Installation

The nimbus_splash package and its command line interface are designed to be installed on Bath’s Nimbus HPC system.

Unfortunately, the copy of python 3.8 that comes as default on Nimbus is too old for nimbus_splash, so instead it’s better to use a newer version of python in an Anaconda conda environment.

Depending on your level of python knowledge, follow either the short instructions or the long instructions.

Short Instructions

  1. Load Anaconda module load Anaconda3/2022.10 - Optionally add this to your ~/.bashrc file for automatic loading.

  2. Create a conda environment or pyenv - Optionally set this to automatically load every time you log in using ~/.bashrc.

  3. Install pip with conda install pip.

  4. Install nimbus_splash using pip

  5. Check your installation was sucessful with splash -h. You should see a help screen.

  6. Set the SPLASH_RAID environment variable to your Research Allocation ID in ~/.bashrc - export SPLASH_RAID=<RA_ID_HERE>

  7. Optional: Set the SPLASH_EMAIL environment variable to your email address to get job updates ~/.bashrc - export SPLASH_EMAIL=<Email_Here>

Long Instructions

To install splash, you will need to create a conda environment. This contains a sandboxed installation of python that is separate from the system version, so if anything bad happens you can just delete the environment and start again without affecting anything. You will then install splash in this environment.

Enabling Anaconda

First, log into Nimbus, and add the Anaconda module load command to ~/.bashrc by doing the following.

Open your ~/.bashrc file in nano using the following command

nano ~/.bashrc

Then go to the bottom of the file using your arrow keys or mouse, and paste in the following lines

module load Anaconda3/2022.10

Then save and exit nano using ctrl+o, enter, then ctrl+x, and then run the command

source ~/.bashrc

to reload your bashrc file.

Creating a conda environment

Now create a conda environment called nimbus_base, this is a sandboxed copy of python that you can use as a default and are free to mess around with in the knowledge that it can just be deleted if something breaks!

Run the following command

conda create -n nimbus_base

answering Y to any questions.

You’ll probably get a message about initialising your shell for conda, so run

conda init bash

This adds some configuration information to your ~/.bashrc, to make sure it works properly, exit your ssh window (close the connection), and then reconnect to Nimbus.

Upon reconnection, you should see the word (base) at the start of your terminal prompt. This is the base conda environment which you don’t want to use. To stop this base environment loading every time you open a shell, run the following command

conda config --set auto_activate_base false

and then deactivate this environment using

conda deactivate

Now (base) should be gone.

To instead start your new nimbus_base environment every time you connect, open ~/.bashrc with nano, and add the following to the bottom of the file.

conda activate nimbus_base

then save and exit nano using ctrl+o, enter, then ctrl+x, and then run the command

source ~/.bashrc

in your terminal.

If everything is working correctly, (nimbus_base) will appear at the start of your prompt.

You now have a(n) (updatable) conda environment to use!

Now, to set up this environment and install python, run the command

conda install pip

answering Y to any questions.

Installing nimbus_splash

Install nimbus_splash with

pip install nimbus_splash

Now, set your Research Allocation ID using the instructions below.

Setting your Research Allocation ID

To select your Research Allocation ID, add the following environment variable in your Nimbus ~/.bashrc file and replace <name_here> with your Research Allocation ID.

export SPLASH_RAID=<name_here>

save and exit, and then run

source ~/.bashrc

If you don’t do this, nimbus_splash will tell you to!

Note

If you want to switch over to using a different Research Allocation ID, you’ll need to update this line in ~/.bashrc and run source ~/.bashrc. Alternatively, you can temporarily change the value for the current session by running export SPLASH_RAID=<name_here> in your terminal.

You’re now ready to use nimbus_splash - head to Usage to get started.

Optional: Setting your notification email

To recieve emails on your job status, add the following environment variable in your Nimbus ~/.bashrc file and replace <email_here> with your email address.

export SPLASH_EMAIL=<email_here>

Updating

To update nimbus_splash run the following command

pip install --upgrade nimbus_splash