Q: "Macintosh HD" partition is not mounted properly

There might be bad sectors on the drive.

I tend to use SpinRite to solve and prevent disk issues. It's a life saver.

https://www.grc.com/sr/spinrite.htm

I don't think Parallels messes with the existing partitions, at least it shouldn't.

I'm no expert on core system functionality but it almost seems as if the disk is ok.

The system will correctly boot but then the index table of the OS itself is messed up.

I don't know the specifics of UNIX mounting or OS X volume indexing to give you any answers.

Interesting tho!

I think the OS indexing/reading of the disk info itself is messed up.

Did you use Disk Utility from the recovery/DVD or in OS X self? Try the recovery one.

Back up all data immediately if you haven't already done so.

Please read this whole message before doing anything.

This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.

The purpose of the test is to determine whether the problem is caused by third-party software that loads automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.

Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards, if applicable. Start up in safe mode and log in to the account with the problem.

Note: If FileVault is enabled in OS X 10.9 or earlier, or if a firmware password is set, or if the startup volume is a software RAID, you can’t do this. Ask for further instructions.

Safe mode is much slower to start up and run than normal, with limited graphics performance, and some things won’t work at all, including sound output and Wi-Fi on certain models. The next normal startup may also be somewhat slow.

The login screen appears even if you usually login automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.

Test while in safe mode. Same problem?

After testing, restart as usual (not in safe mode) and verify that you still have the problem. Post the results of the test.

I suggest you back up all data, then turn off FileVault. If that's successful, try turning it back on.

While you could spend hours monkeying around with partition tables, corestorage setups, and volume formatting routines, your best bet here is going to be to set up your drive from scratch. The Fusion Drive is a combination of two separate hard drives (an SSD and a HDD--your SSD is disk0 and your HDD is disk1, with the corestorage volume being disk2 in the "diskutil list" output above), and thereby employ both classic partitioning and corestorage volume management to provide your Mac with a single storage medium upon which to store OS X and your data.

It appears you have some corruption in your Mac's corestorage setup. If you want, you can run the following command to see the structure of corestorage on the systems:

     diskutil cs list

However, I suspect this is not going to give any details that will help address this problem. Ultimately, if you back up your system and format it, then you will ensure the drive's setup is healthy. To do this, after backing up your Mac, boot to Recovery mode by holding the Command-R keys at startup, and then use Disk Utility to erase the partition on there. For fusion drives on supported Macs (those that ship with Fusion drives), Disk Utility should clear the corestorage partition and rebuild the Fusion drive setup. You can then use either OS X's backup recovery tools, or your cloning software, to restore OS X to the system.

Above everything, though, be sure you get your files backed up.

Apple has not provided an easy way to recover from this condition. If you don't feel able to carry out these instructions, get someone more experienced to help you. One option is to make a "Genius" appointment at an Apple Store.

You need at least two complete, independent backups of all data before proceeding. There are ways to back up a computer that isn't fully functional. Ask if you need guidance.

Start up in Internet Recovery mode by holding down the key combination command-option-R at the startup chime. Release the keys when you see a spinning globe.

Note: You need an always-on Ethernet or Wi-Fi connection to the Internet to use Recovery. It won’t work with USB or PPPoE modems, or with proxy servers, or with networks that require a certificate for authentication.

When the OS X Utilities window appears, select

          Utilities ▹ Terminal

from the menu bar at the top of the screen—not from any of the items in the OS X Utilities window.

Follow the procedure in this thread to split up the Fusion Drive. The long string of letters, numbers, and dashes that you will have to enter will be different in your case. Copy and paste it from the Terminal window into the command.

This operation will remove all data from the Fusion Drive, so you had better be sure of your backups.

Quit Terminal, then repair the Fusion Drive (see under "Troubleshooting" on the linked page.)

Quit Disk Utility. You should then be able to restore the data from a backup in the main screen.

There are several ways to back up a Mac that is not fully functional. You need an external hard drive or other storage device to hold the data.

1. Start up from the Recovery partition, from Internet Recovery, or from a local Time Machine backup volume (option key at startup.) Launch Disk Utility and follow the instructions in this support article, under “Instructions for backing up to an external hard disk via Disk Utility.” The article refers to starting up from a DVD, but the procedure in Recovery mode is the same. You don't need a DVD if you're running OS X 10.7 or later.

If you use FileVault 2, then you must first unlock the startup volume. Select its icon ("Macintosh HD," unless you gave it a different name.) It will be nested below another disk icon, usually with the same name. Click the Unlock button in the toolbar. Enter your login password when prompted.

2. If Method 1 fails because of disk errors, then you may be able to salvage some of your files by copying them in the Finder. If you already have an external drive with OS X installed, start up from it. Otherwise, if you have Internet access, follow the instructions on this page to prepare the external drive and install OS X on it. You'll use the Recovery installer, rather than downloading it from the App Store.

3. If you have access to a working Mac, and both it and the non-working Mac have FireWire or Thunderbolt ports, start the non-working Mac in target disk mode. Use the working Mac to copy the data to another drive. This technique won't work with USB, Ethernet, Wi-Fi, or Bluetooth.

4. If the internal drive of the non-working Mac is user-replaceable, remove it and mount it in an external enclosure or drive dock. Use another Mac to copy the data.