Category: OSX

Fix lagging display performance on retina MacBook Pro

This weekend my Mac suddenly started behaving strangely: moving windows around occurred with a nearly psychodelic delay, mission control (aka exposé) was “jerky”, and scrolling was not fun. Forcing the graphics card to the discrete NVIDIA GT 650 instead of integrated Intel GPU sped things up, but the overall experience still didn’t feel right. Since the onset was sudden I immediately though: imminent hardware failure! But thankfully that turned out not to be the case.

Scouring forums for answers led me here, which worked for me!. The basic idea: delete some preferences files and reset the PRAM:

  • Delete /Library/Preferences/
  • Delete ~/Library/Preferences/ByHost/*.plist
  • Shutdown OSX
  • Startup, immediately press and hold the P and R keys while holding down the option (⌥) and command (⌘) keys before the gray boot screen appears, which resets the PRAM
  • You may have to reset your display preferences (resolution) once you login
  • Done!

2013-08-12: fixed typo in preference plist filename.

Recover a failed TimeMachine backup

I recently received an unpleasant warning message after TimeMachine routinely tried to perform a backup:

Time Machine completed a verification of your backups on “matmos”. To improve reliability, Time Machine must create a new backup for you.
Click Start New Backup to create a new backup. This will remove your existing backup history. This could take several hours.
Click Back Up Later to be reminded tomorrow. Time Machine won’t perform backups during this time.Time Machine completed a verification of your backups on 'matmos'. To improve reliability, Time Machine must create a new backup for you.  Click Start New Backup to create a new backup. This will remove your existing backup history. This could take several hours.  Click Back Up Later to be reminded tomorrow. Time Machine won’t perform backups during this time.

Googling around for others with the same problem I found quite a few tips (like this one, or this one). The basic idea is to mount the sparsebundle image, run a disk check/repair, and hope for the best. In my case (as you will see in a bit), my sparsebundle appeared to be hosed. My options: lose my old backups or look for a way to recover the old backups. But first up, turn off TimeMachine, and then try to run a standard disk check.

Run disk check/repair

  • Unlock and mount the TimeMachine sparsebundle from the already-mounted server share (of course your server name, network share, sparsebundle names will not be the same as mine):

    $ sudo chflags nouchg /Volumes/TimeMachine-David/fünke.sparsebundle
    $ sudo chflags nouchg /Volumes/TimeMachine-David/fünke.sparsebundle/token
    $ sudo hdiutil attach -nomount -noverify -readwrite -noautofsck /Volumes/TimeMachine-David/fünke.sparsebundle
    /dev/disk2          	GUID_partition_scheme          	
    /dev/disk2s1        	EFI                            	
    /dev/disk2s2        	Apple_HFS
  • The disk check utility fsck may now be running, so get the PID of it and kill the process so we can manually run it:

    $ ps auxwww | grep fsck
    $ kill PID
  • Now run fsck with some repair options on the correct disk partition (use the “Apple_HFS” partition as listed in the mount step above (/dev/disk2s2 in my example):

    $ sudo fsck_hfs -dryf /dev/disk2s2
    journal_replay(/dev/disk2s2) returned 0
    ** /dev/rdisk2s2
    	Using cacheBlockSize=32K cacheTotalBlock=65536 cacheSize=2097152K.
       Executing fsck_hfs (version diskdev_cmds-557~393).
    ** Checking Journaled HFS Plus volume.
       Invalid number of allocation blocks
    (4294967295, 0)
    	IVChk - volume header total allocation blocks is greater than device size 
    	volume allocation block count 102374400 device allocation block count 97630464 
    ** The volume could not be verified completely.
    	volume check failed with error 7 
    	volume type is pure HFS+ 
    	primary MDB is at block 0 0x00 
    	alternate MDB is at block 0 0x00 
    	primary VHB is at block 2 0x02 
    	alternate VHB is at block 781043710 0x2e8dc7fe 
    	sector size = 512 0x200 
    	VolumeObject flags = 0x07 
    	total sectors for volume = 781043712 0x2e8dc800 
    	total sectors for embedded volume = 0 0x00 
    CheckHFS returned -1317, fsmodified = 1
  • The disk check did not do anything, so let’s unmount the sparsebundle:

    $ sudo hdiutil detach /dev/disk2s2
  • You can try running the disk check (fsck) multiple times. Some have reported that does the trick! In my case, it didn’t help. I had to try something else.

