./run_stacks.sh executable fails

[AleruDivine]

Following the readme instructions, I copied the ./.env.TEMPLATE file content and pasted it into an ./.env file, and I tried running the ./run_stacks.sh executable, but it fails with the following output:

dependency failed to start: container molevolvr20-db-1 exited (1)

I need help starting the project. My OSTYPE is darwin24.0, and the following is the log output from running the executable:

$ ./run_stack.sh
* Inferred target environment: dev (via DEFAULT_ENV)
* Pulling images for dev (tag: dev)
[+] Pulling 7/7
 ✔ worker Skipped - Image is already being pulled by master                                                                                                                                                                                                                                                                               0.0s
 ✔ dev-db Skipped - Image is already being pulled by db                                                                                                                                                                                                                                                                                   0.0s
 ✔ master Pulled                                                                                                                                                                                                                                                                                                                          4.3s
 ✔ db Pulled                                                                                                                                                                                                                                                                                                                              2.8s
 ✔ backend Pulled                                                                                                                                                                                                                                                                                                                         3.6s
 ✔ accounting Pulled                                                                                                                                                                                                                                                                                                                      2.8s
 ✔ frontend Pulled                                                                                                                                                                                                                                                                                                                        3.8s
* Building images for dev (tag: dev)
[+] Building 5.6s (65/74)                                                                                                                                                                                                                                                                                                 docker:desktop-linux
 => [backend internal] load build definition from Dockerfile                                                                                                                                                                                                                                                                              0.0s
 => => transferring dockerfile: 4.60kB                                                                                                                                                                                                                                                                                                    0.0s
 => [worker internal] load build definition from Dockerfile                                                                                                                                                                                                                                                                               0.0s
 => => transferring dockerfile: 5.06kB                                                                                                                                                                                                                                                                                                    0.0s
 => WARN: FromPlatformFlagConstDisallowed: FROM --platform flag should not use constant value "linux/amd64" (line 2)                                                                                                                                                                                                                      0.0s
 => [master internal] load build definition from Dockerfile                                                                                                                                                                                                                                                                               0.0s
 => => transferring dockerfile: 5.06kB                                                                                                                                                                                                                                                                                                    0.0s
 => WARN: FromPlatformFlagConstDisallowed: FROM --platform flag should not use constant value "linux/amd64" (line 2)                                                                                                                                                                                                                      0.0s
 => [backend] resolve image config for docker-image://docker.io/docker/dockerfile:1.7                                                                                                                                                                                                                                                     1.7s
 => [backend internal] load metadata for docker.io/rocker/tidyverse:4.3                                                                                                                                                                                                                                                                   3.5s
 => [backend auth] docker/dockerfile:pull token for registry-1.docker.io                                                                                                                                                                                                                                                                  0.0s
 => [worker auth] rocker/tidyverse:pull token for registry-1.docker.io                                                                                                                                                                                                                                                                    0.0s
 => CACHED [backend] docker-image://docker.io/docker/dockerfile:1.7@sha256:a57df69d0ea827fb7266491f2813635de6f17269be881f696fbfdf2d83dda33e                                                                                                                                                                                               0.0s
 => [worker internal] load .dockerignore                                                                                                                                                                                                                                                                                                  0.0s
 => => transferring context: 2B                                                                                                                                                                                                                                                                                                           0.0s
 => [master internal] load .dockerignore                                                                                                                                                                                                                                                                                                  0.0s
 => => transferring context: 2B                                                                                                                                                                                                                                                                                                           0.0s
 => [backend internal] load .dockerignore                                                                                                                                                                                                                                                                                                 0.0s
 => => transferring context: 2B                                                                                                                                                                                                                                                                                                           0.0s
 => [master] importing cache manifest from us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-slurm-node:dev                                                                                                                                                                                                     0.0s
 => [backend slurm-build  1/14] FROM docker.io/rocker/tidyverse:4.3@sha256:7854ac4af0ab36a0b457a266dd41db04cbf004150ea6074e7ce3b8a155f77ba2                                                                                                                                                                                               0.0s
