mypresto_screening.md

myPresto5 Screening Tutorial on AWS ParallelCluster with SGE

based on myPresto5.0 -in silico screening- tutorial 180112

set up AWS ParallelCluster

install AWS ParallelCluster

sudo pip install aws-parallelcluster

create config file for AWS ParallelCluster

• ~/.parallelcluster/config

replace <KEY_NAME>, <VPC_ID>, <MASTER_SUBNET_ID>, <COMPUTE_SUBNET_ID>

[aws]
aws_region_name = us-east-1

[global]
cluster_template = default
update_check = true
sanity_check = true

[aliases]
ssh = ssh {CFN_USER}@{MASTER_IP} {ARGS}

[cluster default]
key_name = <KEY_NAME>
base_os = centos7
scheduler = sge

master_instance_type = c5.xlarge
compute_instance_type = c5.12xlarge
max_queue_size = 10
maintain_initial_size = true

master_root_volume_size = 200

vpc_settings = default
dcv_settings = dcv1

tags = {"Project": "ParallelCluster-myPresto"}

[vpc default]
vpc_id = <VPC_ID>
master_subnet_id = <MASTER_SUBNET_ID>
compute_subnet_id = <COMPUTE_SUBNET_ID>

[dcv dcv1]
enable = master

• create cluster

pcluster create mypresto-cluster

connect to the cluster by NICE-DCV

pcluster dcv connect -k <KEY_NAME>.pem mypresto-cluster

screening_org_server

• bin/make_grid.csh

qsub -b y -N "G_${protein_name}" -cwd -o make_grid_${protein_name}.log "${sievgene} < ${protein_name}.inp"

• bin/make_docking_score.csh

qsub -b y -cwd -o D_${docking_name}.log -N D_${docking_name} $CMD  

• bin/RUN_docking.pl

chmod +x bin/RUN_docking.pl

• bin/run_group_MTS.pl

# system("bsub -o $output_file -i $input_file -q $que -J D_$code $CMD");       
system("qsub -b y -o D_${code}.log -N D_${code} -cwd \"$CMD < $input_file\"")