Topaz in sbatch

Hi - we have cryoSPARC running in our HPC environment with slurm and sbatch. We’re wondering what the best way to start the topaz environment to pass the Path to Executable in the UI? Has anyone done this before? Also is there any plans for updating from Python 2.7 to Python 3.x


we are also using slurm and sbatch to run cryoSPARC. We are also thinking about setting up topaz in this environment so we are also interested in the topic that @hansenbry brought up.

We are using singularity to pack cryoSPARC into a container. For now the idea is to just add topaz to the cryoSPARC worker container. But topaz uses quite a lot of CPU cores for processing and we have to figure out how to automatically reserve the additional (CPU) resources.

Any ideas are welcome!