online_preproc_baremetal.sh

# Copyright (c) 2023 Intel Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

root_home=$1 # e.g. /home/<your-username>, root path that holds all intermediate IO data
data_dir=$2 # e.g. $root_home/af2data, path that holds all reference database and model params, including mgnify uniref etc.
input_dir=$3 # e.g. $root_home/samples, path of all query .fa files (sequences in fasta format)
out_dir=$4 # e.g. $root_home/experiments, path that contains intermediates output of preprocessing, model inference, and final result

suffix=".fa"
log_dir=$root_home/logs # root of logs
n_sample=`ls ${input_dir}|grep ${suffix}|wc -l`
n_core=`lscpu|grep "^Core(s) per socket"|awk '{split($0,a," "); print a[4]}'`
n_socket=`lscpu|grep "^Socket(s)"|awk '{split($0,a," "); print a[2]}'`
((n_sample_0=$n_sample-1))
((core_per_instance=$n_core*$n_socket))
script="python run_preprocess.py"
workdir=`pwd`

export TF_CPP_MIN_LOG_LEVEL=3
lo=0
((hi=$core_per_instance-1))
((ncpu=$core_per_instance))
for f in `ls ${input_dir} | grep ${suffix}`; do
  fpath=${input_dir}/${f}
  # echo preprocessing ${fpath} on cores $lo to $hi on full sockets
  # numactl -C $lo-$hi -m 0,1 $script \
  $script \
    --n_cpu=$ncpu \
    --fasta_paths=${fpath} \
    --output_dir=${out_dir} \
    --model_names=model_1 \
    --bfd_database_path=${data_dir}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
    --uniref30_database_path=${data_dir}/uniref30/UniRef30_2021_03 \
    --uniref90_database_path=${data_dir}/uniref90/uniref90.fasta \
    --mgnify_database_path=${data_dir}/mgnify/mgy_clusters_2022_05.fa \
    --pdb70_database_path=${data_dir}/pdb70/pdb70 \
    --template_mmcif_dir=${data_dir}/pdb_mmcif/mmcif_files \
    --data_dir=${data_dir} \
    --max_template_date=2022-01-01 \
    --obsolete_pdbs_path=${data_dir}/pdb_mmcif/obsolete.dat \
    --hhblits_binary_path="$PWD/hh-suite/build/release/bin/hhblits" \
    --hhsearch_binary_path="$PWD/hh-suite/build/release/bin/hhsearch" \
    --jackhmmer_binary_path="$PWD/hmmer/release/bin/jackhmmer" \
    --kalign_binary_path=`which kalign` \
    --run_in_parallel=true
done
cd $workdir