run_all_experiments.sh

#!/usr/bin/env bash
###############################################################################
# StepProbe — Master driver for all follow-up experiments.
#
# Runs the six GPU-gated experiment scripts in their priority order (the
# tallest reviewer-risk items first), then regenerates every paper figure
# and LaTeX table so the paper source is up to date.
#
# Every step is skip-if-exists, so if you Ctrl-C mid-run, just re-run and
# it resumes from where it stopped. A single failure halts the master
# script (set -e), but individual sub-scripts tolerate resumption.
#
# Total runtime if everything runs from scratch: ~10-12 hours on one 3090 Ti.
# Re-runs after partial completion are proportionally shorter.
#
# Usage:
#   bash run_all_experiments.sh              # run the default priority order
#   bash run_all_experiments.sh --dry-run    # print the plan, run nothing
#   bash run_all_experiments.sh --skip baselines multi_seed    # skip by tag
#   bash run_all_experiments.sh --only prompt_prefix           # run one phase
#   OPENAI_API_KEY=sk-... bash run_all_experiments.sh          # include A3 validation
#
# Phase tags (for --skip / --only):
#   baselines     — sampling-strategy baselines (A4)
#   multi_seed    — 3-seed robustness on primary cell (A1)
#   classifier    — LLM-judge classifier validation (A3) — API KEY REQUIRED
#   llama_lr      — Llama LR sensitivity sweep (A5)
#   prompt_prefix — training-free intervention (B2-a)
#   scale_up      — 14B scale-up experiment (B1)
#   paper         — regenerate figures + tables (always runs at the end)
###############################################################################
set -euo pipefail

PROJECT_DIR="$(cd "$(dirname "$0")" && pwd)"
cd "$PROJECT_DIR"

export CUDA_VISIBLE_DEVICES="${CUDA_VISIBLE_DEVICES:-1}"
export HF_HUB_DOWNLOAD_TIMEOUT=300

# ========================== CONFIG =========================================
LOG_DIR="${PROJECT_DIR}/logs"
TIMESTAMP=$(date +%Y%m%d_%H%M%S)
LOG_FILE="${LOG_DIR}/run_all_experiments_${TIMESTAMP}.log"
PY="${PY:-python}"
GPU_MEM="${GPU_MEM:-0.55}"

mkdir -p "$LOG_DIR"

# ========================== ARG PARSING ====================================
DRY_RUN=false
CONTINUE_ON_ERROR=false
ONLY_TAGS=()
SKIP_TAGS=()

while [[ $# -gt 0 ]]; do
    case $1 in
        --dry-run)            DRY_RUN=true; shift ;;
        --continue-on-error)  CONTINUE_ON_ERROR=true; shift ;;
        --skip)               shift; while [[ $# -gt 0 && "$1" != --* ]]; do SKIP_TAGS+=("$1"); shift; done ;;
        --only)               shift; while [[ $# -gt 0 && "$1" != --* ]]; do ONLY_TAGS+=("$1"); shift; done ;;
        --help|-h)
            grep -E "^#( |$)" "$0" | sed 's/^# \?//' | head -40
            exit 0 ;;
        *) echo "Unknown option: $1"; exit 1 ;;
    esac
done

FAILED_TAGS=()

should_run() {
    local tag=$1
    # If --only was passed, only those tags run.
    if [[ ${#ONLY_TAGS[@]} -gt 0 ]]; then
        for t in "${ONLY_TAGS[@]}"; do
            [[ "$t" == "$tag" ]] && return 0
        done
        return 1
    fi
    # Otherwise, skip tags listed in --skip.
    for t in "${SKIP_TAGS[@]}"; do
        [[ "$t" == "$tag" ]] && return 1
    done
    return 0
}

# ========================== LOGGING ========================================
log() {
    local msg="[$(date '+%H:%M:%S')] $1"
    echo "$msg" | tee -a "$LOG_FILE"
}

section() {
    log ""
    log "=============================================="
    log "$1"
    log "=============================================="
}

# Run one phase. $1 = tag, $2 = description, $3 = runtime estimate, $4 = command.
run_phase() {
    local tag=$1 desc=$2 eta=$3 cmd=$4

    if ! should_run "$tag"; then
        log "[skip $tag] $desc"
        return 0
    fi

    section "PHASE: $desc  [tag=$tag, ETA $eta]"
    if $DRY_RUN; then
        log "  [DRY-RUN] $cmd"
        return 0
    fi

    local phase_start=$(date +%s)
    # Disable `set -e` around the eval so a non-zero exit doesn't kill us;
    # we want to check the status ourselves. Restore immediately after.
    set +e
    eval "$cmd" 2>&1 | tee -a "$LOG_FILE"
    local rc=${PIPESTATUS[0]}
    set -e

    local phase_end=$(date +%s)
    local dur=$((phase_end - phase_start))

    if [[ $rc -ne 0 ]]; then
        log "FAILED [$tag] after $((dur / 60))m $((dur % 60))s — exit=$rc"
        FAILED_TAGS+=("$tag")
        if $CONTINUE_ON_ERROR; then
            log "  continuing to next phase (--continue-on-error set)"
            return 0
        fi
        log "  Resume with: bash $0 --only $tag"
        log "  Or skip and continue the remaining queue: bash $0 --continue-on-error --skip $tag"
        log "  (Individual scripts are skip-if-exists so restart is cheap.)"
        exit 1
    fi
    log "PHASE COMPLETE [$tag] in $((dur / 60))m $((dur % 60))s"
}

