Local machine: advanced

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This article provides additional options for running Datagrok on your local machine using Docker Compose. By following these instructions, you can customize your local Datagrok stand or even start the second one.

Hardware requirements

Minimal hardware requirements: 60 GB of free disk space, 4 CPUs, 8 GB RAM.

Prerequisites

1. Install and launch the latest Docker Desktop application for your operating system:

   • Docker Desktop for Windows
   • Docker Desktop for MacOS
   • Docker Desktop for Linux

2. Clone public repository with docker-compose file

3. Open the command-line interface and navigate to the directory where you cloned the repository.

Installing Datagrok

1. Get latest Datagrok docker images

   docker compose -f docker\localhost.docker-compose.yaml --profile all pull

   docker compose -f docker/localhost.docker-compose.yaml --profile all pull

2. Run the basic Datagrok stand

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all up -d

   note

   If you encounter an error related to a WriteFile function when running docker-compose up on Windows, try running the command prompt (cmd) in Administrator mode. This is a known issue with Docker on certain computers.

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all up -d

3. After the docker compose process is completed, wait for approximately 1 minute for the Datagrok server to spin up. Once the server is up and running, open http://localhost:8080 in your browser and log in.

Log in to Datagrok

1. Once the server is up and running, open your browser and go to http://localhost:8080.
2. On the login page, use the following credentials to login:
   • Login or Email: admin
   • Password admin

note

If you see the message Datagrok server is unavailable, wait for approximately 1 minute for the server to start, and then reload the page.

CVM features

If you do not need CVM features, you can run only Datagrok application containers to save space and resources:

docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
  --profile datagrok --profile db up -d

docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
  --profile datagrok --profile db up -d

If you need CVM features only, you can run only CVM application containers:

docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
  --profile cvm up -d

docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
  --profile cvm up -d

To run Datagrok with exact CVM features, specify them in the command line using the --profile flag

• Cheminformatics

  docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
   --profile datagrok --profile db --profile chem up -d

  docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
   --profile datagrok --profile db --profile chem up -d

• Jupyter notebook

  docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
   --profile datagrok --profile db --profile jupyter_notebook up -d

  docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
   --profile datagrok --profile db --profile jupyter_notebook up -d

• Scripting

  docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
   --profile datagrok --profile db --profile scripting up -d

  docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
   --profile datagrok --profile db --profile scripting up -d

• Modeling

  docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
   --profile datagrok --profile db --profile modeling up -d

  docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
   --profile datagrok --profile db --profile modeling up -d

• Features can be enabled in any combination

  docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
    --profile datagrok ^
    --profile db ^
    --profile chem ^
    --profile scripting ^
    --profile jupyter_notebook ^
    --profile modeling ^
    up -d

  docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
    --profile datagrok \
    --profile db \
    --profile chem \
    --profile scripting \
    --profile jupyter_notebook \
    --profile modeling \
    up -d

• Datagrok container is not required to be started for any feature, so you can omit it in run parameters

  docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
    --profile chem ^
    --profile scripting ^
    --profile jupyter_notebook ^
    --profile modeling ^
    up -d

  docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
    --profile chem \
    --profile scripting \
    --profile jupyter_notebook \
    --profile modeling \
    up -d

Multiple stands

It is possible to run multiple stands of Datagrok on one host machine. To do so:

1. Run the first stand as described in instruction.

2. Set the Docker images versions with the environment variables. It can be any tag from Docker Hub.

   Environment variable	Default value
   DATAGROK_VERSION	latest
   GROK_SPAWNER_VERSION	latest
   GROK_CONNECT_VERSION	latest
   GROK_COMPUTE_VERSION	latest

    set DATAGROK_VERSION=latest
    set GROK_SPAWNER_VERSION=latest
    set GROK_CONNECT_VERSION=latest
    set GROK_COMPUTE_VERSION=latest

    export DATAGROK_VERSION='latest'
    export GROK_SPAWNER_VERSION='latest'
    export GROK_CONNECT_VERSION='latest'
    export GROK_COMPUTE_VERSION='latest'

3. Set environment variables for mapped ports:

   Environment variable	Default value
   DATAGROK_PORT	8080
   DATAGROK_DB_PORT	5432
   DATAGROK_CVM_PORT	8090
   DATAGROK_H2O_PORT	54321
   DATAGROK_H2O_HELPER_PORT	5005
   GROK_SPAWNER_PORT	8000
   GROK_CONNECT_PORT	1234
   DATAGROK_DEMO_POSTGRES_NORTHWIND_PORT	5433
   DATAGROK_DEMO_POSTGRES_CHEMBL_PORT	5434
   DATAGROK_DEMO_POSTGRES_UNICHEM_PORT	5435
   DATAGROK_DEMO_POSTGRES_STARBUCKS_PORT	5436
   DATAGROK_DEMO_POSTGRES_WORLD_PORT	5437

