Gadi FAQs

Gadi FAQs#

Debugging:

How to debug issues with gadi jupyter

The script submitted to PBS and the PBS logs are saved under the directory tmp/runjp directory under the user’s /scratch directory for the group used to run the script. These will often have more information if the script was started alright but you can’t seem to be able to connect to the Jupyer Notebooks. This usually happens when the job started alright but exited due to an error in the script.

For example, let’s say I (ccc561) requests gadi_jupyter to run using the project w35. The information will then be stored under ‘’’/scratch/w35/ccc561/tmp/runjp’’’

If I then run gadi_jupyter again but this time running on w40, the information will be stored under ‘’’/scratch/w40/ccc561/tmp/runjp’’’

Why do I get segfaults?

A segmentation fault means the program you are using has tried to read or write a memory location it does not have access to. This can mean there is an error in the code, or there is a system limit set. If the program runs for others, but not you, it may well be a system limit issue. This seems to be quite common when trying to write netcdf files. In some cases this can be overcome by setting your stack size to unlimited

For tcsh/csh add this to your .cshrc:

limit stacksize unlimited

For bash add this to your .bashrc:

ulimit -s unlimited

Note: you must log out and log back in again for this change to take effect.

I cannot see a project folder under /g/data and/or /scratch

You need to be a member of a project to access or even just list the project folder. So if you cannot see a project folder, it doesn’t mean that it doesn’t exist or it was removed, it simply means that you are not a member of that project. Go to my.nci.org.au if you want to request access.

Weird errors for a script that was previously working

Make sure you have loaded the right modules and only them! Avoid to load modules directly in your .bash_profile, .bashrc files . They will be loaded every time and occasionally interfere with the modules you are loading for a specific task.

It is useful and safe to add instructions as

module use /g/data/hh5/public/modules

as this is making the modules available without loading any.

Sometimes you need to install a python module in your user space ($HOME/.local/...) as it is not available in a managed conda environment. Again, occasionally modules stored in your local user space can interfere with other loaded modules, for example if they have different dependencies. If you find this is causing issues you can exclude the local environment by setting this environment variable

PYTHONNOUSERSITE=x (=True and =1 should also work as values)