Running HTTomo at Diamond

Running HTTomo at Diamond#

HTTomo can be run at Diamond in two ways:

  • in parallel on the wilson compute cluster, using the httomo_mpi launcher; or

  • serially on a Diamond workstation, using the httomo run command.

Parallel execution on the compute cluster is the recommended and most common way to process tomography data at Diamond.

Commands are entered in a terminal, also called a shell or command line. Before running HTTomo, load its software module:

$ module load httomo

The module configures executable and library paths for the current terminal. List the installed versions with module avail httomo. To select a specific version, unload the current one and load the required version:

$ module unload httomo
$ module load httomo/<version>

Running HTTomo in parallel#

Parallel HTTomo jobs run on the wilson production compute cluster. The httomo_mpi launcher is integrated with the SLURM workload manager and submits the requested processing job to the cluster.

Submitting from a Diamond workstation#

On a Diamond workstation, load the HTTomo environment if it is not already loaded:

$ module load httomo

Then submit the processing job:

$ httomo_mpi IN_FILE YAML_CONFIG OUT_DIR

Alternatively, log in to wilson, load the HTTomo module and submit the job from there:

$ ssh wilson
$ module load httomo
$ httomo_mpi IN_FILE YAML_CONFIG OUT_DIR

The command takes the following arguments:

IN_FILE

The path to the HDF5 file containing the input tomography data.

YAML_CONFIG

The path to the YAML file that defines the processing pipeline.

OUT_DIR

The directory in which HTTomo will write its output.

To see the available launcher options, run:

$ httomo_mpi --help

Running HTTomo serially on workstation#

For smaller jobs or testing pipelines, HTTomo can be run serially on a Diamond workstation.

First, load the HTTomo environment:

$ module load httomo

Then run the pipeline locally:

$ httomo run IN_FILE YAML_CONFIG OUT_DIR

This command runs HTTomo on the workstation itself and does not submit a job to the compute cluster.