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I had troubles with my client on a Raspberry because it was using the wrong configuration file and I could not find any entry in the configuration file that referred to the right location of the data directory, but I knew it was beeing used correctly in the past.
I was trying to use -printtoconsole to debug the problem but that did also not work.
On command line bitcoin can be started in several ways
bitcoind starts a process with the current user. This way the home directory of this user will be searched for a config file and will be used as data directory as default.
service bitcoin start will use the startup script /etc/systemd/system/bitcoind.service. This might contain a link to a configuration file. In my case this config file did not contain of a data directory which I found troubling. But the solution is that it contains a user. This user's home directory is then automatically referred to.
So, in my case I was using the terminal as user pi and had to start the process as user bitcoin instead. This can be done by
sudo runuser -l bitcoin -c 'bitcoind'