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TL;DR: Your home directory might be over its quota. Either move data from there to your research data directory or contact SESYNC cyberhelp for assistance.
Help! I’m locked out of the server!
If you try to log in to the RStudio or Jupyter server, enter your username and password, and then get an error message saying something like “Error occurred during transmission,” don’t panic. This is probably because your research home directory is above its quota. The quota is set to 20 GB per user by default.
Your home directory should not be used to store data. A relatively small disk space is set aside for all users’ home directories. Home directories are for code and software installations like R packages. See our cyber resources infographic to learn more about the difference between home and data directories.
But I didn’t put any data in my home directory!
It is possible that the quota can be exceeded by temporary hidden RStudio or Jupyter session files you might not even be aware of. In that case please contact SESYNC cyberhelp and we can help you troubleshoot and figure out ways to avoid that situation in the future.
But I don’t know how to move data without logging into the RStudio server first!
It’s possible to connect to the SESYNC server with SSH and move data between your home directory and research data directory using text commands on the command line e.g., if your username is jdoe you might have a directory called /research-home/jdoe/big-directory and you want to move it to your group’s research data directory, /nfs/cooltrees-data/. Open a terminal window (See: FAQ on accessing Linux resources if you don’t know how to access a terminal window on your computer.)
Log into the SESYNC server by entering the following command:
ssh jdoe@ssh.sesync.org
You’ll be prompted to enter your password and possibly add SESYNC to your list of known hosts. Once you do, you’ll be connected to the SSH gateway (sshgw00) on the SESYNC server. The current working directory will be /research-home/jdoe, which can be confirmed by entering pwd to see something like:
jdoe@sshgw00:~$ pwd
/research-home/jdoe
To find out how much space is being used by the subdirectories in your home directory, enter du -h --max-depth=1. It will list all top-level subdirectories and the space they are using to look something like:
jdoe@sshgw00:~$ du -h --max-depth=1
10M ./.cache
5M ./.local
1G ./R
100M ./.rstudio
40K ./.ipynb_checkpoints
35G ./big-directory
36G .
The final line shows the total across all subdirectories.
To copy big-directory to your group’s data directory, enter:
cp -r /research-home/jdoe/big-directory/ /nfs/cooltrees-data/big-directory/
The cp means copy, and the -r means recursive so it will copy the entire directory and everything in it.
Once this is finished (it will take a few minutes if it’s a big folder) delete the one on your home directory:
rm -rf /research-home/jdoe/big-directory/
Here the rm means remove (i.e., delete), and the -rf is an option that ensures everything inside that directory will be deleted. If your home directory is under the quota of 20 GB you will be able to access all SESYNC resources again!
I’ve tried everything and I still can’t log in! What do I do?!? Email SESYNC cyberhelp
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