Part C1: How to submit VASP jobs to Slurm: Adsorber submit

Once you have run the Adsorber partC command, you can submit your jobs. If you use a computer cluster that run the Slurm Workload Manager, you can submit all your jobs at the same time by changing directory into the Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP folder and running a command called Adsorber submit.

cd Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP
Adsorber submit

Running the Adsorber submit command in the terminal will look through all subdirectories that this program is executed from and looks for folders that contain a 'submit.sl' file.

  • This program will not submit VASP jobs that are currently running or have been run. This program will only submit VASP jobs that do not contain a ``OUTCAR`` file. Any job that is running or has already run will contain an OUTCAR file, which tells the Adsorber program that that VASP job is currently running or has already been run.

  • Run_Adsorber_submitSL_slurm.py will execute all folders that contain a 'submit.sl' file. However, Adsorber submit will not run any 'submit.sl' files from previously run calculations, which are found in the Submission_Folder folders.

If you dont want to run all the jobs in Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP but just a select few, you want to move into that folder and then type Adsorber submit into the terminal. For example, lets say that I only want to run the jobs that are in the directory Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP/COOH_symmetric/Bridge_Sites/Other_5_fold_Sites_Blue, then we want to move into this directory and then type Adsorber submit into the terminal:

cd Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP/COOH_symmetric/Bridge_Sites/Other_5_fold_Sites_Blue
Adsorber submit

Adsorber submit settings that can be changed

Write this once I am happy with how the program works here.

Adsorber check_submit: Other useful commands to see how many jobs are running and the number of jobs that you will submit

Before you run Adsorber submit you can see how many jobs you are submitting to the queue by running typing Adsorber check_submit into the terminal in the directory you are in.

Adsorber check_submit

This will show all the VASP jobs that would be submitted if you were to run the Adsorber submit command.

A command to determine the number of jobs you have already running in slurm

To find out the number of jobs that are running or are waiting in the queue in slurm, you can type no_of_jobs_running_or_queued into the terminal. To use this command, you need to enter this alias into your ~/.bashrc:

alias no_of_jobs_running_or_queued='squeue -u $USER | wc -l'

Note: This will give you the number of jobs you have in your slurm queue, plus 1. So whatever number you get from no_of_jobs_running_or_queued, minus 1 from it to get the actual number of jobs in your queue. Not suer how to fix this yet.

NOTE: You CAN enter more than 1000 jobs into the slurm queue with Run_Adsorber_submitSL_slurm.py. If you reach 1000 jobs queued in slurm, Run_Adsorber_submitSL_slurm.py will patiently wait for current running jobs to complete and add more of your jobs into the slurm queue as current jobs are completed.

What to do if some jobs need to be resubmit for some reason

If you would like to resubmit one or many jobs for some particualy reason, see Part C2: What To Do If Some Jobs Have Not Finished/Converged for information about the programs for doing this.