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.
If you try to log in to the RStudio or Jupyter server, enter your username and password, and then get an error message that says 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.
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.
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. For example, 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 on your computer. (See our FAQ on accessing Linux resources if you do not know how to access a terminal window on your computer.)
Log into the SESYNC server by entering the following command:
You will be prompted to enter your password and possibly to add SESYNC to your list of known hosts.
Once you do, you will be connected to the SESYNC server and the current working directory will be
/research-home/jdoe, which you can confirm by entering
pwd. You will see something like:
jdoe@sshgw02:~$ pwd /research-home/jdoe
To find out how much space is being used by the different subdirectories in your home directory, enter
du -h --max-depth=1 and it will list all the top-level subdirectories and how much space they are taking up. It might look something like:
jdoe@sshgw02:~$ 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.
big-directory to your group’s data directory, enter:
cp -r /research-home/jdoe/big-directory/ /nfs/cooltrees-data/big-directory/
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/
rm means remove (i.e., delete), and the
-rf is an option that ensures everything inside that directory will be deleted.
Now if your home directory is under the quota of 20 GB you will be able to access all SESYNC resources again!
Please email SESYNC cyberhelp and we will be happy to assist you.