[Discuss] Disk partitioning

[John Blomfield]

I have an Intel NUC mini desktop computer that has caused me to curse a 
lot and consider returning it. The symptoms have been for the BIOS to 
fail to recognize the Hard Drive intermittently.

My NUC has an SSD and a mechanical HD. The NUC comes as a barebones box 
to which you can add the RAM, SSD, HD, wireless card and no OS (no 
Windows). I chose it precisely because of this flexibility to. So I have 
16 GB RAM, a 250GB SSD (mSata) and a 1TB HD (SATAIII). It has a very low 
power consumption, no fans and almost silent.

Initially I installed Linux (OpenSuse) using Legacy MBR partitioning on 
the SSD and found that I could not get it to boot from the SSD MBR even 
after setting the boot priority for it to do so. It would only boot with 
the MBR on the HD, unless of course I removed the HD when it would then 
boot from the SSD. This was when the intermittent behaviour started. The 
BIOS would suddenly stop recognizing the HD so it then booted from the 
SSD. However the HD would be accessible by the OS. I also received boot 
messages saying that "an error had been detected on the HD". After 
running all the usual checks on the HD and finding nothing wrong I 
bought another HD anyway transferred all the data and updated the BIOS, 
which seemed to fix things for a few weeks. Then the trouble started again.

With the most up-to-date BIOS I moved the MBR to the SSD (which has the 
OS on it) using the HD just for data but I still got the HD error 
messages and an intermittent failure of the BIOS to recognize the HD 
(new or original). Then purely by chance I notice when I ran:

fdisk -l

I got warnings about the HD "Partition does not start on physical sector 
boundary" on several of the partitions. I found this link referencing 
the problem 
http://askubuntu.com/questions/156994/partition-does-not-start-on-physical-sector-boundary

The HD is in fact a Western Digital which accounts of the 4096 byte 
sector issue although its reported as 512 bytes. I noted that my first 
partition on the HD started at 63. Experimenting I found that this 
occurs when using GParted with the starting byte set at 0MiB. If you set 
it to 1 MiB it starts at sector 2048. By chance I had partitioned my SSD 
starting at 2048 sector which may be why I have not had a problem with 
that drive.

Anyway I fixed the HD to start at 2048 copied back all my data (took 
hours) and so far so good. No more error messages on the BIOS or when 
running fdisk -l. The BIOS also enables me to change the boot order as 
it should.

My question; why would a BIOS be so sensitive to the start byte on a HD 
when it works in every other way? When the HD is put in a external USB 
case, fdisk does not report and warnings about "physical boundaries". 
Maybe this is not the real problem? Any ideas?

John

-- 
John Blomfield
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