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My system has been running smoothly, with no changes for months, but this morning when I turned it on it hung on AHCI init.

I narrowed it down to being some kind of issue with my second HDD (boot drive is SSD), it would boot fine with the second HDD unplugged.

Strangely, if I plug in the second HDD after windows has started (at login screen) it is detected and seems to run fine. But, on reboot, the same issue occurs (still, can hot plug at login screen).

I assume my hard disk is starting to fail, so I should replace the drive ASAP. But I cannot find much about this kind of issue (all I read is about installing windows and drivers - this is a bios thing).

Are there any other causes? Or is my drive on its final legs.

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The very first thing you should do is to run S.M.A.R.T. test of your drive.

There are many Windows graphics utilities which can use SMART. I actually prefer to use command line smartctl utility from smartmoontools (they have Windows executable as well). Passmark has free graphical tool which can provide pretty much the same information as smartctl: DiskCheckup, but probably easier to use.

SMART test should give you report like this:

smartctl -a /dev/sda

SMART Attributes Data Structure revision number: 16
Vendor Specific SMART Attributes with Thresholds:
  1 Raw_Read_Error_Rate     0x002f   200   200   051    Pre-fail  Always       -       0
  3 Spin_Up_Time            0x0027   216   147   021    Pre-fail  Always       -       6158
  4 Start_Stop_Count        0x0032   100   100   000    Old_age   Always       -       75
  5 Reallocated_Sector_Ct   0x0033   200   200   140    Pre-fail  Always       -       0
  7 Seek_Error_Rate         0x002e   200   200   000    Old_age   Always       -       0
  9 Power_On_Hours          0x0032   056   056   000    Old_age   Always       -       32390
 10 Spin_Retry_Count        0x0032   100   253   000    Old_age   Always       -       0
 11 Calibration_Retry_Count 0x0032   100   253   000    Old_age   Always       -       0
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       74
192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always       -       72
193 Load_Cycle_Count        0x0032   200   200   000    Old_age   Always       -       303
194 Temperature_Celsius     0x0022   100   087   000    Old_age   Always       -       52
196 Reallocated_Event_Count 0x0032   200   200   000    Old_age   Always       -       0
197 Current_Pending_Sector  0x0032   200   200   000    Old_age   Always       -       0
198 Offline_Uncorrectable   0x0030   200   200   000    Old_age   Offline      -       0
199 UDMA_CRC_Error_Count    0x0032   200   200   000    Old_age   Always       -       0
200 Multi_Zone_Error_Rate   0x0008   200   200   000    Old_age   Offline      -       0

If there is any metric with low value (below 100 or close to threshold), then it is reason to worry. Especially troublesome are metrics UDMA_CRC_Error_Count, Multi_Zone_Error_Rate, Reallocated_Event_Count, Current_Pending_Sector, Offline_Uncorrectable - they should be exactly 0.

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Ran a test, it looks to be okay to me (first time looking at SMART other than just Pass/Fail status!) – Adam Heath Sep 28 '13 at 4:21
You have red flags: G-Sense_Error_Rate=3 (g-sense is number of errors caused by externally-induced shock or vibration), and Multi_Zone_Error_Rate=3 - typically, if it is not 0, I would be very worried. – mvp Sep 28 '13 at 4:25
Looks like I shall be going shopping for a replacement drive then! Thanks so much for your help :) – Adam Heath Sep 28 '13 at 4:26
One more thing to try - run long smart test using smartctl /dev/sda -t long - it takes 2-3 hours, but can find more serious issues – mvp Sep 28 '13 at 4:32
Thanks @mvp running it now and will see what it says. – Adam Heath Sep 28 '13 at 4:37

Check the disk for bad sectors. If the HD's ok, check to see if there are any updated device drivers for the HD.

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CHKDSK showed no errors. The hard drive seems to be working okay, I can access all just won't boot while plugged in :( – Adam Heath Sep 28 '13 at 4:26
Have you checked the settings in the hardware BIOS/UEFI? It seems as if your SSD could be set up as the primary hard disk. – Frank R. Sep 28 '13 at 4:29
Yup my SSD is primary and my boot disk. So my computer can thankfully boot to Windows without the second HDD. – Adam Heath Sep 28 '13 at 4:36

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