OS X - Repair disk errors like invalid node structure

If you're an OS X user you may have run into a problem like this before. When you power on the machine it just sits on the Apple logo screen but won't get any further. Other boot up problems may be fixed by this as well. If you try to boot from the install CD and run disk utility to repair permissions or repair the disk, you may get an error such as invalid node structure or something similar that will cause the repair to fail. One solution to this is to reformat the hard drive, reinstall the OS, and then reinstall all the programs. This is time consuming, and you'll lose all of your data if it hasn't been backed up. Instead, there's something else to try that could solve the problem and you won't have to worry about reinstalling anything. You can manually run the Apple file system consistency check (fsck) and have it repair errors it finds. To do this you'll need an OS X install disk, which you should have gotten with the computer.

1. Put the install disk in the computers CD/DVD drive
2. Restart the computer
3. When it comes back on, hold down the C key on the keyboard to force it to boot from the CD
4. Once it gets to the point where the Apple logo is on the screen and the progress spinner has appeared and is moving underneath the logo, you can release the C key.
5. It will ask you which language you want to use, so select your language choice and continue
6. Don't continue with the installation from this point on. Instead, on the menu at the top I believe there is an entry for "Utilities" (or something like that). Click on it and go to Disk Utility. If that's not where it is, check the other menu options until you can find it
7. When Disk Utility opens, click on the hard drive partition that has the operating system installed, then click on Unmount at the top
8. Close Disk Utility
9. Go back into the "Utilities" menu (or wherever you had found Disk Utility) and open up the Terminal application
10. Enter the command diskutil list and press Enter. This will list all the partitions on the computer. You're looking for the name of the partition that contains the operating system files, which will most likely be disk0s2 or disk0s3. I think the defaults may be disk0s2 for Intel Macs, and disk0s3 for PPC Macs, but I'm not sure if that's correct which is why you should use the diskutil program to find it
11. Once you know the partition name, enter the command /sbin/fsck_hfs -yprd /dev/partitionName where you substitute the partition name that you found in step 10 for partitionName. This will run the HFS+ version of the file system consistency check on the partition you specified, and will repair and "normal" errors it finds while outputting what it's doing. You could use -ypr instead if you don't want to know what it's doing, but if you're like me you'll be curious to see what it finds. This step may take a while to run
12. After the fsck_hfs command is done running, you can close Terminal
13. Go back into Disk Utility
14. Click on the hard drive partition you unmounted in step 7, then click on Mount at the top
15. Now you could try running the Repair Permissions and Repair Disk within Disk Utility to see if you have any better luck
16. Close Disk Utility and restart the computer.

At this point your problem should be gone and the system should act normally. If not, then there is probably something much deeper wrong with the disk/partition and you may want to turn to professional help. There is always DiskWarrior too if you'd rather try another utility, but since that's not a free tool I'll leave it up to you. The only other thing I can think of is going into Startup Disk before restarting in step 16 and making sure that the computer is set to startup from the partition that you just fixed. Hopefully you'll never need this, but I actually used it this afternoon on a OS X 10.4 machine that Disk Utility wouldn't fix, and afterwards everything was fine. If you want to see the original article where I found this, click here. It's down in the comments because the original poster has something about cloning drives which you can hopefully avoid with this other solution. Good luck!

UPDATE: 6/30/14

It's been over 5 1/2 years since I published this article, and it still is the most popular for comments. I'm glad it has helped so many people and hope it continues to.

A lot has changed in that time though, and it would be even better to avoid the problem by having backups of your data. It is usually such a pain to keep up with backups. Plugging in a USB drive, waiting for the backup to finish, blah blah blah. I have problems with it on my personal machines because it ends up taking too much time and is a hassle. When you run into an issue like this though you realize just how important it is to have those backups.

The reason I'm adding this to the article is because I've started using an application called CrashPlan for offsite backups for business and am very happy with it. So much so that I may just bite the bullet and start using it for my personal machines too. I'm not affiliated with them in any way and am just a happy customer willing to promote their product of my own accord because I have this article and web traffic. There are other similar paid services out there (Mozy, Carbonite, etc), and some free options with a set amount of storage (e.g. Dropbox). If you're reading this article it's most likely because you've experienced some sort of failure with data loss and are probably in a mild panic if you didn't have a backup. These cloud-based services are good options that run all the time without the typical hassle, and will help you avoid that feeling of panic thinking you lost all your photos, work, or whatever else it was on your hard drive. Definitely do your own due diligence on them to find the right one for you.

The much wider adoption of cloud-based services over the past 5+ years and a severe reduction in the cost to utilize those services make them a very viable option for you and I to protect our ever important data.