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I'm running geth on a distant linux Ubuntu machine, I have a total of 12Gb disk space, I thought that would be enough, but it wasn't. I only had the minimal LAMP settings, I installed Geth with these instructions, (I didn't check then but I'm not sure it took that much space). I started syncing and tried installing solC at the same time, and I reached size limit.

This is more of an open question because I can't seem to find convincing answer about WHERE the files are located when I run geth console or geth --testnet console. The chaindata folders are way too small, the whole .ethereum directory is only 2.1Gb. What is the difference between .ethereum/chaindata and .ethereum/geth/chaindata ?

Bottomline is is there plan of the geth file architecture for linux ? It seems to be everywhere and I have no idea how to delete everything. I'd also like to know why /usr/ got filled 5 Gb while all the blockchain data is in /<username>/.ethereum.

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12 GB is pretty tight for a full Ubuntu installation. And this issue is not fully related to Ethereum in first place. Let's answer this bottom-up:

I'd also like to know why /usr/ got filled 5 Gb while all the blockchain data is in ~/.ethereum.

/usr is where all your linux applications are installed to. Most likely /usr/bin or /usr/local/bin contains all binaries for your Ubuntu installation. 5GB is actually pretty small for a whole /usr directory. I just checked mine on ArchLinux and it's 6.4GB:

 $ du -sh /usr
6.4G    /usr

So, this has nothing to do with Ethereum in first place.

To cleanly remove all Ethereum data, all you need to do is

  1. Backup your keys in ~/.ethereum/keystore/ or ~/.parity/keys/.
  2. Remove everything in ~/.ethereum/ or ~/.parity/.

There is not much more to it.

And because you asked about the confusing directory structure: geth recently integrated a Swarm node and therefore the chaindata/ got moved from ~/.ethereum/ to ~/.ethereum/geth/. After launching and attaching a Swarm node, you will see there is a ~/.ethereum/swarm/ directory, too. That's pretty much it.

Whith one exception: If you have the Ethereum Wallet or Mist Browser installed, there are additional user data stored in ~/.config/Ethereum\ Wallet/ or ~/.config/Mist/ respectively. This contains logs and sometimes node binaries for geth (and/or eth).

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