Drive Genius 3 and OS X Yosemite
With Drive Genius 3, a native OS X disk repair application from Prosoft Engineering, you can thoroughly check a hard drive for both physical errors (such as faulty electronics or a bad sector on the disk surface) and logical errors (incorrect folder data and glitches in the file structure).
Disk Utility, which is included with OS X, does a fine job of checking the latter, but it doesn’t perform the physical testing — and Drive Genius 3 does both.
More than just about any other type of application, use a disk maintenance program built “from the ground up” for OS X. Never attempt to repair an OS X disk using an older repair utility that wasn’t designed for Yosemite.
Drive Genius 3 also takes care of disk optimization, which is a feature that’s been conspicuously absent from OS X since the beginning. Defragmenting a traditional magnetic hard drive results in better performance and a faster system overall. (Defragmenting shouldn’t be used on a solid-state [SSD] or Fusion drive.)
Drive Genius 3, which will set you back about $100, comes as both an application (that you download and use directly) and as a disc image that you can use to create a self-booting DVD-ROM; so if your Mac has an optical drive, you can easily fix your start-up volume by booting your system from the Drive Genius 3 disc.