This thread is a tad old, but I dislike leaving threads hanging. That is almost as bad as the suits at the SyFy channel suspending episodes for three and half months during the middle of the winter.
When I posted this problem I had little time to troubleshoot because of a busy schedule. Basically I tolerated the problem for several months, but I was using the computer only a little bit during that period.
Last month I finally had meaningful time to investigate.
Sometimes I would see the freeze two or three times in one day. Sometime I'd go two days without a hiccup. I don't recall surviving longer than two days.
Sometimes I'd see the freeze when running VirtualBox. I decided that was not the cause because I'd see the freeze when I was not running VirtualBox. Further, whenever I saw the freeze I always saw something in the system logs. When VB freezes for many long seconds there would be nothing in the logs.
I tried many things. I tested RAM over night. I ran many short and long SMART tests. I ran fsck many times. I swapped cables. I swapped SATA ports.
I did notice something strange. I never had a problem with any drive connected to the SATA 2 port. I always saw some kind of freeze with any device connected to SATA ports 1, 3, or 4. The logs always verified that behavior.
In the end I decided I likely had a funky SATA port controller or possibly something like sold solder joints. There is the possibility of a problem with the sata_nv driver in the kernel too. I really don't know the root cause.
Yet all was not lost.
In my many tests I also tried various kernel parameters. The one parameter that proved successful was libata.force=1.5Gbps
. That parameter limited the SATA ports to 1.5 Gbps rather than allow them to run at 3.0 Gbps. After many days of quiet with that boot parameter, I next fine-tuned the limitation: libata.force=1:1.5Gbps
. This limited only SATA port 1 to 1.5 Gbps. After all, SATA port 2 did not have the problem.
As I never saw an error report in the logs related to SATA port 2, I left that second drive running at 3 Gbps. Only the primary drive at port 1 is throttled. Pleasantly, the machine has not experienced a freeze for about a week now.
I am presuming the problem is solved, but I won't tag the thread as such because I don't know the true root cause of the problem. Nonetheless, I hope this information helps others.