transfer/code/prompt_selection/submit_all.sh

#!/bin/bash
# Master submission script for all perturbation conditions.
#
# Usage:
#   Phase 1: bash code/prompt_selection/submit_all.sh shared
#            (Submit shared steps, wait for completion)
#
#   Phase 2: bash code/prompt_selection/submit_all.sh perturbations
#            (Submit all per-perturbation pipeline + baseline jobs)
#
#   Phase 3: bash code/prompt_selection/run_eval_all.sh
#            (Run evaluation on login node after all GPU jobs complete)

cd /home/hp250092/ku50001222/qian/aivc/lfj/transfer
mkdir -p logs

PERTURBATIONS=(
    "Belinostat"
    "CHIR-99021"
    "Crizotinib"
    "Dabrafenib"
    "Dactolisib"
    "Foretinib"
    "Idelalisib"
    "LDN 193189"
    "Linagliptin"
    "O-Demethylated Adapalene"
    "Palbociclib"
    "Penfluridol"
    "Porcn Inhibitor III"
    "R428"
)

case "$1" in
    shared)
        echo "=== Submitting shared steps ==="
        pjsub code/prompt_selection/run_shared.sh
        echo ""
        echo "Wait for the shared job to complete, then run:"
        echo "  bash code/prompt_selection/submit_all.sh perturbations"
        ;;

    perturbations)
        echo "=== Submitting per-perturbation jobs ==="
        for PERT in "${PERTURBATIONS[@]}"; do
            echo "Submitting: $PERT"
            # Pipeline (prompt selection)
            pjsub -x PERT_NAME="$PERT" code/prompt_selection/run_pert.sh
            # Baseline (random prompt)
            pjsub -x PERT_NAME="$PERT" code/prompt_selection/run_baseline_pert.sh
        done
        echo ""
        echo "Submitted ${#PERTURBATIONS[@]} pipeline + ${#PERTURBATIONS[@]} baseline jobs."
        echo "After all jobs complete, run evaluation:"
        echo "  bash code/prompt_selection/run_eval_all.sh"
        ;;

    *)
        echo "Usage: $0 {shared|perturbations}"
        echo ""
        echo "  shared         Submit shared steps (run first)"
        echo "  perturbations  Submit all per-perturbation jobs (run after shared completes)"
        exit 1
        ;;
esac