OneScience-Group/SurfDock

1#!/bin/bash2 3source ~/anaconda3/bin/activate SurfDock4 5path=$(readlink -f "$0")6SurfDockdir="$(dirname "$(dirname "$(dirname "$(dirname "$path")")")")"7echo SurfDockdir : ${SurfDockdir}8 9export TORCH_DISTRIBUTED_DEBUG=INFO10# path of precomputed arrays11export precomputed_arrays="~/precomputed_arrays"12####################################    Setup Parameters    ############################13export CUDA_VISIBLE_DEVICES="6"14main_process_port=2950615num_processes=116# model version17version_num=618gussions=2019ns=4020nv=1021num_conv_layers=422bs_arrays=(64)23valset=224batch_size=3225mdn_dist_threshold_train=726mdn_dist_threshold_test=527lr=1e-328project="V${version_num}_surface"29time=`date +%Y_%m_%d_%H_%M_%S`30########################################################################################31save_dir="/home/house/caoduanhua/${project}"32 33for i in ${bs_arrays[@]}34do35batch_size=${i}36echo batch_size : ${batch_size}37command=`accelerate launch \38--multi_gpu \39--main_process_port ${main_process_port} \40--num_processes ${num_processes} \41${SurfDockdir}/scripts/train_mdn_accelarete.py \42--project ${project} \43--run_name project_${project}_valset_${valset}_RunTime_${time}_ns_${ns}_nv_${nv}_layer_${num_conv_layers}_lr_${lr}_gussions_${gussions}_train_dist_${mdn_dist_threshold_train}_test_dist_${mdn_dist_threshold_test}_bs_${batch_size}_use_orig_pos_mdn_inter_loss_atom_type_loss_bond_type_loss \44--test_sigma_intervals \45--data_dir ~/PDBBIND/PDBBind_pocket_8A/ \46--cache_path ~/PDBBIND/cache_RTMScoreFeature_Surface_PDBBIND_pocket_8A_randomsplit_rtmscore_valset_${valset} \47--esm_embeddings_path ~/PDBBIND/esm_embedding/esm_embedding_pocket_for_train/esm2_3billion_embeddings.pt \48--split_test ~/data/splits/timesplit_test \49--split_train ~/data/splits/timesplit_no_lig_overlap_train \50--split_val ~/data/splits/timesplit_no_lig_overlap_val \51--log_dir ${save_dir}/workdir \52--wandb_dir ${save_dir} \53--num_dataloader_workers 1 \54--wandb \55--num_workers 1 \56--lr ${lr} \57--tr_sigma_min 0.000000000000000001 \58--tr_sigma_max 0.00000000000000000001 \59--rot_sigma_min 0.000000000000000001 \60--rot_sigma_max 0.000000000000000000001 \61--tor_sigma_min 0.000000000000000000001 \62--tor_sigma_max 0.00000000000000000000001 \63--no_torsion \64--batch_size ${batch_size} \65--ns ${ns} \66--nv ${nv} \67--distance_embed_dim 32 \68--cross_distance_embed_dim 32 \69--sigma_embed_dim 32 \70--num_conv_layers ${num_conv_layers} \71--dynamic_max_cross \72--scheduler plateau \73--scale_by_sigma \74--dropout 0.1 \75--remove_hs \76--c_alpha_max_neighbors 24 \77--receptor_radius 15 \78--cudnn_benchmark \79--val_inference_freq 5 \80--num_inference_complexes 500 \81--scheduler_patience 30 \82--model_type mdn_model \83--bond_type_prediction \84--atom_type_prediction \85--model_version version${version_num} \86--mdn_dist_threshold_train ${mdn_dist_threshold_train} \87--mdn_dist_threshold_test ${mdn_dist_threshold_test} \88--mdn_dropout 0.1 \89--topN 1 \90--n_gaussians ${gussions} \91--n_epochs 850`92state=$command93done94