUID: grep swap /etc/fstab ; you should see a line starting with UUID=b4e6e... - note that UUID; let us assume our UUID is b4e6e5d8-8854-4a3e-8edb-f423ded31e2a
2. Identify swap partition device. If you are using Debian or Ubuntu, device might have been shown to you when running command #1 as a comment of the form
   

   # /dev/sdX4 none swap sw 0 0

   Just to be sure, run cat /proc/swaps (or sudo swapon -s), to be shown something like this:

   Filename Type Size Used Priority
/dev/sdX4 partition 2104504 0 -1

   You can also use partition managers to identify swap device, e.g. sudo fdisk -l. Let us assume our partition device is sdX4.

3. If that swap partition is in use, you need to disable it first: sudo swapoff /dev/sdX4
4. Now that you have both the UUID and the device, run
   sudo mkswap -L new_swap_label -U b4e6e5d8-8854-4a3e-8edb-f423ded31e2a /dev/sdX4
   Do not forget replacing sample values above (label, UUID and device) with your actual values.
5. Enable swap: sudo swapon /dev/sdX4

Now, if you wish so, you may proceed to edit /etc/fstab and replace UUID=.... with LABEL=your_new_swap_label, leaving all other spaces and values in that line untouched.

UPDATE `table_name` SET `table_field` = REPLACE(`table_field`,'string to search for and replace','replacement string');

If you need a database-wide search-and-replace, you could try this script (I haven't tested/used it myself).

Beware of the following gotchas:

1. wrong query syntax may ruin the field you are performing replace on, so always backup first!
2. be sure to provide "search-for" string as specific as possible, or you will get unexpected replacements (e.g. replacing mini with little will also convert all minivans into littlevans); also, do use WHERE clause when necessary to limit the number of rows modified
3. the function in the example is case-sensitive, so replacing all minivans with vehicles won't replace Minivans. However, I believe there exists a case-insensitive version of REPLACE function

Development: see http://www.ruzee.com/blog/2009/01/apache-virtual-hosts-a-clean-setup-for-php-developers. This setup works very well, unless you need to create several virtual hosts every day - in which case necessary actions could be partially scripted.

I'm sure that you are aware of the fact that floats representation in any programming language is limited by the precision of the internal binary representations. In other words, you can never have an exact float representation - there will always be some precision associated with the float you are working with. The simplest example is the difference in precision between the float and double types in C.

Suppose I have the following code fragment:

Both result.score and input->raw_cut_off are of type float, and can have positive and negative values. When compared with the greater than or equal ( >= ) operator, it is not always that condition is true - for the precision reasons shortly mentioned above.

As I already said, there is no precision specification for equality operators in C. But it is quite simple to "invent" precision specification; e.g. if I wanted to test for equality only, I could write

In this example, I'm effectively asking for 6-digit precision for the equality comparison of floating-point values. Note, that if you replace that 0.000001 with the actual precision limit of the floating type you are using, you will be "exactly" comparing floating-point numbers - up to that type's precision, of course .

The first-most example with the >= operator can be rewritten as

where precision is exactly what it is named, e.g. precision = 0.000001.

Sources used:

• comment by Randy A. Ynchausti
• scientific programming

Recursively set directories only to drwx-rx-rx (755):

find . -type d -exec chmod 755 {} \;

Recursively set files only to rwx-r-r (644):

find . -type f -exec chmod 644 {} \;

Recursively remove carriage returns (^M) from the end of all *.php files:

find . -type f -name "*.php" -exec /home/user/dos2unix.sh {} \;

In all these cases, {} is replaced with the filename/directory find has found matching your parameters; \; at the end just stops exec processing.

This is how to do that in Drupal 7 (Views 3):

1. edit the view which makes the block available (follow http://your.site/admin/build/views/viewname/edit)
2. in the Sort Criteria section (under Filter), look for and add Global:Random.

This is how to do that in Drupal 6 (Views 2):

1. edit the view which makes the block available (follow http://your.site/admin/build/views/viewname/edit)
2. in the Sort Criteria section, add the Random criteria.

It can't be simpler than that.

cat styles.css | tr -d "\r" > styles-nocarriage.css

will create styles-nocarriage.css with ^M's removed.

Alternative syntax:

tr -d "\r" < styles.css > styles-nocarriage.css

Most editors have global replace features which allow to get rid of control characters using regular expressions (exact instructions are editor-specific).

For multiple files, try this:

for f
do
mv $f ${f}~ && tr -d "\r" <${f}~ >$f
rm ${f}~
done

Save this shell script as a file (e.g. dos2unix.sh), then do ./dos2unix.sh . This script accepts wildcards (e.g. ./dos2unix.sh *.php), so be careful!

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.

