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Can I take a backup of Oracle home directory (with cp -r) before upgrade while the instances using the home are running or is it required to shutdown instances first?

Trace files/alert logs are in different directory structure and all data files, redo log files, control files and spfiles are in ASM.

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Yes you can do that. There's nothing dynamically changeable here in normal circumstances. All the files here are not touched except in case you apply some patch.

Files specific to the particular database resides in:

$ORACLE_HOME/dbs
$ORACLE_HOME/network/admin

I do that now and then to create test environment. Just for such more complex directory structure I prefer rsync. With it you can resume copying if you run into some disk space or network issues.

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