Integrate your own workflow with job automation APIs

OAsis offers job automation APIs that allow you to enqueue and inspect jobs easily. This means you can seamlessly integrate HPC into your workflow engine as a component. For example, you can use it to finetune machine learning models with new data or set up simulation jobs using your own tooling.

This article will use the Molecular Dynamics Simulation case as an example, but the concept should generally apply to all types of workloads.

For the simulation of the ApoA1 protein in a water box and the study of energy changes, we will be using NAMD. NAMD is available in various distributions, with OAsis offering it as both the Lmod system and the container version packaged by NVIDIA NGC. We will use the container version in this article.

Run the simulation using quick job

We can run container-based jobs easily in the web portal. Access Jobs > Run container and fill in the following:

Enqueue the job, and you should see the job output in(log file) on the following screen:

Please wait until the job is completed. Once that's done, repeat step 1 but this time, click on the "Export job script" button. This will allow you to download a quickjob.sbatch file. This file is a standard SLURM job script that can be enqueued using the sbatch command.