A molecular modeling run rarely ends when you click “start.” You may need to check its progress, pause or stop it, find the output files, and make sure a collaborator can access the right job. When several calculations are underway, keeping those steps straight can become a task of its own.
SAMSON’s Job manager brings those parts of the workflow together. It is useful for cloud jobs launched from SAMSON, including protein structure prediction with AlphaFold or NVIDIA BioNeMo Services and molecular dynamics simulations using GROMACS. Here’s a practical way to use it as a control point for your work.
Start with one place to review your jobs
Open the Job manager from Interface > Job manager. From there, you can create jobs through extensions that support the feature, execute cloud jobs, monitor them, and retrieve results into SAMSON. The manager gives you a place to check on ongoing work instead of relying on memory or hunting through unrelated files.
When you need to inspect a particular run, select it to show its details on the right side of the Job manager. Use that view to orient yourself before taking action: confirm which job you have selected, review its available details, and then start, pause, or stop it as needed. This small pause can help prevent mistakes when multiple calculations have similar names.
Make jobs easier to recognize later
A useful job name should tell you more than the software or method used. Include a distinguishing detail that will still matter when you return to the run—for example, the system or purpose of the calculation. Use the notes field for extra context that does not fit neatly into the name, such as what you intended to compare or what you want to inspect when the results arrive.
You can edit a job’s name and notes in the Job manager. These changes are automatically synced with your SAMSON Connect account, which makes descriptive labels helpful beyond your local view as well.
Retrieve files deliberately
Getting a result back is not always the same as knowing where its files are. To download all files for a job, double-click the job in the Job manager. Once files have been downloaded, the job’s context menu provides access to local files; it also provides access to remote files stored in the cloud. That distinction is useful when you are checking whether a file is already on your computer or still needs to be retrieved.
Before moving on to analysis, it can help to make a quick handoff checklist:
- Confirm the intended job is selected and review its details.
- Give the job a recognizable name and add notes about its purpose.
- Download the files you need, then use the context menu to distinguish local files from remote ones.
- If someone else needs to review the run, check its access and sharing options on SAMSON Connect.
Share the job, not just a file
Cloud jobs launched from SAMSON are accessible from SAMSON Connect, where you can control who has access to them. This can make collaboration clearer than sending a file without the surrounding job context. The context menu also provides a route to the job’s view on SAMSON Connect, alongside access to local and remote files.
Cloud calculations in SAMSON require Computing Credits, so check your available credits when planning work. For an example of launching cloud jobs with GROMACS, see the GROMACS Wizard cloud computing guide.
For the complete guide to the Job manager and cloud workflows, read the SAMSON cloud computations documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.