pvdamme

Alright, so far everything seems to be under control.
 
I'll do a short recap and mark this post as the solution so it might help people who come across the same problem.
 
The issue
I restarted my router which lead to Unraid to become inaccessible over ethernet. Unraid could still be accessed by attaching a monitor and keyboard to the server. Running "ifconfig eth0 down && ifconfig eth0 up" restored network access All disks connected through my PCI-E SATA (ASM1166) adapter were listed as "missing" and the log displayed SATA Link errors A regular reboot did not restore the drives but a shutdown and restart did restored everything back to normal. The cause
When the router reset, the network adapter on my motherboard (ASUS Prime N100I-D D4), a Realtek Gigabit Ethernet controller entered a power saving state couldn't wake up by what I can tell. Since, all drives attached to the SATA adapter were spun down, nothing kept all the PCI stuff from going to sleep as well. This appears to cause the SATA Link errors and I could not figure out how to recover from this state other that doing a full shutdown and restart (reboot doesn't work) The solution
I was aware of issues with ASM1166 SATA adapters so I didn't use powertop auto tune, but instead used the script provided by @mgutt and adapted it. Everything appeared to work fine until I restarted my router, which I don't do often. (Pulling the ethernet cable will cause the same issue) So I went through the script, turned things on and off and discovered that by not setting the power management of the network adapter to auto, everything works fine and c states are still working alright.  Quick way to find the device address of the network adapter is by going to the tunable section of powertop and tuning the device. The path, which includes the address, is listed at the top of the window, which in this case was "/sys/bus/pci/devices/0000\:03\:00.0/power/control" The simplest way to change everything to auto but this one device I could think of was to turn everything including it to auto and then removing it from this one device again and then setting it to "on" (There is probably a better way but this is simple and works):  
# Runtime PM for PCI devices echo auto | tee /sys/bus/pci/devices/????:??:??.?/power/control > /sys/bus/pci/devices/0000\:03\:00.0/power/control echo on | tee /sys/bus/pci/devices/0000\:03\:00.0/power/control  
 
Some notes
So if you happen to have the same hardware as I do, the following version of the script might work for you as well:
 
# ------------------------------------------------- # Set power-efficient CPU governor # ------------------------------------------------- /etc/rc.d/rc.cpufreq powersave # ------------------------------------------------- # Disable CPU Turbo # ------------------------------------------------- #[[ -f /sys/devices/system/cpu/intel_pstate/no_turbo ]] && echo "1" > /sys/devices/system/cpu/intel_pstate/no_turbo [[ -f /sys/devices/system/cpu/cpufreq/boost ]] && echo "0" > /sys/devices/system/cpu/cpufreq/boost # ------------------------------------------------- # Enable power-efficient ethernet # ------------------------------------------------- # enable IEEE 802.3az (Energy Efficient Ethernet): Could be incompatible to LACP bonds! for i in /sys/class/net/eth?; do dev=$(basename $i); [[ $(echo $(ethtool --show-eee $dev 2> /dev/null) | grep -c "Supported EEE link modes: 1") -eq 1 ]] && ethtool --set-eee $dev eee on; done # Disable wake on lan for i in /sys/class/net/eth?; do ethtool -s $(basename $i) wol d; done # ------------------------------------------------- # powertop tweaks # ------------------------------------------------- # Enable SATA link power management echo med_power_with_dipm | tee /sys/class/scsi_host/host*/link_power_management_policy # Runtime PM for I2C Adapter (i915 gmbus dpb) echo auto | tee /sys/bus/i2c/devices/i2c-*/device/power/control # Autosuspend for USB device echo auto | tee /sys/bus/usb/devices/*/power/control # Runtime PM for disk echo auto | tee /sys/block/sd*/device/power/control # Runtime PM for PCI devices echo auto | tee /sys/bus/pci/devices/????:??:??.?/power/control > /sys/bus/pci/devices/0000\:03\:00.0/power/control echo on | tee /sys/bus/pci/devices/0000\:03\:00.0/power/control # Runtime PM for ATA devices echo auto | tee /sys/bus/pci/devices/????:??:??.?/ata*/power/control # Activate ASPM for some devices setpci -s 03:00.0 0x80.B=0x42 setpci -s 00:1c.6 0x50.B=0x42  
In powertop, it looks like this on the tunables:

 
And like this for the c-states under idle stats (which I think is quite alright)

 
I hope my struggle with this problem will help others.