iterative_alignment_experiment_structure/create_sbatch_scripts.sh

#!/bin/bash

# # Define the base directory containing subdirectories
BASE_DIR="./lightning_logs_round_1"

# # Get a sorted list of subdirectories
subdirs=($(ls -d "$BASE_DIR"/*/ | sort))

# Generate sbatch scripts
for i in {0..9}; do
    # Extract the version number (subdirectory name)
    version_number=$(basename "${subdirs[$i]}")

    # Define the sbatch filename
    sbatch_filename="alignment_dataset_2_96_from_ESM3_${i}.sh"

    # Write the sbatch file
    cat <<EOL > "$sbatch_filename"
#!/bin/bash
#SBATCH -N 1
#SBATCH -G 4
#SBATCH -C gpu&hbm80g
#SBATCH -q regular
#SBATCH -t 12:00:00
#SBATCH -A m4235
#SBATCH -J alignment

source /global/u2/s/si264/mambaforge/etc/profile.d/conda.sh
conda activate proera

pera_train \\
    "train.lightning_model_args.eval_type=era" \\
    "train.lightning_model_args.beta=10.0" \\
    "train.lightning_model_args.gamma=0" \\
    "train.trainer_args.devices=4" \\
    "train.trainer_args.max_epochs=25" \\
    "train.trainer_args.log_every_n_steps=1" \\
    "train.trainer_args.enable_progress_bar=True" \\
    "train.lightning_model_args.interval=epoch" \\
    "train.lightning_model_args.monitor=val/ERALoss" \\
    "train.lightning_model_args.lr_scheduler=ReduceLROnPlateau" \\
    "++train.lightning_model_args.lr_scheduler_args.patience=5" \\
    "train.lightning_model_args.optimizer=AdamW" \\
    "train.lightning_model_args.optimizer_args.lr=1.0e-6" \\
    "++train.lightning_model_args.optimizer_args.betas=[0.9,0.99]" \\
    "++train.lightning_model_args.optimizer_args.weight_decay=0.01" \\
    "train.lightning_model_args.on_step=false" \\
    "global_args.dataset_filename=alignment_dataset_2_96_from_ESM3_${i}.hdf5" \\
    "nn.batch_size=4" \\
    "nn.load_model=$BASE_DIR/$version_number/checkpoints/best_model.ckpt" \\
    "++nn.model_args.unified_transformer_args.ida_layer_indices=[]" \\
EOL

    echo "Created $sbatch_filename"
done