For molecular modelers running simulations with GROMACS in the cloud through the SAMSON GROMACS Wizard, a recurring concern is visibility and control. What happens after submitting a job? How can one monitor progress, pause, or cancel a simulation if something’s off? And, perhaps most importantly, how do you make sure you don’t lose track of credits or forget about running jobs?
This post introduces a key but sometimes overlooked feature in SAMSON: the Job manager. If you’ve ever run a Molecular Dynamics (MD) simulation in the cloud and felt uncertain about its current state or longevity—this short guide is for you.
What is the Job Manager?
The Job manager is your central hub for managing all cloud-based simulations you launch with the GROMACS Wizard. It lets you view the status of current jobs, inspect detailed progress, events, and output, and take actions like pausing or canceling jobs—right from within the interface.
Opening the Job Manager
You can open it through:
- Interface > Job manager menu
- or simply press
Ctrl/Cmd + 6
Monitoring Jobs in Real-Time
Once you start a simulation, SAMSON automatically opens the Job manager, displaying all jobs (make sure the Running checkbox is selected to view active jobs). Each job provides valuable information:
- Progress status (Initializing, Running, Completed)
- Creation date
- Estimated completion time
- Cost in computing credits
You can also click the Events button to launch the full event log, which shows status updates, estimated completion time (as projected by GROMACS), and any important messages.
Pausing or Canceling a Job
If something doesn’t look right or if you want to free up credits, SAMSON offers full control. Via the job’s context menu:
- Select Pause to temporarily stop the simulation
- Select Cancel to terminate it completely
- You can later Restart paused jobs
Managing Completed Jobs and Costs
Once a job completes, the status will change and you’ll receive an email and a notification in Home > News within SAMSON.
Be sure to check the Non-running checkbox to see finished jobs. From here, you can download results or delete old jobs to free up Cloud storage and avoid credit usage over time.
Tips to Keep Track
- Give each job a meaningful name and description for quick filtering
- Regularly review the Events section to check on progress
- Sort jobs by start time or status to find what you’re looking for
- Delete jobs you’re done with to save credits 🔍
For modelers juggling multiple simulations or large datasets, the Job manager is an indispensable tool for staying organized and avoiding waste.
To learn more, read the full tutorial on cloud computations with GROMACS Wizard at this documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.