Not sure what you mean when you say “without submitting continuously new jobs”, since you will have to submit more. Here’s a few notes on that:
mdrun command, make sure to include the options
-cpi -maxh 24 along with your other options.
-cpi will resume from the last checkpoint,
-maxh 24 ensures that
mdrun stops and finishes writing all files before the 24 hours are up.
For SLURM, you can specify that your new job depends on a previous job to finish. This is how you can queue up multiple jobs to execute after each other, without running simultaneously. The documentation lists the various options to specify this. I usually submit with “singleton”, which uses the submitted job name as a check – if a job with the same name is already running, it’ll wait for that to finish. So I’ll just repeat my
sbatch command to submit my job script a few times, which creates the queue since the name will be the same for all.
You can set the dependency in the job script with the
SLURM_JOB_DEPENDENCY variable or use it with