The current workflow no longer requires users to interact with AWS via the command line.

All you have to do is open the relion2 GUI on your local linux machine, and then submit the job using the following commands:

When you want to submit a job to run on AWS for 2D classification, 3D classification, and 3D refinement:

• Submit to queue? YES
• Queue name: {not used, leave default}
• Queue submit command: qsub_aws
• Standard submission script: /home/michaelc/Scripts/AWS/relion/relion_qsub.sh {Should be default}
• Click Run now!

You'll see the output in the relion GUI update with information on data being uploaded to AWS. Then, once the job is running, all output files will be synced back to the relion working directory in real time. When the job finishes, the instance will be automatically shut down.

• NONE of the job parameters in the GUI are include in the AWS command. The AWS command on the back end takes care of all of that, so don't worry about setting any flags / GPUs / MPI processes

For the given job that you are monitoring, select 'Job actions > Edit note'.

Then, onto the last line of note, include the text Kill job. {Case sensitive, must include a capital 'K'}

This will terminate the job and stop the instance.