simulation_checker

Slurm job names for simulation needs to be in following format {project}_{condition}_v{version #}_{rep #}

Setup

1. Clone the repository into your home directory.

    cd ~
    git clone https://github.com/lxpowers33/simulation_checker.git
   

2. Add your simulation information to run_config.py file using the appropriate format. The run_config.py file contains a list of dictionaries. Just add a new dictionary on a new line:

    {'c':['MK6_WT'], 'max':1000, 'v':[1], 'r':[1,2,3,4,5,6], 'p':'GPR40', 'd': '/oak/stanford/groups/rondror/projects/MD_simulations/amber/GPR40/jpaggi'},
   

   Above 'MK6_W' is the condition name, '1' is the condition version, '1000' is the max number of time to run the simulations in nanoseconds, '1,2,3,4,5,6' are the rep directories, 'GPR40' is the project name used in your job names, '/oak/stanford/groups/rondror/projects/MD_simulations/amber/GPR40/jpaggi' is the directory containing the condition directory.

3. Then run sbatch run-checker.sbatch to start the recurring job:

    sbatch run-checker.sbatch
   

4. Jobs should start running in 8 hours. If you wish to start jobs immediatley:

    sbatch run-checker-now.sbatch
   

5. As jobs run, the running time should be written to the log file called log_file.txt.