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strange behaviour after upgrading from Jessie to Stretch



My "server" is a bit of an antique. It's a Gigabyte MA790GP-UD4H with a Phenom II 940 processor, an SSD and 4 2T drives in a RAID 6 array plus 8G of DDR2 ram.

A while back I found it necessary to add a Vantec PCIe SATA 6Gbps card with 2 internal SATA ports after ports 4 & 5 on the motherboard stopped recognizing the drives attached to them. It's been running with that configuration for at least a year.

This morning I upgraded from Jessie to Stretch and things went haywire. I could successfully boot into the system using SystemRescueCD but the 2 drives attached to the add-in card weren't recognized. My RAID 6 array was running degraded on the two drives attached to ports 2 & 3. Attempts to boot into Debian/Stretch were largely unsuccessful, with the computer usually locking up after reporting an error on an ATA device.

After a lot of fiddling I discovered that the HDs themselves were all OK but could only be accessed using SATA ports 0 - 3. However my boot/system SSD and the BluRay writer both operate fine off of ports 4 & 5. They also work when attached to the add-in card. I removed the add-in card and it now successfully boots into Debian/Stretch.

Both SystemRescueCD and Debian/Stretch are using 4.9 kernels but the former seemed able to boot while the latter wouldn't. I'm also confused by the problems I've been having with HDs not working when attached to some ports. Can any hardware gurus explain what's going on?


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