What to do next?

So, “The volume could not be verified completely” says that disk check is not going to repair my sparsebundle. But one good thing to note: the sparsebundle can be mounted read-only, so the old backups should still be there. So the plan: make a new sparsebundle, mount it, mount the old sparsebundle, and then copy all files from the old sparsebundle into the new. Sounds easy, right?
Making a new sparsebundle is not rocket science, however copying the files from TimeMachine backups can be quite challenging. I learned quite a bit when trying various methods to copy the files across (Finder, cp, rsync, ditto, etc). TimeMachine is quite ingenious: it uses a combination of file hard links and directory hard links (the latter is a new one to me!) in order to keep the backup size at a mininum. Unfortunately, all the methods I tried could not reconcile the directory hard links: instead of the links being created, the actual directory contents were copied. Furthermore, Apple has made it difficult to work directly with files in TimeMachine backups by making use of sandboxing and an access control “safety net” (see this or this). So I did some more digging and found a great product that can deal with TimeMachine backups, directory hard links, and this safety net: SuperDuper.

Recover contents of failed sparsebundle

Move failed sparsebundle to a new location

I tried restoring the failed sparsebundle to a new sparsebundle while both were on a network drive (connected to my machine via gigabit ethernet) and the backup was painfully slow (wasn’t finished after 24 hours) meaning the bottleneck was random access/seek time of my poor, slow network drives. I cancelled the restore operation, moved the failed sparsebundle to an external USB drive.

Create new sparsebundle

With the failed sparsebundle no longer in my TimeMachine network share, I created a new sparsebundle. Since I encrypt my backups, I used TimeMachine to create a new sparsebundle on the network share:

  • Enable TimeMachine, select the network share, select “encrypt backups”, then “use disk”
    select network share in TimeMachine
  • Provide encryption password:
    create sparsebundle encryption key
  • Let the backup run, then cancel after a few minutes. This will create a new sparsebundle on the network share.
    backing up...

Mount both sparsebundles

  • Mount the failed sparsebundle (from the external/USB drive). Unfortunately, you can’t use the paste command in the encryption password field 😦
    field does not allow pasting!
  • Note that the sparsebundle will be mounted read-only (which is just fine):
    Mac OSX can't repair the disk 'Time Machine Backups'. You can still open or copy files on the disk, but you can't save changes to files on the disk. Back up the disk and reformat it as soon as you can.
  • Now that both sparsebundles are mounted and have the same name (Time Machine Backups), we need to make sure we know which is the source (external drive) and which is the destination (network share). A little commandline magic:

    $ mount
    /dev/disk4s2 on /Volumes/Time Machine Backups (hfs, local, nodev, nosuid, read-only, mounted by david)
    /dev/disk5s2 on /Volumes/Time Machine Backups 1 (hfs, local, nodev, nosuid, journaled, mounted by david)
  • So, “Time Machine Backups” is the source (it’s read-only) and “Time Machine Backups 1” is the destination.

Copy files from the failed sparsebundle to the new sparsebundle

  • Open “SuperDuper!”
    Select copy: “Time Machine Backups”
    to: “Time Machine Backups 1”
    using: “Backup – all files”
  • Select “Options…” and choose “Smart Update” (this prevents SuperDuper from reformatting the destination sparsebundle, ask me how i know 😉 )
    Smart Update
  • Advanced options are left as the default:
  • Start the copy process:
    Start copy
  • Let it run for a long time…

Enable TimeMachine

Enable TimeMachine and start the backups. When the backups first started, the “Oldest backup” date was not listed. But when the backup finished, TimeMachine successfully recognized the oldest backup. Success!
Backing up

Updated 2013-07-06: updated fsck step to not be recursive, can try to run fsck multiple times, thanks to comments!

