[Discuss] Disk partitioning

[Alan W. Irwin]

On 2015-05-02 16:30-0700 John Blomfield wrote:

> 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?

Hi John:

I ran into the issue of partitions not starting on physical sector
boundaries a couple of years back, and my understanding at the time
was it was important to solve the issue because of efficiency
concerns.  Also, I am not too surprised that a BIOS might not produce
very good results in that situation; BIOS firmware is notorious for
being simple-minded.

One result you got that surprised me was fdisk quit complaining about
the partitioning if you accessed the drive externally. Maybe you have
a smaller physical block size = logical block size for that particular
way of accessing the disk? But that different result doesn't really
matter; if fdisk starts complaining about partitioning in any context,
I would pay close attention and fix the issue like it appears you have
done in this case.

Alan
__________________________
Alan W. Irwin

Astronomical research affiliation with Department of Physics and Astronomy,
University of Victoria (astrowww.phys.uvic.ca).

Programming affiliations with the FreeEOS equation-of-state
implementation for stellar interiors (freeeos.sf.net); the Time
Ephemerides project (timeephem.sf.net); PLplot scientific plotting
software package (plplot.sf.net); the libLASi project
(unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
and the Linux Brochure Project (lbproject.sf.net).
__________________________

Linux-powered Science
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