1. cd gitosis-admin && git pull - enter your gitosis administrative repository and ensure it is up-to-date
2. $EDITOR gitosis.conf
3. add [group newreponame] section (newreponame is the name of your new repository being added); add yourself with members = yourlogin@yourhost line; also add writable = newreponame line:
   

   [group newreponame]
   members = yourlogin@yourhost
   writable = newreponame

4. based on my assumption of a correctly setup gitosis-admin repository, you should already have the appropriate public key in the keydir directory, but if not - copy your user's ssh public key to keydir in the form of yourlogin@yourhostname.pub, then do git add keydir/yourlogin@yourhostname.pub
5. git commit -am 'new repository: newreponame'; git push;
6. now that you have the new repo permissions configured, let's actually create it. Navigate to the directory holding the files of your project (e.g. cd ~/newreponame), and do git init; git add . - this initializes empty git repository, and then adds all the files to it. If you have no files - you can skip the 'git add .' command, as it will do nothing for you.
7. git commit -m 'initial commit'. If you had no files added to the commit, git will complain that it cannot create an empty commit. In this case use the command git commit ––allow-empty -m 'initial commit'
8. git remote add origin ssh://gitosis@yourGitosisServerName/newreponame.git
9. git push ––all
10. final thing: git config ––add branch.master.remote origin && git config ––add branch.master.merge refs/heads/master; alternatively, cd .git && $EDITOR config, and then add these lines:
    

    [branch "master"]
    remote = origin
    merge = refs/heads/master

    Without these lines, you won't be able to git pull.

I assume that the problem is caused by Google Analytics, namely the "track outgoing clicks" feature (as recalled, might be inaccurate feature name). "Track outgoing links" adds some JavaScript code to all outgoing links, and that script has tick characters like this one ' which, incidentally, are also used for delimiting the values of comment anchor tags.

To fix:

1. locate file wp-includes/comment-template.php
2. in that file, find the get_comment_author_link function (lines 140-150 in WP 2.7.1)
3. replace the line
   PLAIN TEXT
   PHP:

   1. $return = "<a href='$url' rel='external nofollow' class='url'>$author</a>";

   with

   PLAIN TEXT
   PHP:

   1. $return = '<a href="'.$url.'" rel="external nofollow" class="url">'.$author.'</a>';

This helped me and might help you.

I have found the solution at stackoverflow (see also this question).

This method worked for me, but I couldn't push my rebased repository to the gitosis. I would need to re-init the gitosis repository from my rebased, but I'm not yet prepared to do that.

There is also a slightly different method (which relies on a temporary tag instead of a temporary branch), documented in Git online manual pages; I prefer the temporary branch method.

Below is a full copy-paste of the winning answer by Charles Bailey:

# create and check out a temporary branch at the location of the bad merge
git checkout -b tmpfix

# remove the incorrectly added file
git rm somefile.orig

# commit the amended merge
git commit --amend

# go back to the master branch
git checkout master

# replant the master branch onto the corrected merge
git rebase tmpfix

# delete the temporary branch
git branch -d tmpfix

Also, in my case this thread at stackoverflow was highly useful. I start enjoying the concise and compact style of Charles Bailey :

# detach head and move to D commit
git checkout

# move HEAD to A, but leave the index and working tree as for D
git reset --soft

# Redo the D commit re-using the commit message, but now on top of A
git commit -C

# Re-apply everything from the old D onwards onto this new place
git rebase --onto HEAD master

Note: this example is for a branch of commits R--A--B--C--D--E--HEAD, where commits B & C should be removed from commit history.

Another option is to use git rebase --interactive (for the same example):

git rebase -i HEAD~5

Unfortunately, rebasing on a public (pushed out) branch has no effect for other users of the current gitosis repository.

An alternative to re-initializing gitosis repository from rebased scratch could be switching to a different (rebased) branch, and deleting the outdated master branch; but I haven't investigated if this works.

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.

To extract a single page (or a range of pages), I used pdftops:

pdftops -f 187 -l 187 -paper A4 abstract_book.pdf page_187.ps

Here, -f is the first page, -l is the last, and -paper is paper size.

Alternatives include using pdf2ps (which relies on GhostScript and accepts the same options) and acroread -toPostScript (which uses non-free Adobe Reader in CLI mode to convert PDF to PS).

Now that I have a single-page PS file, I can print it:

cupsdoprint -P S200 -o Resolution=720dpi,Copies=2,PageSize=A4 page_187.ps

Printing options will vary depending on your printer model (use lpoptions -l -P PrinterName to find out possible options and their default values). In the sample line above, S200 is the printer to use for printing, Resolution/Copies/PageSize are all self-explanatory printing options.

Alternative (and, actually, more standard) way to print is by using lpr, but if you run CUPS and KDE then cupsdoprint isn't any worse.

For more details this FAQ might be helpful. Also, keep in mind that simple shell scripts can automate routine sequential tasks, and that piping helps.

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.

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!

When right-clicking many links in FF3/IW3, it quite often happens so that a random action is performed instead of opening the context menu (bug report).

One of the solutions work-arounds (suggested by Andre Pirard) is to slow-right-click, that is to hold the right mouse button down until the menu actually appears, then - and only then - release it. Or, you can even slow-right-click, move the pointer over the desired menu item, and then release - that will perform the desired action in a single long right click (instead of more common single right click with a following single left click.)

Alternative workaround (found at the bug report page): install the mouse gestures add-on, and restart firefox. Tested: works for me.

This bug/behaviour is otherwise unsolved.