Recommended Way to Use (ESRF) SLURM Cluster

There are several ways to use the SLURM cluster at ESRF. Given the limited resources (especially GPUs), here is the recommended approach to use the SLURM cluster with Tomwer:

1. Connect to the SLURM cluster front-end:

   ssh -XC cluster-access
   

2. Connect to the ‘interactive’ partition in ‘interactive’ mode:

   salloc --partition interactive --x11 srun --pty bash -l
   

3. On the node, activate the version of Tomwer that you want to use and start the `canvas` application:

   module load tomotools
   tomwer canvas
   

   You should now see the ‘canvas’ interface.

   

   Hint

   You can specify a version of Tomotools when you load the module (like dev or stable):

   module load tomotools/{dev|stable|1.x}
   

4. Trigger all jobs requiring a GPU (e.g., Nabu reconstructions) remotely.

   Here are two examples:

   • Reconstructing one slice over SLURM:

     

   • Reconstructing one slice and a full volume over SLURM:

     

   Remember that some examples of workflows using SLURM are available in examples/remote processing with SLURM, and a video demonstrating this use case is available:

   • https://youtu.be/HYufV7Ya9v8

   Warning

   Please remember that all ‘Nabu’ tasks will require a GPU, so you will not be able to run them locally on the ‘interactive’ partition or any node without a dedicated GPU.