FAQ: Software

Q: How do I compile my own software on the HPC

A: Our Software Installation Guide will provide you with the information on how to compile your own software on the HPC.

Q: How do I add my own Python modules or R packages?

A: We have provided specific instructions on installing additional Python modules and R packages in your own home directory. Additionally, on Python, you can also opt to build your own Python virtual environment.

Q: I work with both R and Python at the same time. Can I use RStudio and Spyder simultaneously in the HPC Cluster?

A: Yes, you should reserve a compute node with enough resources and, within the gcc/6.3.0 + openmpi/2.0.1 hierarchy, you should be able to run both at the same time. It is recommended that you use two different terminal sessions: once you have allocated enough resources and after getting an interactive session, you can directly SSH into the corresponding compute node from a new terminal session.

Q: My Jupyter Notebook will not launch and says "database locked"

A: This can happen if something interferes with Jupyter while it is modifying data that tracks notebooks (e.g. if the hard quota is reached in the middle of launching a notebook). We recommend you try the following:

1. End your current Jupyter session

2. mv $HOME/.local/share/jupyter $HOME/backup_jupyter

3. Start a new Jupyter session and try to launch start a Notebook

If you have kernels in $HOME/.local/share/jupyter/kernels you might want to put those back depending on if they are important.

This issue has been reported on github: https://github.com/jupyter/nbformat/issues/52 and you may want to review the discussion depending on your use case.