Should I stop using my Mac while the hard disk is being cloned?

As one of my backup solutions, I use an app (SuperDuper!, if it makes any difference) to make a clone of my Mac at the same time every evening. Sometimes I am still working at that time. What I want to know is: should I stop using my Mac while the clone is in progress? Why or why not?

Intuitively it seems that if a file is being modified while it is being copied to the clone drive that could affect the integrity of the backup. However, it would be good to have a definitive answer from someone who knows.

Thanks for reading.

Your instincts are correct.

If a file is being modified when the program reads it, you will end up with a copy of it in a transient state (or perhaps some programs like iPhoto that have a database that tracks files - the structure might not be correct to run with after a restore.)

This is why Time Machine makes two passes - it copies everything and then runs a second copy to pick up any files that were in the process of being modified during the first pass. Of course, a file under constant change might not get saved in either case, but it reduces the odds of a critically vital file that doesn't get changed often will be caught in a delicate moment.

To be safe, you want to boot to another OS (the recovery HD or an external drive) to run imaging if you need to ensure a perfect copy and all files being closed and flushed properly to storage.

I don't know if this applies to SuperDuper!, but here's a KB entry from Carbon Copy Cloner's website:

Can I run a backup while I'm using my computer? If I have open files, will they be backed up?

Yes and no, it really depends. Performance will be affected during the clone (especially the first one) as CCC reads the entire source volume and writes to the destination volume. If your work is "disk bound" -- that is your applications are reading or writing to either the source or destination, then you'll notice a performance hit. If you're just reading email or writing a Pages document, then you probably won't notice the performance hit.

Affecting the accuracy of the backup task is something else that should be considered. Typically it's OK to work from the source volume while you're copying it, with the understanding that if CCC copied a file, then you open it, make changes, save it, then CCC completes the backup task, the modified version of your document is not backed up (this time around). Typically that's no big deal, the modifications will get backed up the next time the backup task runs. More importantly, though, if you're working with large files (mounted disk image, Entourage email database, VMWare/Parallels container) during the backup operation, it is possible that those large files could be modified while CCC is backing up that file. This won't affect the source file, but there's a good chance that the backup version of that file will be corrupt. For this reason it is a good idea to stop using applications that may be modifying large files.