forked from PaddlePaddle/PaddleHelix
-
Notifications
You must be signed in to change notification settings - Fork 0
/
gpu_infer.sh
60 lines (54 loc) · 2.53 KB
/
gpu_infer.sh
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
#!/bin/bash
cd "$(dirname $0)"
root_path="$(pwd)"
demo=$1
export PYTHONPATH=$root_path:$PYTHONPATH
export FLAGS_use_cuda_managed_memory=true
#DATA_DIR="$root_path/data"
DATA_DIR="/root/paddlejob/workspace/env_run/alphafold_data"
fasta_file="$root_path/demo_data/casp14_demo/fasta/${demo}.fasta"
OUTPUT_DIR="$root_path/demo_data/casp14_demo/output"
MODELS="model_1,model_5"
USE_DAP=false
if [ $USE_DAP == true ]; then
distributed_args="--run_mode=collective --log_dir=${log_dir}"
python -m paddle.distributed.launch ${distributed_args} \
--gpus="0,1,2,3,4,5,6,7" \
run_helixfold.py \
--distributed \
--dap_degree 8 \
--fasta_paths=${fasta_file} \
--data_dir=${DATA_DIR} \
--bfd_database_path=${DATA_DIR}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--small_bfd_database_path=${DATA_DIR}/small_bfd/bfd-first_non_consensus_sequences.fasta \
--uniclust30_database_path=${DATA_DIR}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--uniref90_database_path=${DATA_DIR}/uniref90/uniref90.fasta \
--mgnify_database_path=${DATA_DIR}/mgnify/mgy_clusters_2018_12.fa \
--pdb70_database_path=${DATA_DIR}/pdb70/pdb70 \
--template_mmcif_dir=${DATA_DIR}/pdb_mmcif/mmcif_files \
--obsolete_pdbs_path=${DATA_DIR}/pdb_mmcif/obsolete.dat \
--max_template_date=2020-05-14 \
--model_names=${MODELS} \
--output_dir=${OUTPUT_DIR} \
--preset='reduced_dbs' \
--random_seed=0 \
${@:2}
else
CUDA_VISIBLE_DEVICES=0 python run_helixfold.py \
--fasta_paths=${fasta_file} \
--data_dir=${DATA_DIR} \
--bfd_database_path=${DATA_DIR}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
--small_bfd_database_path=${DATA_DIR}/small_bfd/bfd-first_non_consensus_sequences.fasta \
--uniclust30_database_path=${DATA_DIR}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
--uniref90_database_path=${DATA_DIR}/uniref90/uniref90.fasta \
--mgnify_database_path=${DATA_DIR}/mgnify/mgy_clusters_2018_12.fa \
--pdb70_database_path=${DATA_DIR}/pdb70/pdb70 \
--template_mmcif_dir=${DATA_DIR}/pdb_mmcif/mmcif_files \
--obsolete_pdbs_path=${DATA_DIR}/pdb_mmcif/obsolete.dat \
--max_template_date=2020-05-14 \
--model_names=${MODELS} \
--output_dir=${OUTPUT_DIR} \
--preset='reduced_dbs' \
--random_seed=0 \
${@:2}
fi