You should synchronize your backup (copy).  Try surrounding it with an 
exclusive transaction.

Stan Bielski wrote:
> Sorry for the repost, but the original thread was hijacked by another
> list user. This is a serious problem IMHO; it looks like the DB can't
> be backed-up without rendering the machine unusable if a query hits it
> while a copy is in progress.
>
> Hello,
>
> In the course of copying a largish (20 GB) database file while
> accessing it via sqlite3, the machine became very unresponsive. I
> opened task manager and found that the system was using a huge amount
> of virtual memory, causing it to thrash. Per-process memory usage
> looked normal and did not add up to anywhere near system-wide VM
> usage.
>
> I ran into this issue at a customer site and was able to reproduce it
> using a local Windows 2008 installation. I have not installed any
> backup software or a virus scanner. Storage is local disk, SQLite
> version is 3.3.17.
>
> At first I thought that this was a general Windows problem involving a
> process accessing a file that is being copied, but other binaries I
> tested do not cause the same behavior that sqlite3 does. I performed
> the following experiments to try to diagnose the issue.
>
> Case 1:
>
> * I copy a 20 GB sqlite DB using Windows' own copy utility (e.g. via 
> explorer).
> * At any point during the copy, I open the file being copied in sqlite3
> * I exit sqlite3.
> * During the rest of the copy the OS will consume virtual memory
> linear (seemingly identical) to the amount of data copied since the
> process opened the file.
>
> I repeated this experiment using a similarly-sized file created from
> /dev/zero (i.e. an invalid DB) and the results were the same.
>
> Case 2:
>
> * I copy the sqlite DB using Windows' own copy utility (e.g. via explorer).
> * At any point during the copy, I run 'strings' with the file as an argument.
> * I exit strings.
> * The copy does not result in the OS consuming additional virtual memory.
>
> Case 3:
>
> * I open the DB in sqlite3
> * I let sqlite3 idle and do not input any commands.
> * I copy a sqlite DB using Windows' own copy utility (e.g. via explorer).
> * I continue to let sqlite3 idle and do not input any commands.
> * During the rest of the copy the OS will consume virtual memory
> linear (seemingly identical) to the amount of data copied since the
> process opened the file.
>
> Is there a workaround for this issue? Any assistance or info is appreciated.
>
> Thanks,
> -Stan
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