HDD not being detected by AHCI after HDD cloning; only by IDE

Question

I've done a 1:1 HDD copy, containing Ubuntu 16.04, from a IDE drive to a 1 TB SATA HDD, using Clonezilla. The 1 TB HDD was previously used for Windows.

The 1 TB HDD isn't being recognized by the BIOS anymore, if the controller is set to AHCI. (But it works if the controller is set to IDE.) It stalls on "detecting AHCI Port XXX", in which Port, does not matter at all. AHCI recognition used to work, as long Windows was installed (NTFS). It also recognizes FAT32 Drives without problems.

Since this is the second hard disk which fails after being cloned/filled with an Ext4 file system (the previous one that I've tried was a smaller SATA HDD), I ask myself if the AHCI drive recognition routine needs additional information from the hard disk in order to give the "ok" to boot and if there is no NTFS/FAT32, it stalls.

Machine used is a Q6600, 8GB RAM, ASUS P5K Pro, latest BIOS. In addition, the BIOS also contains Asus EZFlash, which uses NTFS/FAT32/FAT16 routines to access the BIOS update files on USB flash drives or CDs. Maybe the AHCI routine uses the file system access routine from EZFlash.

Is this problem a common error with "older" AHCI controllers? Or any suggestions?

Answer 1

The problem is a bug in the BIOS. It happens to some computers which use the ICH9 chipset (mabye others too). The BIOS routines search on offset 0x1c3 on the hard disk for the end address of the entire HDD and if these do not match a certain value (FE FF FF), the entire routine hangs with "Detecting AHCI Port XXX....". Resizing the partition to the max did the trick. Filling with "FE FF FF" at 0x1C3 not, GRUB did not like that at all and refused to come up.

I ask myself why the AHCI routines have to get their information from the HDD Surface instead of flash entries of the HDD controller.

Answer 2

I have had a similar problem. First try new SATA cable, switch around. I've had bad cables also dirty terminals on board and HDD. Also power to HDD both bad/dirty.

I'm assuming your clone file is good. Can you test it?

If your original HDD boots up fine with your new Bios flash then I would install both HDDs. I would format the HDD in question (NTFS). Test it, if fine make a bootable flash with Ubuntu. Set up a dual boot HDDs. Reboot to install Ubuntu. If it runs fine, then setup your partitions the why you like.

I have read about bad bios updates, but never dealt with it. If this happened after that.