 => [worker internal] load build context                                                                                                                                                                                                                                                                                                  0.0s
 => => transferring context: 944B                                                                                                                                                                                                                                                                                                         0.0s
 => [master internal] load build context                                                                                                                                                                                                                                                                                                  0.0s
 => => transferring context: 944B                                                                                                                                                                                                                                                                                                         0.0s
 => [backend] importing cache manifest from us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-backend:dev                                                                                                                                                                                                       0.0s
 => [backend internal] load build context                                                                                                                                                                                                                                                                                                 0.0s
 => => transferring context: 1.77kB                                                                                                                                                                                                                                                                                                       0.0s
 => CACHED [worker slurm-build  2/14] RUN groupadd -g 981 munge   && useradd  -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u 981 -g munge  -s /sbin/nologin munge   && groupadd -g 982 slurm   && useradd  -m -c "Slurm workload manager" -d /var/lib/slurm -u 982 -g slurm  -s /bin/bash slurm   && groupadd -g 1005 worker     0.0s
 => CACHED [worker slurm-build  3/14] RUN apt-get update                                                                                                                                                                                                                                                                                  0.0s
 => CACHED [worker slurm-build  4/14] RUN DEBIAN_FRONTEND=noninteractive apt-get install -y     munge libmunge-dev     lua5.4 liblua5.4-dev     libhttp-parser-dev libjson-c-dev libyaml-dev libjwt-dev     mailutils     hwloc libhwloc-dev     libmariadb-dev     libbpf-dev libdbus-1-dev     libpam0g-dev     libreadline-dev         0.0s
 => CACHED [worker slurm-build  5/14] RUN apt-get install -y wget gcc make bzip2     && cd /tmp     && wget https://download.schedmd.com/slurm/slurm-24.05.1.tar.bz2     && tar -xvf slurm-24.05.1.tar.bz2     && cd slurm-24.05.1     && ./configure         --with-lua         --sysconfdir=/etc/slurm/         --with-systemdsystemun  0.0s
 => CACHED [worker slurm-build  6/14] COPY ./install.R /tmp/install.r                                                                                                                                                                                                                                                                     0.0s
 => CACHED [worker slurm-build  7/14] RUN   Rscript /tmp/install.r                                                                                                                                                                                                                                                                        0.0s
 => CACHED [worker slurm-build  8/14] RUN apt-get update && apt-get install -y curl stress cgroup-tools cron                                                                                                                                                                                                                              0.0s
 => CACHED [worker slurm-build  9/14] RUN curl -L -o envsubst     "https://github.com/a8m/envsubst/releases/download/v1.2.0/envsubst-$( uname -s )-$( uname -m )" &&     chmod +x envsubst &&     mv envsubst /usr/local/bin                                                                                                              0.0s
 => CACHED [worker slurm-build 10/14] COPY ./slurm-config/ /opt/templates/                                                                                                                                                                                                                                                                0.0s
 => CACHED [worker slurm-build 11/14] COPY ./system-v/init.d/ /etc/init.d/                                                                                                                                                                                                                                                                0.0s
 => CACHED [worker slurm-build 12/14] COPY ./system-v/default/ /etc/default/                                                                                                                                                                                                                                                              0.0s
 => CACHED [worker slurm-build 13/14] RUN mkdir -p /var/spool/slurmd /var/spool/slurmctld                                                                                                                                                                                                                                                 0.0s
 => CACHED [master slurm-build 14/14] COPY ./entrypoint/ /var/slurm-init/                                                                                                                                                                                                                                                                 0.0s
 => [master] exporting to image                                                                                                                                                                                                                                                                                                           0.0s
 => => exporting layers                                                                                                                                                                                                                                                                                                                   0.0s
 => => preparing layers for inline cache                                                                                                                                                                                                                                                                                                  0.0s
 => => writing image sha256:237dd74dbd55081f4a7a59039d51544106581e2059b0f95fbd3902d704dfc58c                                                                                                                                                                                                                                              0.0s
 => => naming to us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-slurm-node:dev                                                                                                                                                                                                                               0.0s
 => [worker] exporting to image                                                                                                                                                                                                                                                                                                           0.0s
 => => exporting layers                                                                                                                                                                                                                                                                                                                   0.0s
 => => preparing layers for inline cache                                                                                                                                                                                                                                                                                                  0.0s
 => => writing image sha256:fca83ef5cc098d17dc3d909358e6baeb0964d06f41e45fbb6d005ba5b8bb23a3                                                                                                                                                                                                                                              0.0s
 => => naming to us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-slurm-node:dev                                                                                                                                                                                                                               0.0s
 => CACHED [backend backend-base 2/7] RUN apt-get update && apt-get install -y ccache                                                                                                                                                                                                                                                     0.0s
