File size: 4,940 Bytes
7a0d051 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 | #!/bin/bash
# Wait for Kermany SD-VAE stage2, then sample and run C-sdvae downstream.
set -euo pipefail
export https_proxy=http://10.140.15.68:3128 http_proxy=http://10.140.15.68:3128
export HF_DATASETS_CACHE=/data/temp/qinshengqian/c3/hf_cache
export PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
BASE=/data/temp/qinshengqian/c3
CODE=$BASE/Code/RAEv2
PIPE=$BASE/kermany_pipeline
DOWN=$BASE/kermany_downstream
SYN=$DOWN/synth/sdvae
JSONS=$DOWN/jsons
LOGS=$DOWN/logs
CFGS=$DOWN/cfgs
mkdir -p "$SYN" "$JSONS" "$LOGS" "$CFGS"
FINAL_EPOCH=${FINAL_EPOCH:-50}
STOP_TRAINING_AFTER_FINAL=${STOP_TRAINING_AFTER_FINAL:-1}
FINAL=$(printf "%s/results/stage2/KERMANY_sdvae/checkpoints/ep-%07d.pt" "$CODE" "$FINAL_EPOCH")
RUNLOG=$DOWN/sdvae_completion.log
exec >>"$RUNLOG" 2>&1
ts() { date '+%Y-%m-%d %H:%M:%S'; }
echo "[$(ts)] waiting for $FINAL"
while [ ! -f "$FINAL" ]; do
if ! pgrep -f "configs/stage2/training/KERMANY/sdvae" >/dev/null 2>&1; then
echo "[$(ts)] sdvae training process not found before final checkpoint; abort"
exit 1
fi
sleep 120
done
echo "[$(ts)] final checkpoint found"
if [ "$STOP_TRAINING_AFTER_FINAL" = "1" ]; then
echo "[$(ts)] stopping SD-VAE training after checkpoint ep-$FINAL_EPOCH"
pkill -TERM -f "configs/stage2/training/KERMANY/sdvae_8gpu_gb64.yaml" || true
sleep 30
pkill -KILL -f "configs/stage2/training/KERMANY/sdvae_8gpu_gb64.yaml" || true
fi
CSV=$SYN/synth.csv
if [ ! -f "$CSV" ] || [ "$(tail -n +2 "$CSV" 2>/dev/null | wc -l)" -lt 8000 ]; then
SCFG=$CFGS/sample_sdvae.yaml
cd "$CODE"
/root/miniconda3/envs/rae_v2/bin/python "$PIPE/build_kermany_sample_cfg.py" sdvae "$SCFG"
rm -f "$SYN"/synth_*.csv "$CSV"
CLASSES=(CNV DME DRUSEN NORMAL)
for i in "${!CLASSES[@]}"; do
c=${CLASSES[$i]}
CUDA_VISIBLE_DEVICES=$i PYTHONPATH=src /root/miniconda3/envs/rae_v2/bin/python sample_perclass_kermany.py \
"$SCFG" "$SYN" 2000 80 "$c" "$c" >"$LOGS/sample_sdvae_${c}.log" 2>&1 &
echo "[$(ts)] launched SD-VAE sampling class=$c gpu=$i pid=$!"
done
sample_fail=0
for pid in $(jobs -rp); do
wait "$pid" || sample_fail=$((sample_fail + 1))
done
[ "$sample_fail" -eq 0 ] || { echo "[$(ts)] sampling failed count=$sample_fail"; exit 1; }
head -1 "$SYN/synth_CNV.csv" > "$CSV"
for c in "${CLASSES[@]}"; do tail -n +2 "$SYN/synth_${c}.csv" >> "$CSV"; done
fi
rows=$(tail -n +2 "$CSV" | wc -l)
echo "[$(ts)] synth csv rows=$rows"
[ "$rows" -ge 8000 ] || { echo "[$(ts)] synth csv too small"; exit 1; }
DOSES=(0.05 0.25 1.0)
SEEDS=(0 1 2)
GPUS=(0 1 2 3 4 5 6 7)
MAXJOBS=8
wait_for_slot() {
while [ "$(jobs -rp | wc -l)" -ge "$MAXJOBS" ]; do
sleep 10
done
}
for seed in "${SEEDS[@]}"; do
out="$JSONS/A_full_s${seed}.json"
if [ -f "$out" ]; then
echo "[$(ts)] skip existing full-train baseline $out"
continue
fi
wait_for_slot
gpu=${GPUS[$((seed % ${#GPUS[@]}))]}
log="$LOGS/A_full_s${seed}.log"
/root/miniconda3/envs/rae_v2/bin/python "$PIPE/kermany_dose_rn50.py" \
--dose 1.0 --regime A --seed "$seed" --device "cuda:$gpu" \
--real-cap-per-class 0 --epochs 15 --out-json "$out" >"$log" 2>&1 &
echo "[$(ts)] launched A_full seed=$seed gpu=$gpu pid=$! out=$out"
sleep 3
done
i=0
for dose in "${DOSES[@]}"; do
for seed in "${SEEDS[@]}"; do
out="$JSONS/C-sdvae_d${dose}_s${seed}.json"
if [ -f "$out" ]; then
echo "[$(ts)] skip existing $out"
continue
fi
wait_for_slot
gpu=${GPUS[$((i % ${#GPUS[@]}))]}
log="$LOGS/C-sdvae_d${dose}_s${seed}.log"
/root/miniconda3/envs/rae_v2/bin/python "$PIPE/kermany_dose_rn50.py" \
--dose "$dose" --regime C --seed "$seed" --device "cuda:$gpu" \
--synth-csv "$CSV" --epochs 15 --out-json "$out" >"$log" 2>&1 &
echo "[$(ts)] launched C-sdvae d=$dose seed=$seed gpu=$gpu pid=$! out=$out"
i=$((i + 1))
sleep 3
done
done
for seed in "${SEEDS[@]}"; do
out="$JSONS/C-sdvae_full_s${seed}.json"
if [ -f "$out" ]; then
echo "[$(ts)] skip existing full-train $out"
continue
fi
wait_for_slot
gpu=${GPUS[$((i % ${#GPUS[@]}))]}
log="$LOGS/C-sdvae_full_s${seed}.log"
/root/miniconda3/envs/rae_v2/bin/python "$PIPE/kermany_dose_rn50.py" \
--dose 1.0 --regime C --seed "$seed" --device "cuda:$gpu" \
--real-cap-per-class 0 --synth-csv "$CSV" --epochs 15 --out-json "$out" >"$log" 2>&1 &
echo "[$(ts)] launched C-sdvae full seed=$seed gpu=$gpu pid=$! out=$out"
i=$((i + 1))
sleep 3
done
fail=0
for pid in $(jobs -rp); do
wait "$pid" || fail=$((fail + 1))
done
/root/miniconda3/envs/rae_v2/bin/python "$PIPE/aggregate_kermany.py" --arms sdvae --metric macro >"$DOWN/SUMMARY_sdvae_macro.txt"
/root/miniconda3/envs/rae_v2/bin/python "$PIPE/aggregate_kermany.py" --arms sdvae --metric disease_mean >"$DOWN/SUMMARY_sdvae_disease_mean.txt"
echo "[$(ts)] KERMANY_SDVAe_COMPLETION_DONE fail=$fail"
echo "KERMANY_SDVAe_COMPLETION_DONE fail=$fail $(date)" > "$DOWN/SDVAE_COMPLETION_DONE"
exit "$fail"
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