Datasets:
Languages:
English
Size:
10M<n<100M
Tags:
biomedical
negative-results
benchmark
drug-target-interaction
clinical-trials
protein-protein-interaction
License:
| # Submit all CT LLM benchmark jobs on Cayuga. | |
| # | |
| # Grid: 5 models × 4 tasks × (1 zero-shot + 3 three-shot seeds) = 80 jobs | |
| # | |
| # Provider routing (CT-specific SLURM templates): | |
| # llama70b, qwen32b → run_ct_llm_local.slurm (GPU, vLLM) | |
| # gpt-4o-mini → run_ct_llm_openai.slurm (CPU, API) | |
| # gemini-2.5-flash → run_ct_llm_gemini.slurm (CPU, API) | |
| # claude-haiku-4-5 → run_ct_llm_anthropic.slurm (CPU, API) | |
| # | |
| # Usage: | |
| # bash slurm/submit_ct_llm_all.sh [--dry-run] | |
| set -euo pipefail | |
| SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)" | |
| PROJECT_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)" | |
| SBATCH="/opt/ohpc/pub/software/slurm/24.05.2/bin/sbatch" | |
| DRY_RUN=false | |
| if [[ "${1:-}" == "--dry-run" ]]; then | |
| DRY_RUN=true | |
| echo "=== DRY RUN ===" | |
| fi | |
| CT_TASKS=("ct-l1" "ct-l2" "ct-l3" "ct-l4") | |
| CONFIGS=("zero-shot" "3-shot") | |
| FEWSHOT_SETS=(0 1 2) | |
| # Model definitions: short_name → model_arg, slurm_template, extra_flags | |
| # For local models: short name matches SLURM case statement | |
| # For API models: model name is passed directly to --model | |
| declare -A MODEL_ARG | |
| declare -A MODEL_SLURM | |
| declare -A MODEL_EXTRA | |
| MODEL_ARG["llama70b"]="llama70b" | |
| MODEL_SLURM["llama70b"]="run_ct_llm_local.slurm" | |
| MODEL_EXTRA["llama70b"]="" | |
| MODEL_ARG["qwen32b"]="qwen32b" | |
| MODEL_SLURM["qwen32b"]="run_ct_llm_local.slurm" | |
| MODEL_EXTRA["qwen32b"]="" | |
| MODEL_ARG["gpt-4o-mini"]="gpt-4o-mini" | |
| MODEL_SLURM["gpt-4o-mini"]="run_ct_llm_openai.slurm" | |
| MODEL_EXTRA["gpt-4o-mini"]="" | |
| MODEL_ARG["gemini-2.5-flash"]="gemini-2.5-flash" | |
| MODEL_SLURM["gemini-2.5-flash"]="run_ct_llm_gemini.slurm" | |
| MODEL_EXTRA["gemini-2.5-flash"]="" | |
| MODEL_ARG["claude-haiku-4-5"]="claude-haiku-4-5" | |
| MODEL_SLURM["claude-haiku-4-5"]="run_ct_llm_anthropic.slurm" | |
| MODEL_EXTRA["claude-haiku-4-5"]="" | |
| TOTAL=0 | |
| SUBMITTED=0 | |
| for MODEL in "${!MODEL_ARG[@]}"; do | |
| MODEL_NAME="${MODEL_ARG[$MODEL]}" | |
| SLURM_TMPL="${MODEL_SLURM[$MODEL]}" | |
| EXTRA="${MODEL_EXTRA[$MODEL]}" | |
| for TASK in "${CT_TASKS[@]}"; do | |
| for CONFIG in "${CONFIGS[@]}"; do | |
| if [[ "$CONFIG" == "zero-shot" ]]; then | |
| FS_SETS=(0) | |
| else | |
| FS_SETS=("${FEWSHOT_SETS[@]}") | |
| fi | |
| for FS in "${FS_SETS[@]}"; do | |
| TOTAL=$((TOTAL + 1)) | |
| JOB_NAME="ct_${TASK}_${MODEL}_${CONFIG}_fs${FS}" | |
| if $DRY_RUN; then | |
| echo " [DRY] $JOB_NAME → $SLURM_TMPL" | |
| else | |
| echo " Submitting: $JOB_NAME" | |
| $SBATCH \ | |
| --job-name="$JOB_NAME" \ | |
| --export="ALL,TASK=$TASK,MODEL=$MODEL_NAME,CONFIG=$CONFIG,FS=$FS,EXTRA=$EXTRA" \ | |
| "$SCRIPT_DIR/$SLURM_TMPL" | |
| SUBMITTED=$((SUBMITTED + 1)) | |
| fi | |
| done | |
| done | |
| done | |
| done | |
| echo "" | |
| echo "Total jobs: $TOTAL" | |
| if $DRY_RUN; then | |
| echo "(Dry run — no jobs submitted)" | |
| else | |
| echo "Submitted: $SUBMITTED" | |
| fi | |