Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
Remove internal script: slurm/submit_eval_checkpoints.sh
Browse files
slurm/submit_eval_checkpoints.sh
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#!/bin/bash
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# Evaluate timed-out checkpoints:
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# drugban_balanced_random_uniform_random_seed{seed}
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# drugban_balanced_random_degree_matched_seed{seed}
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# Optional:
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# SEEDS="42 43" bash slurm/submit_eval_checkpoints.sh
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set -euo pipefail
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SBATCH=/opt/ohpc/pub/software/slurm/24.05.2/bin/sbatch
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NEGBIODB=${SCRATCH_DIR:-/path/to/scratch}/negbiodb
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LOGDIR=$NEGBIODB/logs
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SCRIPT=$NEGBIODB/slurm/eval_checkpoint.slurm
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DATASET=${DATASET:-balanced}
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SEEDS_STR=${SEEDS:-42}
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submit() {
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local model=$1 split=$2 neg=$3 dataset=${4:-balanced} seed=${5:-42}
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local name="negbio_eval_${model}_${dataset}_${split}_${neg}_seed${seed}"
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local sbatch_out job_id
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sbatch_out=$(
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"$SBATCH" \
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--job-name="$name" \
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--output="$LOGDIR/${name}_%j.out" \
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--error="$LOGDIR/${name}_%j.err" \
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--export=MODEL="$model",SPLIT="$split",NEG="$neg",DATASET="$dataset",SEED="$seed" \
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"$SCRIPT" 2>&1
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)
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job_id=$(echo "$sbatch_out" | grep -oP 'batch job \K\d+')
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if [[ -z "$job_id" ]]; then
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echo "ERROR: Failed to submit $name"
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echo "$sbatch_out"
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exit 1
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fi
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echo "Submitted $name → job $job_id"
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}
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echo "=== Submitting eval-only jobs for timed-out checkpoints ==="
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echo "Timestamp: $(date)"
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echo "Dataset: $DATASET"
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echo "Seeds: $SEEDS_STR"
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echo ""
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for seed in $SEEDS_STR; do
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submit "drugban" "random" "uniform_random" "$DATASET" "$seed"
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submit "drugban" "random" "degree_matched" "$DATASET" "$seed"
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done
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echo ""
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echo "=== Done ==="
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