# ========================== PREFLIGHT ======================================
section "StepProbe — full follow-up experiment sweep"
log "  Project dir: $PROJECT_DIR"
log "  Log file:    $LOG_FILE"
log "  GPU:         $(nvidia-smi --query-gpu=name --format=csv,noheader 2>/dev/null | head -1 || echo 'unknown')"
log "  CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES"

if [[ ${#ONLY_TAGS[@]} -gt 0 ]]; then
    log "  Running ONLY: ${ONLY_TAGS[*]}"
elif [[ ${#SKIP_TAGS[@]} -gt 0 ]]; then
    log "  Skipping:     ${SKIP_TAGS[*]}"
fi
if $DRY_RUN; then
    log "  Mode:         DRY-RUN"
fi

OVERALL_START=$(date +%s)

# ========================== PHASE 1 — BASELINES (A4) ======================
# Tallest reviewer-risk: if silver_bullet ≈ random, the novelty claim collapses.
run_phase "baselines" \
    "Sampling-strategy baselines (silver_bullet vs failed_only vs random)" \
    "~90 min" \
    "bash ${PROJECT_DIR}/run_baselines.sh"

# ========================== PHASE 2 — MULTI-SEED (A1) =====================
# Reviewer-rigor blocker for NeurIPS-tier submission.
run_phase "multi_seed" \
    "Multi-seed robustness (3 seeds at T=0.6 on primary cell)" \
    "~2 h" \
    "bash ${PROJECT_DIR}/run_multi_seed.sh"

# ========================== PHASE 3 — CLASSIFIER (A3) =====================
# LLM-judge validation. Requires OPENAI_API_KEY or ANTHROPIC_API_KEY.
if [[ -n "${OPENAI_API_KEY:-}" ]]; then
    run_phase "classifier" \
        "Error-type classifier validation (OpenAI judge, gpt-4o)" \
        "~5 min + API cost" \
        "$PY ${PROJECT_DIR}/scripts/validate_classifier.py \
            --judge openai --judge-model gpt-4o --n-samples 200"
elif [[ -n "${ANTHROPIC_API_KEY:-}" ]]; then
    run_phase "classifier" \
        "Error-type classifier validation (Anthropic judge, claude-3-5-sonnet)" \
        "~5 min + API cost" \
        "$PY ${PROJECT_DIR}/scripts/validate_classifier.py \
            --judge anthropic --judge-model claude-3-5-sonnet-latest --n-samples 200"
elif should_run "classifier"; then
    log "[skip classifier] set OPENAI_API_KEY or ANTHROPIC_API_KEY to include LLM-judge validation"
fi

# ========================== PHASE 4 — LLAMA LR SWEEP (A5) =================
# Converts the §8 regression discussion into evidence-backed narrative.
run_phase "llama_lr" \
    "Llama-family learning-rate sweep (5e-5, 1e-4, 2e-4)" \
    "~2.5 h" \
    "bash ${PROJECT_DIR}/run_llama_lr_sweep.sh"

# ========================== PHASE 5 — PROMPT PREFIX (B2-a) ================
# Headline figure for the reframed paper: training-free intervention.
run_phase "prompt_prefix" \
    "Prompt-prefix injection sweep (k = 0..4)" \
    "~80 min" \
    "bash ${PROJECT_DIR}/run_prompt_prefix.sh"

# ========================== PHASE 6 — 14B SCALE-UP (B1) ===================
# Answers the inevitable "does it scale?" reviewer question.
run_phase "scale_up" \
    "14B scale-up experiment" \
    "~90 min" \
    "bash ${PROJECT_DIR}/run_scale_up.sh"

# ========================== PHASE 7 — PAPER ARTIFACTS =====================
# Always regenerate — this is cheap and ensures every figure/table reflects
# whatever new experiments succeeded above.
run_phase "paper" \
    "Regenerate paper figures + LaTeX tables" \
    "~1 min" \
    "$PY ${PROJECT_DIR}/scripts/compute_ci.py \
        --diagnosis ${PROJECT_DIR}/results/diagnosis \
        --output ${PROJECT_DIR}/results/metrics --n-boot 5000 && \
     $PY ${PROJECT_DIR}/scripts/make_paper_figures.py \
        --metrics ${PROJECT_DIR}/results/metrics \
        --diagnosis ${PROJECT_DIR}/results/diagnosis \
        --segmented ${PROJECT_DIR}/results/segmented \
        --output ${PROJECT_DIR}/figures/paper && \
     $PY ${PROJECT_DIR}/scripts/make_tables.py \
        --metrics-dir ${PROJECT_DIR}/results/metrics \
        --output-dir ${PROJECT_DIR}/figures/paper"

# ========================== DONE ===========================================
OVERALL_END=$(date +%s)
TOTAL=$((OVERALL_END - OVERALL_START))

if [[ ${#FAILED_TAGS[@]} -gt 0 ]]; then
    section "RUN FINISHED WITH FAILURES"
    log "  Failed phases: ${FAILED_TAGS[*]}"
    log "  Resume any of them with: bash $0 --only <tag>"
else
    section "ALL EXPERIMENTS COMPLETE"
fi
log "  Total time:  $((TOTAL / 3600))h $(((TOTAL % 3600) / 60))m"
log "  Log file:    $LOG_FILE"
log ""
log "  Next:"
log "    1. Open figures/paper/ to review all figures and tables."
log "    2. Recompile paper/: cd paper && make   (or upload to Overleaf)."
log "    3. Read §6.3 (baselines), §7 (interventions), §8 (limitations) first"
log "       — those are the sections whose content depends on these runs."