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jax

User documentation

The JAX container is developed by AMD specifically for LUMI and contains the necessary parts to run JAX on LUMI, including the plugin needed for RCCL when doing distributed AI, and a suitable version of ROCm for the version of JAX.

Note that JAX is still very much in development. Moreover, we sometimes have to use newer version of ROCm than the drivers on LUMI support, so there is no guarantee that this container will work for you (even though it did pass some tests we did), and there might be problems that cannot be fixed by the support team. This is software for users with a development spirit, not for users who expect something that simply and always works.

The EasyBuild installation with the EasyConfigs mentioned below will do four things:

  1. It will copy the container to your own file space. We realise containers can be big, but it ensures that you have complete control over when a container is removed again.

    We will remove a container from the system when it is not sufficiently functional anymore, but the container may still work for you. E.g., after an upgrade of the network drivers on LUMI, the RCCL plugin for the LUMI Slingshot interconnect may be broken, but if you run on only one node PyTorch may still work for you.

    If you prefer to use the centrally provided container, you can remove your copy after loading of the module with rm $SIF followed by reloading the module. This is however at your own risk.

  2. It will create a module file. When loading the module, a number of environment variables will be set to help you use the module and to make it easy to swap the module with a different version in your job scripts.

    • SIF and SIFPYTORCH both contain the name and full path of the singularity container file.

    • SINGULARITY_BINDPATH will mount all necessary directories from the system, including everything that is needed to access the project, scratch and flash file systems.

    • RUNSCRIPTS and RUNSCRIPTSPYTORCH contain the full path of the directory containing some sample run scripts that can be used to run software in the container, or as inspiration for your own variants.

  3. It creates the $RUNSCRIPTS directory with scripts to be run in the container:

    • conda-python-simple: This initialises Python in the container and then calls Python with the arguments of conda-python-simple. It can be used, e.g., to run commands through Python that utilise a single task but all GPUs.

  4. It creates a bin directory with scripts to be run outside of the container:

    • start-shell: Serves a double purpose:

      • Without further arguments, it will start a shell in the container with the Conda environment used to build the container activated.

      • With arguments it simply runs a shell in the container, but the Conda environment will not be activated.

    The bin directory is not mounted in the container, but if you would, the scripts would recognise this and work or print a message that they cannot be used in that environment.

The container uses a miniconda environment in which Python and its packages are installed. That environment needs to be activated in the container when running, which can be done with the command that is available in the container as the environment variable WITH_CONDA (which for this container it is source /opt/miniconda3/bin/activate jax).

Example of the use of WITH_CONDA: Check the Python packages in the container in an interactive session:

module load LUMI jax/0.4.13-rocm-5.6.1-python-3.10-singularity-20240207
singularity shell $SIF

which takes you in the container, and then in the container, at the Singularity> prompt:

$WITH_CONDA
pip list

An example of the use of start-shell that even works on the login nodes is:

module load LUMI jax/0.4.13-rocm-5.6.1-python-3.10-singularity-20240207
start-shell -c '/runscripts/conda-python-simple -c "import numpy ; import scipy ; import jax ; print( f'"'JAX {jax.__version__}, NumPy {numpy.__version__}, SciPy {scipy.__version__}.'"' )"'

The container (when used with SINGULARITY_BINDPATH of the module) also provides one or more wrapper scripts to start Python from the conda environment in the container. Those scripts are also available outside the container for inspection after loading the module in the $RUNSCRIPTS subdirectory and you can use those scripts as a source of inspiration to develop a script that more directly executes your commands or does additional initialisations.

Example (in an interactive session):

salloc -N1 -pstandard-g -t 30:00
module load LUMI jax/0.4.13-rocm-5.6.1-python-3.10-singularity-20240207
srun -N1 -n1 --gpus 8 singularity exec $SIF /runscripts/conda-python-simple \
    -c 'import jax; print("I have these devices:", jax.devices("gpu"))'

Installation

To install the container with EasyBuild, follow the instructions in the EasyBuild section of the LUMI documentation, section "Software", and use the dummy partition container, e.g.:

module load LUMI partition/container EasyBuild-user
eb jax-0.4.13-rocm-5.6.1-python-3.10-singularity-20240207.eb

To use the container after installation, the EasyBuild-user module is not needed nor is the container partition. The module will be available in all versions of the LUMI stack and in the CrayEnv stack (provided the environment variable EBU_USER_PREFIX points to the right location).

Singularity containers with modules for binding and extras

Install with the EasyBuild-user module in partition/container: 

module load LUMI partition/container EasyBuild-user
eb <easyconfig>
The module will be available in all versions of the LUMI stack and in the CrayEnv stack.

To access module help after installation use module spider jax/<version>.

EasyConfig:

Archived EasyConfigs

The EasyConfigs below are additonal easyconfigs that are not directly available on the system for installation. Users are advised to use the newer ones and these archived ones are unsupported. They are still provided as a source of information should you need this, e.g., to understand the configuration that was used for earlier work on the system.