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Issue Installing and Running Atlas

Developers
#1

I am trying to install Atlas on my server. At the moment I have a dockerize OMOP database and WebAPI up and running. My goal is to setup little by little all the OHDSI tooling.

My database includes schemas required for WebAPI:

  • 1 CDM source + Vocabulary tables
  • Result schema and populated with tables from endpoint (/WebAPI/ddl/results?dialect=postgresql&schema[…])
  • OHDSI Schema: seems well populated first time running WebAPI with Flyaway (includes the source and source daimon table that point to my cdm, vocabulary and result schemas)
  • 1 temp schema

It seems that the database and WebAPI are well working together, I am able to use a bunch of WebAPI endpoints to create cohort definition, search vocabulary…

Now I encounter difficulties to setup Atlas on top of this, I assume I am missing some steps. I am using a minimal docker file as define below:

version: '3'
services:
  atlas:
    image: ohdsi/atlas
    container_name: atlas
    ports:
      - "7070:80"
    environment:
      - WEBAPI_URL=http://webapi:8080/WebAPI
    networks:
      - omop_network

networks:
  omop_network:
    external: true

All my containers are on the same network.

When I try a docker compose up, atlas setup stay stuck forever on:

[+] Running 1/0
 ✔ Container atlas  Created                                                                                                                                                                                                                                                                                    0.0s 
Attaching to atlas
atlas  | /docker-entrypoint.sh: /docker-entrypoint.d/ is not empty, will attempt to perform configuration
atlas  | /docker-entrypoint.sh: Looking for shell scripts in /docker-entrypoint.d/
atlas  | /docker-entrypoint.sh: Launching /docker-entrypoint.d/10-listen-on-ipv6-by-default.sh
atlas  | 10-listen-on-ipv6-by-default.sh: info: can not modify /etc/nginx/conf.d/default.conf (read-only file system?)
atlas  | /docker-entrypoint.sh: Launching /docker-entrypoint.d/20-envsubst-on-templates.sh
atlas  | /docker-entrypoint.sh: Launching /docker-entrypoint.d/30-atlas-env-subst.sh
atlas  | /docker-entrypoint.sh: Launching /docker-entrypoint.d/30-tune-worker-processes.sh
atlas  | /docker-entrypoint.sh: Configuration complete; ready for start up
atlas  | 2024/09/26 09:42:22 [notice] 1#1: using the "epoll" event method
atlas  | 2024/09/26 09:42:22 [notice] 1#1: nginx/1.23.3
atlas  | 2024/09/26 09:42:22 [notice] 1#1: built by gcc 12.2.1 20220924 (Alpine 12.2.1_git20220924-r4)
atlas  | 2024/09/26 09:42:22 [notice] 1#1: OS: Linux 5.15.153.1-microsoft-standard-WSL2
atlas  | 2024/09/26 09:42:22 [notice] 1#1: getrlimit(RLIMIT_NOFILE): 1048576:1048576
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker processes
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 27
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 28
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 29
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 30
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 31
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 32
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 33
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 34
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 35
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 36
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 37
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 38
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 39
atlas  | 2024/09/26 09:42:22 [notice] 1#1: start worker process 40

At the moment I am trying to run this locally on my WSL machine to make sure I do not break anything on my server.

Does anyone experienced the same issue? Do you see anything missing in my setup process?

t