Linux – APIC error on CPU1: 60(60) in dmesg what does it mean

It's AppArmor loading it's profiles as applications start up.

For those that don't know, apparmor is similar to selinux in that it monitors and restricts based on a set of profiles, usually configured in /etc/apparmor.d.

The log entries you are seeing are good log entries and are showing that AppArmor is loading up and doing it's thing. Generally you can ignore them but it's always a good idea to remember AppArmor exists as it can bite you.

e.g. I reconfigured MySQL on a Ubuntu system to use /home/mysql for its data files and it wouldn't start, because AppArmor was blocking access to it. The MySQL logs just said "Permission Denied", whereas syslog told me that AppArmor was stopping it.

I would use rsync as it means that if it is interrupted for any reason, then you can restart it easily with very little cost. And being rsync, it can even restart part way through a large file. As others mention, it can exclude files easily. The simplest way to preserve most things is to use the -a flag – ‘archive.’ So:

rsync -a source dest

Although UID/GID and symlinks are preserved by -a (see -lpgo), your question implies you might want a full copy of the filesystem information; and -a doesn't include hard-links, extended attributes, or ACLs (on Linux) or the above nor resource forks (on OS X.) Thus, for a robust copy of a filesystem, you'll need to include those flags:

rsync -aHAX source dest # Linux
rsync -aHE source dest  # OS X

The default cp will start again, though the -u flag will "copy only when the SOURCE file is newer than the destination file or when the destination file is missing". And the -a (archive) flag will be recursive, not recopy files if you have to restart and preserve permissions. So:

cp -au source dest