AMITIAE - Wednesday 26 December 2012

End of year Maintenance on OS X: Minor Niggles Worth Tidying up - iMac and MacBook Pro

apple and chopsticks


By Graham K. Rogers


It struck me that, as I was not going in to the office for part of this week because I am home marking exam papers and then the New Year period arrives, it would be an ideal time to carry out some end of year maintenance on my MacBook Pro, so that I could start 2013 with a fresher computer, perhaps returning some of the spring to its step, so to speak.

When I went into my office on Monday, however, I found that the iMac had restarted. There must have been a power cut over the weekend. As there are a couple of accounts, the iMac was displaying the login page. If the login had been automatic (as some prefer) - especially with the ability to restore applications that were running at the time of a shutdown - I might never have known. But I prefer to know: forced shutdowns might still have consequences, even with the improvements in protection that are available with OS X Mountain Lion.

I could have logged in and started work. Instead I restarted the computer, then restarted it again into the Rescue partition, that has been with OS X since 10.7 Lion, using the Command + R keys.

Part 1 - the iMac

When the process is complete, a user is offered 4 choices in a panel: Restore from a Time Machine Backup; Reinstall OS X; Get Help Online; and Disk Utility. I went straight for Disk Utility which has a display almost the same as the version in the Mac's Applications > Utilities folder.

In the left panel I first highlighted the disk icon to check on the S.M.A.R.T. status (Self-Monitoring Analysis and Reporting Technology), although I was confident this was OK as I run SMARTReporter in the background and this checks every 15 minutes. I then highlighted the main partition. Four options are available: Verify Disk, Repair Disk, Verify Disk Permissions and Repair Disk Permissions. When viewed using the Mac's own version, the Repair button is greyed out.


I pressed the button to Repair the disk and after a couple of minutes this gave me a clean bill of health. I then pressed the Repair Disk Permissions button: a couple of minor differences were noted and fixed. I restarted the computer, but took things a little further by inserting my 16 GB USB rescue drive, which has a complete OS X installation. I selected this as startup disk when the Rescue partition gave me the option (when quitting).

The restart with a flash drive is always a little slower than when using the Mac's own hard disk (SSD is even quicker I am told). I also had to connect a USB mouse as the magic trackpad was not recognised.


Eventually a Finder window opened and I started Disk Warrior, which I had installed in the Applications folder on the USB drive. I was offered two disks in the working panel: Macintosh HD (default) and Rescue. I did not waste any time by running the Graph process first, as this was an end of year clean-up. I clicked on the other button available - Rebuild - and the process began.

While it was running, I noticed that the clock was wrong by exactly 15 hours. As the wi-fi was not connected, there was no link to the online Apple Asia time server.

Although Disk Utility on the Rescue Partition had reported a clean bill of health, Disk Warrior found a number of minor problems with directory entries that were all repaired. I (of course) took the offer to replace the directory: small problems can build into large ones.

When this was done, I quit Disk Warrior and shut down the computer. I removed the USB mouse and then restarted. OS X found the correct partition, but I confirmed this using System Preferences > Startup Disk when I was able. As the wi-fi was now on, the time was displayed correctly as the computer was able to link to the Apple Asia time server.

This was a fairly lightly used 500 GB hard disk that was installed a few months back, so probably had few problems. But I did not know that.

Not running maintenance because a system appears to be running perfectly is a short cut to disaster.

Part 2 - the MacBook Pro

A couple of days later, with Xmas Day behind me and a lot of the exam marking finished, I had a look at the MacBook Pro. This is my working machine and as such it is backed up. I am a bit sloppy with the iMac as that is a spare machine and any data on there is synchronised with the MacBook Pro.

I recently bought a 2 TB Western Digital, My Book Studio external disk to replace the reliable, Neil Poulton designed LaCie disk, as the cumulative backups were now too much for the 500 GB disk. I had been running the two together, but retired the older disk this week and will keep it somewhere safe for now.

Before starting any maintenance, I made sure that Time Machine had made 3 or 4 backups for the start of the day, then set to work.

I decided to follow the same basic processes as I had with the iMac. I shut down the major applications running and pressed Restart. When I heard the Startup chime, I pressed Command + R. However, instead of the Rescue partition, I was faced with a padlock icon, a plain grey screen and a text entry box.

I use the Firmware Password Utility, which can now only be accessed from within the Utilities menu of the Rescue partition. Before I can go further, I must enter the Firmware password. When this was done, there was a brief delay then the Rescue options appeared as they had on the iMac: Restore from a Time Machine Backup; Reinstall OS X; Get Help Online; and Disk Utility.

I selected Disk Utility as before, confirmed the S.M.A.R.T. status of the disk, then pressed Start Repair. After a few minutes - longer than on the iMac as there is more data - the utility reported (in red) two faults: "Volume bitmap needs minor repair for orphaned blocks"; and "Invalid volume free block count".

The repairs were made and the checking process ran again automatically. This time there were no comments in red. A green colored text reported that the volume "was repaired successfully." Time to double-check with Disk Warrior.


I shut down the computer. As I was working at home, as well as the rescue USB drive, I also had the latest version of Disk Warrior (4.4) on a DVD. I connected the flash drive, inserted the disk, and pressed the Start button, this time holding down the Option key. After entering the Firmware password, an array of available OS X disks appeared. I selected Disk Warrior and the slow process began.

Disk Warrior panel: screen shot from version on the Mac

Because of this mollasses-like behaviour, I prefer to run Disk Warrior from the flash drive or an external source (hard disk or Mac connected via Firewire). I also like to keep the disk safe: only using it for updates to the utility. The purpose this time was to run Disk Warrior via a different medium - the disk - to remind myself how it all works.

While I was waiting, I made some lunch. Eventually a blue screen appeared (this is a good blue screen), followed by the Disk Warrior panel and a licence agreement. The software scans for disks, this time finding 3: the flash drive, the main disk and the Disk Warrior DVD. I selected the main disk and pressed the Rebuild button.

While I had lunch, Disk Warrior did its thing and then reported 3 minor problems: "24 files had a directory entry with an incorrect text coding value that was repaired"; "21 folders had a directory entry with an incorrect custom icon flag that was repaired"; and "13 files will now become accessible".

Bear in mind that Disk Utility had just done a repair: but it does not examine in the same was as Disk Warrior. I pressed the button to Replace the directory with a new, optimized version. This was completed quickly. I also saved the report. The default location for this is Root, which I do not think is useful, so I saved it to the Desktop in my user account.

I quit Disk Warrior and the computer restarted automatically. I forgot to eject the disk (hold down the trackpad or mouse button at startup), so when all was running again, I dealt with that and the still connected USB drive.

Startup and login to my user account seemed more sprightly, with desktop icons and apps appearing quickly. But maybe my brain is playing tricks with me as this is what I want to see. . . .

Graham K. Rogers teaches at the Faculty of Engineering, Mahidol University in Thailand. He wrote in the Bangkok Post, Database supplement on IT subjects. For the last seven years of Database he wrote a column on Apple and Macs.



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