Bump atom3-py3

Author: amorehead

project/datasets/builder/compile_evcoupling_dataset_on_andes.sh

@@ -4,38 +4,38 @@
 #SBATCH -A BIF135
 #SBATCH -p batch
 #SBATCH -J make_evcoupling_dataset
-#SBATCH -t 0-12:00
+#SBATCH -t 0-24:00
 #SBATCH --mem 224G
 #SBATCH --nodes 4
 #SBATCH --ntasks-per-node 1
 ###############################################################
 
+# Remote paths #
+export PROJDIR=/gpfs/alpine/scratch/"$USER"/bif135/Repositories/Lab_Repositories/DIPS-Plus
+export PSAIADIR=/ccs/home/"$USER"/Programs/PSAIA_1.0_source/bin/linux/psa
+export OMP_NUM_THREADS=8
+
 # Remote Conda environment #
 source "$PROJDIR"/miniconda3/bin/activate
 conda activate DIPS-Plus
 
 # Load CUDA module for DGL
 module load cuda/10.2.89
 
-# Remote paths #
-export PROJDIR=/gpfs/alpine/scratch/"$USER"/bif135/Repositories/Lab_Repositories/DIPS-Plus
-export PSAIADIR=/ccs/home/"$USER"/Programs/PSAIA_1.0_source/bin/linux/psa
-export OMP_NUM_THREADS=8
-
 # Default to using the Big Fantastic Database (BFD) of protein sequences (approx. 270GB compressed)
 export HHSUITE_DB=/gpfs/alpine/scratch/$USER/bif132/Data/Databases/bfd_metaclust_clu_complete_id30_c90_final_seq
 
 # Run dataset compilation scripts
 cd "$PROJDIR"/project || exit
 
-srun python3 "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/parsed "$HHSUITE_DB" "$PROJDIR"/project/datasets/DB5/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type evcoupling --write_file
+srun python3 "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/EVCoupling/interim/parsed "$PROJDIR"/project/datasets/EVCoupling/interim/parsed "$HHSUITE_DB" "$PROJDIR"/project/datasets/EVCoupling/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type evcoupling --read_file
 
-#srun python3 "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim/pairs "$PROJDIR"/project/datasets/DB5/interim/external_feats "$PROJDIR"/project/datasets/DB5/final/raw --num_cpus 32 --rank "$1" --size "$2" --source_type db5
+#srun python3 "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/EVCoupling/raw "$PROJDIR"/project/datasets/EVCoupling/interim/pairs "$PROJDIR"/project/datasets/EVCoupling/interim/external_feats "$PROJDIR"/project/datasets/EVCoupling/final/raw --num_cpus 32 --rank "$1" --size "$2" --source_type EVCoupling
 
-#python3 "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DB5/final/raw --source_type db5 --rank "$1" --size "$2"
-#python3 "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
-#python3 "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
-#python3 "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DB5/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
+#python3 "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --source_type EVCoupling --rank "$1" --size "$2"
+#python3 "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --rank "$1" --size "$2"
+#python3 "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --rank "$1" --size "$2"
+#python3 "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
 
 # Optionally convert each postprocessed (final 'raw') complex into a pair of DGL graphs (final 'processed') with labels
-#python3 "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DB5/final/raw "$PROJDIR"/project/datasets/DB5/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"
+#python3 "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/EVCoupling/final/raw "$PROJDIR"/project/datasets/EVCoupling/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"