Move music library and update iTunes database

I’m doing some reorganization of my network shares. My music is saved on the server under its own share, “Music”. In the new scheme, I want the music folder to be located in a subfolder in the share “Multimedia”. This poses a small problem: I have to update iTunes to recognize the new file locations. I’ve got iTunes 10.6.3 on OS X Mountain Lion 10.8.1.

Edit iTunes Music Library.xml

The simple solution is to modify the Location values in the iTunes Music Library.xml file, mangle the iTunes Library.itl file, then open iTunes. iTunes will then rebuild the database file based on the xml (the .itl file is the active database file, the .xml file is regenerated based on the .itl database).  To find and replace all the locations I tried this:

cat ~/Music/iTunes/iTunes\ Music\ Library.xml | perl -pe 's/\/Volumes\/Music\//\/Volumes\/Multimedia\/music\//i' > itunes.xml

Then quickly checked to see if I was missing any other locations:

cat itunes.xml | grep "Location" | grep -v "/Volumes/Multimedia/music"

Then erase iTunes Library.itl, replace iTunes Music Library.xml with this new copy (making backups of the originals first, of course).

An unfortunate side effect of rebuilding the .itl based on the xml: the Date Added values for the entire library are reset (probably other values are reset as well). I wanted to move my library files and keep all the metadata intact.

Edit iTunes Library.itl

So, instead of editing the xml file, what about editing the itl file? Unfortunately, the .itl file is a proprietary format binary file. Luckily, there are some who have tinkered with the file in order to edit .itl database entries. Enter Tools for iTunes Libraries (titl): excellent! I cloned the mercurial repository, built the code and tried to move some files:

$ hg clone titl
$ cd titl
$ mvn verify
$ java -Xmx512m -XX:MaxPermSize=256m -jar titl-core/target/titl-core-0.3-SNAPSHOT.jar MoveMusic --use-urls ~/Music/iTunes/iTunes\ Library.itl "file://localhost/Volumes/Music" "file://localhost/Volumes/Multimedia/music"

That resulted in a Exception in thread "main", the exact same issue as this one. Downloaded the patch file that the user thankfully uploaded, applied the patch to the code, and tried again (disabling the now broken unit tests with -Dmaven.test.skip=true): success! Excellent!

Final step: rename the iTunes Library.itl.processed file to iTunes Library.itl (making backup first of the original file of course). iTunes works as expected, music files are found, play count still there, “last added” dates still there.

Not that I use iTunes very often (or really at all) anymore to play music. Spotify is the scheisse these days! 😉

Updated 2011-12-16: Uploaded the patched + compiled jar (for those of you who want it)

No more annoying password popups for Cisco VPN on OSX Lion (and Mountain Lion)!

I am currently working on a development project for our office in München. Accessing their internal servers requires connection via VPN (I’m working from Stockholm). I’m using the very handy built-in Cisco IPSEC VPN client in OSX and have had some annoying problems which until today I have not been able to solve. I am documenting these configuration changes so I remember what I did, and hopefully it can also help others out there!

The problem

After being connected via VPN for about 48-54 minutes (seems to vary), OSX will throw up a “please enter password” dialog (I can’t remember the exact wording…). After entering the password, the VPN connection stays active for another 48-54 minutes, at which time another password dialog pops up. Lather, rinse, repeat. Not very fun during a standard work day, especially when my application-in-progress likes to crap out as soon as it loses connectivity to those remote servers (and requires lengthy restarts).

The solution (I thought)

After much googling I found this solution, for which I had high hopes (despite the comments from fellow OSX Lion users who couldn’t get the solution to work). In short, that post goes about showing how to grant /usr/libexec/configd access to your keychain, in order to squelch the password dialog. Well, unfortunately that solution didn’t work for me as well 😦

The working solution (finally!)

After a week or so of still getting that annoying password dialog, I managed to google the correct sequence of terms and I finally found a working solution! Over at the Apple forums, a very clever Mr Geordiadis posts a working solution to the problem. His solution is to modify the racoon configuration files for the VPN connection by tweaking a few settings and increasing the negotiated password timeout value from 3600 seconds to 24 hours (perfectly fine for my intended use). I’ve been connected now for over 8 hours today, haven’t had a password dialog yet! So excellent! Confirmed that it works on Mountain Lion (10.8) as well.

