"Disappearing" HDD when booting

[macstatic]

Now and then I experience something quite alarming and odd when I power up my Mac Pro (model 5,1, 2010, 2.8GHz quad core running OSX 10.6.8): my main hard drive is missing! In other words the Finder disk icon is gone and I get all sorts of "not found" error messages (which I believe are totally legit as this is my "user" drive where I keep all my settings and files).
But if I restart the computer the drive mysteriously reappears and everything works as before!

My Mac Pro is set up with multiple internal hard drives:

• System (an SSD with OSX, all my apps, administrator user area)
• Time Machine (regular Time Machine backups)
• User (my main user area with all my files, settings etc.)
• Emergency backup (a bootable clone of all my drives (using Chronosync) which is automatically done every 2-3 hours)
• Cache (SSD used for Lightroom, Photoshop, Adobe Bridge etc. cache and temporary files)

It's the "User" drive that has had the problems mentioned above, and it happened again today. I decided to try running Disk Utility when the drive had disappeared but couldn't get it to launch. Most likely because I use Alfred for keyboard shortcuts, and my settings were on that drive. I should have launched it directly from the /Applications/ folder on my system drive instead, silly me, to see if the drive was unmounted or simply not there. I'll see about that next time.

S.M.A.R.T. status is OK, but then again I have had past experiences with drives that show "OK" but in reality are starting to fail (resulting in several corrupt files). Could the drive be failing? What do you suggest I do?

 

[Intelligent]

The drive could very well be failing, is it new? Or the hard drive connectors might be broken, SATA/whatever where you put the drive. Do a Backup, (you mention you already do) and if the problems persist, try another hard drive in the same slot, and if that works then its probably your drive.

 

[macstatic]

No, not new. I bought my 2010 Mac Pro used in 2012 and this was the drive that sat inside. What's the general lifespan of drives these days? The drive would have been used around 4 years then. All my other internal drives were bought new by me and are working perfectly.

I've just moved the drive to another bay as you suggested, swapping it with another one to see if the problem persists (or if the other drive suddenly disappears).
Yes, I do take regular backups (I also do (more seldomly though) backups to external drives in addition to the (several times daily) Time Machine and bootable cloning backups, just in case the computer gets stolen etc.), but what worries me is if this drive is slowly failing intermittently I'll get corrupt files which the backups will just copy.
I've experienced this happening to an iMac where things worked fine for a while, then suddenly acted up only to return to its normal state again. The S.M.A.R.T. status showed fine though, so apparently it can't be trusted all the time.

By the way, if I do need to replace the drive, will the Mac Pro 5,1 (2010) take 4TB drives or is there a size limit to the SATA interface? The drive I suspect to be failing is a 3TB Seagate ST3000DM001.

 

[Intelligent]

Yep, a 4 year old drive could be broken. Im pretty sure that theres no max space for Mac Pro hard drives but there is a speed limit. And your files getting corrupted, that doesn't have anything to do with what slot it is in, could you define "corrupted files"?

 

[h9826790]

will the Mac Pro 5,1 (2010) take 4TB drives or is there a size limit to the SATA interface?

4TB HDD is not a problem at all.

 

[macstatic]

Hey, that's a pretty hot hex-core you have there, h9826790! Did you upgrade it yourself by changing the CPU? Thanks for confirming that 4TB works fine.

Intelligent: I wasn't referring to my Mac Pro when talking about those corrupt files, but my wife's iMac. We were having strange problems which were very hard to troubleshoot (it seemed like a hard drive problem but all of a sudden everything was working perfectly again). It took a while to figure out but in the end an Apple tech found out it was the drive which he then replaced. It's been working great ever since. I even checked the SMART status which showed "OK", so that wasn't much help.
As for the corrupt files: there were some image files which I know were fine in the camera, but having transferred them over to the computer and viewing them later I see the transfer must have been during one of the computer's "moody hard drive" periods, so they were only partly viewable. The same thing happened with some video files which were taken and transferred during that time period and were missing audio. I knew they were OK in the camera (a different camera from the above). Unfortunately this meant that all my backups also had the bad copies on them because they were simply copies of the memory-card imports on to that bad drive.
There might have been some damaged text files as well, but I can't remember. Frustrating, but it could have been much worse.

 

[h9826790]

Yes, I did the upgrade by myself. There is no such CPU upgrade option from Apple. You can do this upgrade as well, the CPU required is W3690. The process is very straight forward.

 

[Intelligent]

How did it go with trying another slot, did it fix it? Otherwise id suggest you buy a new hard drive.

 

[macstatic]

I haven't had any more incidents since I posted, but then again this has only occured now and then (sorry to say I haven't taken note of each time but I believe it's been weeks between each time). However, it has been a reoccuring thing which tells me something is wrong.
Yes, if it happens again, with the same drive I'll have to buy another drive.

 

[macstatic]

It happened again yesterday!
All of a sudden I got a "The disk was not ejected properly" error message, my email app crashed and all desktop icons also vanished after a little while.
I noticed that the desktop drive icon was gone as well (same drive as last time, even though it was moved to another slot), so I decided to run "Disk utility". Sure enough the drive wasn't there.

Next thing I did was to log out and in again but I wasn't able to log in, so I decided to do a restart and see what happened. I wasn't able to do that either (the "busy" throbber kept spinning indefinitely) so the only thing left to do was force a shutdown (press and hold the physical power button for several seconds). After that was done I waited a couple of seconds, turned on the computer and I could log in as usual. Everything seemed like nothing had happened and everything worked again.
I started Disk utility once again to check the drive and everything showed up OK.

So, now that I had moved the drive to another slot and this has happened again, does it sound like the drive is about to die or could it be something else? Has anyone else experienced similar things?