File size: 3,944 Bytes
4653e06 | 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 | # bash run.sh Protenix 1
#!/bin/bash
algorithm="$1"
gpu_id="$2"
af3_input_json=./examples/alphafold3_inputs.json
targets_dir=./examples/targets
output_root_dir="./examples/outputs"
time_log_root_dir="./examples/times"
ground_truth_dir="./examples/ground_truths"
overlay_size=2048
prediction_root_dir="$output_root_dir/prediction"
evaluation_root_dir="$output_root_dir/evaluation"
input_root_dir="$output_root_dir/input"
time_log_dir="$time_log_root_dir"
recalculate=false
while getopts ":r" opt; do
case $opt in
r) recalculate=true
;;
\?) echo "Invalid option -$OPTARG" >&2
;;
esac
done
echo "Recalculate all algorithm outputs: $recalculate"
if "$recalculate"; then
# Clean output dir
rm -rf "$prediction_root_dir"
rm -rf "$evaluation_root_dir"
rm -rf "$input_root_dir"
rm -rf "$time_log_dir"
fi
# Create the output directory if it doesn't exist
mkdir -p "$prediction_root_dir"
mkdir -p "$evaluation_root_dir"
mkdir -p "$input_root_dir"
mkdir -p "$time_log_dir"
# start evaluation environment
conda init
. /root/miniconda3/etc/profile.d/conda.sh
conda activate foldbench
# Loop through each algorithm in the algorithms directory
for algorithm_dir in algorithms/*; do
if [ -d "$algorithm_dir" ] && [ $(basename "$algorithm_dir") != "base" ]; then
algorithm_name=$(basename "$algorithm_dir")
# If an algorithm is specified, only continue if algorithm_name matches
if [ -z "$algorithm" ] || [ "$algorithm_name" == "$algorithm" ]; then
prediction_dir="$prediction_root_dir/${algorithm_name}"
time_log_file="$time_log_dir/${algorithm_name}_time.log"
# Check if the output file does not exist
# if [ ! -e "$prediction_dir" ]; then
if [ -e "$prediction_dir" ]; then
echo "Processing algorithm: $algorithm_name"
input_dir="$input_root_dir/${algorithm_name}"
evaluation_dir="$evaluation_root_dir/${algorithm_name}"
# create dirs for prediction, input, evaluation
mkdir -p "$prediction_dir"
mkdir -p "$input_dir"
mkdir -p "$evaluation_dir"
# Remove an existing container overlay, if any
rm -rf "algorithms/${algorithm_name}/overlay.img"
# Create writable overlay for the container
apptainer overlay create --size $overlay_size --sparse "algorithms/${algorithm_name}/overlay.img"
# Calculate predictions
echo "RUN ALGORITHM $algorithm_name"
{ time ( apptainer exec --nv \
--overlay "algorithms/${algorithm_name}/overlay.img" \
-B $af3_input_json:/algo/alphafold3_inputs.json \
-B $output_root_dir:/algo/outputs \
"algorithms/${algorithm_name}/container.sif" \
bash -c "cd /algo \
&& ./make_predictions.sh ${af3_input_json} ${input_dir} ${prediction_dir} ${evaluation_dir} ${gpu_id}" 2>&1 ); } 2> "$time_log_file"
echo "EVALUATE PREDICTIONS"
python evaluate.py --targets_dir ${targets_dir} --prediction_dir ${prediction_dir} --evaluation_dir ${evaluation_dir} --ground_truth_dir ${ground_truth_dir}
python task_score_summary.py --algorithm_names ${algorithm_name}
else
echo "Skipping algorithm: $algorithm_name. Output file already exists."
# Remove an existing container overlay, if any
# FIXME: mb put this part outside if-else statement?
# Now when each dataset has separate container overlays,
# old dataset overlays must be removed if output file already exists.
rm -rf "algorithms/${algorithm_name}/overlay.img"
fi
fi
fi
done |