I hope this information helps you as it helped me!


  • Connect to the VPN so the configuration file is generated
  • Create a location for the VPN configuration files

    $ sudo mkdir /etc/racoon/vpn
  • Copy the auto-generated configuration file into the new configuration folder:

    $ sudo cp /var/run/racoon/ /etc/racoon/vpn/
  • Edit the racoon.conf file:

    $ sudo emacs /etc/racoon/racoon.conf
  • Comment out the include line at the end of the file and include the new configuration folder:

    #include "/var/run/racoon/*.conf" ;
    include "/etc/racoon/vpn/*.conf" ;
  • Edit the VPN configuration file:

    $ sudo emacs /etc/racoon/vpn/
    • Disable dead peer detection:

      dpd_delay 0;
    • Change proposal check to claim from obey:

      proposal_check claim;
    • Change the proposed lifetime in each proposal (24 hours instead of 3600 seconds):

      lifetime time 24 hours;
  • Disconnect VPN and reconnect.

Updated 2012-08-07: added the detailed steps
Updated 2012-08-07: tested on OSX Mountain Lion (10.8)

Reduce the size of MySQL ibdata1 on OSX

So I finally figured out why my TimeMachine backups were becoming bigger and bigger, 3-4GB backing up every day when I come home from work… It seems that my MySQL database file (/usr/local/mysql/data/ibdata1) keeps getting larger and larger, unnecessarily, even if I deleted databases, tables, etc. It seems even if I only update a few rows in a table in a small database, the ginormous idbdata1 file grows and then get marks as a candidate for backup into TimeMachine. Ugh.

I did some digging and found this interesting tutorial on how to clean up InnoDB storage files.  Here I’ll explain what I specifically did on my OSX 10.6.5 machine with MySQL v5.1.38.

  1. If you’re not a cowboy, stop MySQL, backup all files, then start MySQL again (I used the System pref to stop/start MySQL, feel free to use the command-line instead):

    $ sudo cp -R /usr/local/mysql/data /usr/local/mysql/data.bak

  2. Export all data from MySQL:
    $ mysqldump -u root -p --all-databases > alldatabases.sql
  3. Drop databases in MySQL (except “mysql” and “information_schema”):
    $ mysql -u root -p
    mysql> show databases;
    mysql> drop database XXXX;

    or use this great one-liner to delete all databases, modded a bit so it would work for me:

    # measure twice, cut once... make sure we are deleting what we should be deleting
    $ mysql -u root -p  -e "show databases" | grep -v Database | grep -v mysql | grep -v information_schema | awk '{print "drop database " $1 ";select sleep(0.1);"}'
    # now delete them
    $ mysql -u root -p  -e "show databases" | grep -v Database | grep -v mysql | grep -v information_schema | awk '{print "drop database " $1 ";select sleep(0.1);"}' | mysql -uroot -ppassword
  4. Stop MySQL again
  5. Add the following to the [mysqld] section in /etc/my.cnf:
  6. Remove the files:
    $ sudo rm /usr/local/mysql/data/ibdata1
    $ sudo rm /usr/local/mysql/data/ib_logfile0
    $ sudo rm /usr/local/mysql/data/ib_logfile1
  7. Start MySQL again
  8. Reload the databases from the sql dump-file:
    $ mysql -u root -p < alldatabases.sql
  9. Verify that your database(s) are working properly
  10. Delete the backup
    $ sudo rm -rf /usr/local/mysql/data.bak
  11. Done!

After this modification my TimeMachine backups are much more reasonably-sized. Very nice!

Furthermore, I noticed the same infamously large ibdata1 file on our continuous-integration build server at work: it was 40GB! I applied the same modifications as above. That server runs Ubuntu 10.10, the MySQL files are located in /var/lib/mysql/data, but otherwise the steps are pretty much the same. Even build-server bongo seems snappier now, and the total size of the MySQL data folder is 1GB (insane that there was 39GB of “dead” data in the ibdata1-file…)

Very happy.