DOCK on AWS

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DOCK on AWS

  • create an account
  • create an S3 bucket "results2021"
  • within create dockfiles, database.txt output1
  • set up the ability to upload. On your client computer you need awscli. you need to set up your credentials. you need to upload. also work on download.
  • put someproject.dockfiles.tgz into dockfiles.
  • you need to set up credentials for aws.
  • go to AWS Batch. use new batch experience.
  • set up compute environments. env1. managed. env1. enable computer environment. AWSBatchService role. Spot. maximum on demand price 100. minimum vCPUs 0. max vCPUs 256. desired vCPUs 0. BEST_FIT_PROGRESSIVE.
  • set up job queue. queue1.
  • set up job definition. jobdef4. EC2. retry 1. execution timeout 14400. image btingle/dockaws:latest . bash . vcpus 1. memory 2048.
  • S3_DOCKFILES_LOCATION s3://results2021/dockfiles
  • SHRTCACHE /tmp
  • AWS_ACCESS_KEY_ID xxxxx
  • S3_INPUT_LOCATION s3://btingletestbucket/input
  • AWS_SECRET_ACCESS_KEY xxxxx
  • S3_OUTPUT_LOCATION s3://btingletestbucket/output1
  • AWS_DEFAULT_REGION us-east-2
  • Enable privileged mode root.
  • log driver awslogs
  • go to jobs. submit new job.
  • still to follow is
  • a. restart / complete all jobs
  • b. combine blazing fast
  • c. extract mol2 files.
  • d. download data
  • e. at beginning, set up which databases to dock by curating a list.