   To start the second stand properly the values should differ from the ports of the existing stands. For example, you can increment every port value by 11.

   set DATAGROK_PORT=8091
   set DATAGROK_DB_PORT=5444
   set DATAGROK_CVM_PORT=8101
   set DATAGROK_H2O_PORT=54332
   set DATAGROK_H2O_HELPER_PORT=5016
   set GROK_SPAWNER_PORT=8011
   set GROK_CONNECT_PORT=1245
   set DATAGROK_DEMO_POSTGRES_NORTHWIND_PORT=5444
   set DATAGROK_DEMO_POSTGRES_CHEMBL_PORT=5445
   set DATAGROK_DEMO_POSTGRES_UNICHEM_PORT=5446
   set DATAGROK_DEMO_POSTGRES_STARBUCKS_PORT=5447
   set DATAGROK_DEMO_POSTGRES_WORLD_PORT=5448

   export DATAGROK_PORT=8091
   export DATAGROK_DB_PORT=5444
   export DATAGROK_CVM_PORT=8101
   export DATAGROK_H2O_PORT=54332
   export DATAGROK_H2O_HELPER_PORT=5016
   export GROK_SPAWNER_PORT=8011
   export GROK_CONNECT_PORT=1245
   export DATAGROK_DEMO_POSTGRES_NORTHWIND_PORT=5444
   export DATAGROK_DEMO_POSTGRES_CHEMBL_PORT=5445
   export DATAGROK_DEMO_POSTGRES_UNICHEM_PORT=5446
   export DATAGROK_DEMO_POSTGRES_STARBUCKS_PORT=5447
   export DATAGROK_DEMO_POSTGRES_WORLD_PORT=5448

4. The last step is to run the second stand. It is important to change the project name to start the second Datagrok stand. The project name in the standard instructions, which were used for the first stand, is datagrok. For example, you can add an increment to the project name: datagrok_2

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok_2 ^
     --profile all up -d

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok_2 \
     --profile all up -d

Demo Databases

Datagrok offers demo databases that include sample data. To install them locally, run the following command:

docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok_2 ^
  --profile all --profile demo up -d

docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok_2 \
  --profile all --profile demo up -d

Shutting down Datagrok

To shut down Datagrok use this command:

docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
  --profile all --profile demo stop

docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
  --profile all --profile demo stop

All the data is saved in the Docker volumes.

To reset Datagrok to factory settings and remove all stored data, including all created users, projects, connections, etc., run the following command:

docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
  --profile all --profile demo down --volumes

docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
  --profile all --profile demo down --volumes

Troubleshooting

1. In case of any issues, check the settings in the Datagrok (Tools -> Settings...).

   • Connectors
     • External Host: grok_connect
   • Scripting:
     • CVM Url: http://cvm:8090
     • CVM URL Client: http://localhost:8090
     • H2o Url: http://h2o:54321
     • API Url: http://datagrok:8080/api
     • Cvm Split: true
   • Dev:
     • CVM Url: http://localhost:8090
     • Cvm Split: true
     • API Url: http://datagrok:8080/api

2. Check containers logs for any possible errors and report the problem if there are any

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo logs

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo logs

   You can also watch the logs of the desired service in real-time.

   • Replace <service> with the necessary service name
   • Replace <number> with desired log lines to watch or remove --tail <number> at all, if you want to see the full log

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo logs -f --tail <number> <service>

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo logs -f --tail <number> <service>

3. Restart Docker compose stand

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo down
   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo up -d

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo down
   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo up -d

4. For advanced service troubleshooting, you can access the containers shell.

   • Replace <service> with one of the services: db, datagrok, grok_connect, grok_compute, grok_spawner, jupyter_notebook, jupyter_kernel_gateway, h2o, etc.

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo exec <service> /bin/sh

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo exec <service> /bin/sh

5. Docker logs might take up all your free disk space. If such a situation has already taken place:

   • Limit Disk Usage using Docker Desktop Resources Settings
   • Or add to the Docker Daemon configuration log properties.

6. As your last resort, recreate stand completely

   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo down --volumes
   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo pull
   docker compose -f docker\localhost.docker-compose.yaml --project-name datagrok ^
     --profile all --profile demo up -d

   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo down --volumes
   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo pull
   docker compose -f docker/localhost.docker-compose.yaml --project-name datagrok \
     --profile all --profile demo up -d

Useful links

• Basic local machine deployment
• All deployment options
• Infrastructure overview
• Server configuration properties