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Full Hard Drives and Drive Corruption

I recently read a disturbing note by a technician from MicroMat (the makers of TechTool Pro) regarding a potential drive corruption issue on Macintosh HFS and HFS+ volumes. In summary, if your hard drive (or a hard drive partition) is very full (>70% on HFS and >85% on HFS+ volumes) and is very severely fragmented, you run the risk of serious file corruption if you add any more files - ouch! However, before you get too worried, realize that the conditions under which this can occur are pretty extreme and require a huge amount of disk fragmentation, so it is really quite unlikely that you’ll ever run into this. See my detailed technical explanation here...

To make a long story short, the moral here is to avoid filling your hard drive partitions to capacity (luckily hard drives are cheap these days!) and use a disk defragmenting utility on a fairly regular basis. Micromat’s Drive10, Symantec’s Norton Utilities as well as Alsoft’s PlusOptimizer, included when you purchase the excellent DiskWarrior on CD, are ways of obtaining disk defragmenting tools. All are now compatible with OS X volumes but Norton Utilities and PlusOptimizer still need to be run while booted into OS 9. At this point, if you have OS X v10.2.2 (both client or Server) and have file-system journaling enabled (turned off by default), then it is not recommended to run a defragmentation tool (see the companies respective tech support departments for more information on this.)

After discussing this issue with a friend who’s a PC guru, I can reassure you Windows users out there that this specific technical issue cannot occur on PC hard drive file-systems. However, from a performance perspective, there are many good reasons why you should keep a decent amount of free space on your hard drives and keep them defragmented as well.

What the heck is actually going on...
(the long, technical version!)

The technical reason why this HFS/HFS+ corruption can occur requires a little background on how files are actually kept track of on a Macintosh disk drive. Each hard drive volume (complete drive or partition) has a Catalog B-tree (a type of database) of the files that are stored on the drive - images, documents, fonts, system files, every file on your hard drive has an entry in the Catalog B-tree database. The operating system uses this database to keep track of where these files are physically located on the drive volume. For example, when you double-click on a file to open it, behind the scenes, the MacOS is looking up the Catalog B-tree entry for the file you clicked in order to physically locate its data on the drive. If the file is fragmented, things get a little more complicated...

In order to understand what file fragmentation is, imagine the following scenario: Lets say you have a hard drive that is totally full - there is no more free space on it. You decide to free up some space because you have a 10 Mb image you want to save on that drive. You go ahead and delete ten individual 1 Mb files that you don't need anymore from that drive. Now there is enough room to store your 10Mb image. Well, those 10 files that you deleted were scattered all over your hard drive. Now, when you go and copy the 10Mb image over, the OS has to split it up into 10 different 1 Mb chunks in order to save it to the drive. No problem, the OS handles all this seamlessly for you - you never know that it's happened. All you know is that now your image has been successfully copied to the hard drive and everything is fine. Or is it...?

In this scenario, what would actually happen is that the positions of the first 3 chunks, or fragments of data, for this image will be kept track of by the Catalog B-tree. Since the Catalog B-tree is designed to only handle up to a maximum of 3 fragments per file, another database is called into play to handle any additional fragments - the Extents B-tree. When the Extents B-tree database starts getting very large, as it would on a severely fragmented drive, this file corruption issue can arise. What came as a surprise to me was that apparently the Macintosh operating system takes some error-checking shortcuts - potentially disastrous ones - when this Extents B-Tree grows large and the hard drive starts reaching capacity! Let me explain...

Imagine, in our little scenario, that those 10 files we deleted from the drive were not fragmented. This means that they would not have had entries in the Extents B-Tree since all the data for each file was being kept track of in the Catalog B-tree. Now we come along and copy this 10Mb image over and suddenly the OS has to keep track of 7 additional fragments in the Extents B-Tree - remember, the first 3 are being tracked in the Catalog B-tree. Well, our hard drive is now full, so there is no more room for the Extents B-tree to grow. So, rather than report an error and say the disk is full, the Macintosh OS simply overwrites 7 other entries in the Extents B-tree with the data locations for this 10Mb image that you've just copied to the drive! So effectively, the system has just clobbered some Extents B-tree data that it would need to find fragments for some other files elsewhere on the hard drive! So, the next time you try to open some other file, you might suddenly find that it's corrupt, even though it opened fine the last time around. Or, maybe even worse, if a critical system file gets clobbered, you may not even be able to boot your computer anymore! Not a very pretty picture, is it?

So why aren't we constantly having file corruption problems? Well, I oversimplified the above scenario but it serves to illustrate the point I think. Realistically, it is rare that a file will have more than 3 fragments and the Catalog B-tree, which stores the location of these first fragments, seems to be implemented in a more robust fashion than the Extents B-tree. Also, since the amount of data needed to keep track of fragment locations is generally tiny in comparison to the actual data being stored, there is usually plenty of room for the Extents B-tree database to grow to whatever size is needed. Problems will only occur with a severely fragmented drive where the Extents B-tree has grown to an enormous size and the hard drive has only many small "holes" scattered around the drive in which to store fragments for newly added files.

Because of all the variables involved, it is nearly impossible to say when exactly a problem such as this could occur. That is why it is not recommended to fill an HFS+ disk to more than 85% capacity since we generally don't keep track of how fragmented our hard drives are from day to day. If a drive has absolutely no fragmentation at all, then you could likely fill it to 99% capacity or more without encountering any problems whatsoever.

Why did Apple design things this way, you might be asking? Well, that's a good question and believe me, I've been asking myself this as well! I can only imagine that this software design decision, compromise, design flaw or whatever you want to call it, exists because somewhere along the line, many years ago, a software engineer decided that the possibility of this kind of file corruption was too remote and the speed benefits of performing less error checking on Extents B-tree operations were too appealing to pass up. Of course now, in order to retain full backward compatibility, it is likely difficult for Apple to engineer out this little problem without losing the ability to work with older HFS or HFS+ volumes. Hopefully they will find a way to address this issue in the future however...

On a positive note, I have read that under OS X, a freshly formatted drive has more room preallocated for its Catalog and Extents B-tree database files, so this problem may be less likely to occur.

Again, you shouldn't lose too much sleep over all of this. Just make sure that you are not filling your hard drive volumes to capacity and consider investing in one of the defragmentation utilities mentioned at the beginning of this article. Just don't start de-fragging you drives every other day - it really isn't all that necessary! Play it safe, backup your data frequently and you shouldn't have any problems.

Mike Mander
Beau Photo Supplies
November 2002

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