Usually when I come across a system like this, Ijust flash the firmware to an IT mode so we get just an AHCI system with JBOD, but sometimes it is not practical for remote systems or if we fear that flashing is too risky if something goes wrong.
In this case, we unfortunately have to use LSI/Broadcom proprietary CLI tools (megacli) to even make the drives visible.
Step 1 - Download MegaCLI
The official broadcom packages lack .deb packages and only have .rpm for........
Even in new versions of Ubuntu this happens but for me I found out it was because of one feature under "Power Management".
I had "Spindown hard disks when possible" ticked, after disabling that, my computer wakes up from suspension every time now. So if your computer won't unsuspend with any version of Ubuntu/*Nix try disabling the spin down hard disk option as it's obviously the culprit for many situations.........
hdparm -B 255 /dev/sdb
/dev/sdb:
setting Advanced Power Management level to disabled
HDIO_DRIVE_CMD failed: Input/output error
The one thing you can do though is to set hdparm spindown time lower (it doesn't seem to work that well).
-S set standby (spindown) timeout
hdparm -S 251 /dev/sda
/dev/sda:
setti........