 => CACHED [backend backend-base 3/7] RUN apt-get update && apt-get install -y curl                                                                                                                                                                                                                                                       0.0s
 => CACHED [backend backend-base 4/7] RUN mkdir -p /tmp/software/ &&     wget -L -O /tmp/software/drip.zip https://rdrip.netlify.app/builds/drip_0.1.0_linux_amd64.zip &&     unzip /tmp/software/drip.zip -d /tmp/software &&     mv /tmp/software/drip /usr/local/bin &&     chmod +x /usr/local/bin/drip                               0.0s
 => CACHED [backend backend-base 5/7] RUN curl -sSf https://atlasgo.sh | sh                                                                                                                                                                                                                                                               0.0s
 => CACHED [backend backend-base 6/7] COPY ./docker/install.R /tmp/install.r                                                                                                                                                                                                                                                              0.0s
 => CACHED [backend backend-base 7/7] RUN   Rscript /tmp/install.r                                                                                                                                                                                                                                                                        0.0s
 => CACHED [backend backend-slurm 1/7] RUN curl -L -o envsubst     "https://github.com/a8m/envsubst/releases/download/v1.2.0/envsubst-$( uname -s )-$( uname -m )" &&     chmod +x envsubst &&     mv envsubst /usr/local/bin                                                                                                             0.0s
 => CACHED [backend backend-slurm 2/7] RUN groupadd -g 981 munge     && useradd  -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u 981 -g munge  -s /sbin/nologin munge                                                                                                                                                             0.0s
 => CACHED [backend backend-slurm 3/7] RUN apt-get update                                                                                                                                                                                                                                                                                 0.0s
 => CACHED [backend backend-slurm 4/7] RUN DEBIAN_FRONTEND=noninteractive apt-get install -y     munge libmunge-dev     lua5.4 liblua5.4-dev     libhttp-parser-dev libjson-c-dev libyaml-dev libjwt-dev     mailutils     hwloc libhwloc-dev     libmariadb-dev     libbpf-dev libdbus-1-dev     libpam0g-dev     libreadline-dev        0.0s
 => CACHED [backend backend-slurm 5/7] RUN apt-get install -y wget gcc make bzip2     && cd /tmp     && wget https://download.schedmd.com/slurm/slurm-24.05.1.tar.bz2     && tar -xvf slurm-24.05.1.tar.bz2     && cd slurm-24.05.1     && ./configure         --sysconfdir=/etc/slurm/         --enable-slurmd=no --enable-controller=n  0.0s
 => CACHED [backend backend-slurm 6/7] COPY ./cluster_config/slurm.conf.template /opt/config-templates/slurm.conf.template                                                                                                                                                                                                                0.0s
 => CACHED [backend backend-slurm 7/7] RUN mkdir -p /etc/slurm/                                                                                                                                                                                                                                                                           0.0s
 => CACHED [backend backend-final 1/2] WORKDIR /app                                                                                                                                                                                                                                                                                       0.0s
 => CACHED [backend backend-final 2/2] COPY . /app                                                                                                                                                                                                                                                                                        0.0s
 => [backend] exporting to image                                                                                                                                                                                                                                                                                                          0.0s
 => => exporting layers                                                                                                                                                                                                                                                                                                                   0.0s
 => => preparing layers for inline cache                                                                                                                                                                                                                                                                                                  0.0s
 => => writing image sha256:051535fc3a5a23a07923e293a3b070ac63537f7eb075f31ec6bd7dc9c1c1541e                                                                                                                                                                                                                                              0.0s
 => => naming to us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-backend:dev                                                                                                                                                                                                                                  0.0s
 => [worker] resolving provenance for metadata file                                                                                                                                                                                                                                                                                       0.0s
 => [master] resolving provenance for metadata file                                                                                                                                                                                                                                                                                       0.0s
 => [backend] resolving provenance for metadata file                                                                                                                                                                                                                                                                                      0.0s
 => [frontend internal] load build definition from Dockerfile                                                                                                                                                                                                                                                                             0.0s
 => => transferring dockerfile: 1.81kB                                                                                                                                                                                                                                                                                                    0.0s
 => [frontend internal] load metadata for docker.io/oven/bun:1                                                                                                                                                                                                                                                                            1.7s
 => [frontend auth] oven/bun:pull token for registry-1.docker.io                                                                                                                                                                                                                                                                          0.0s
 => [frontend internal] load .dockerignore                                                                                                                                                                                                                                                                                                0.0s
 => => transferring context: 2B                                                                                                                                                                                                                                                                                                           0.0s
 => [frontend] importing cache manifest from us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-frontend:dev                                                                                                                                                                                                     0.0s
 => [frontend internal] load build context                                                                                                                                                                                                                                                                                                0.0s
 => => transferring context: 32.81kB                                                                                                                                                                                                                                                                                                      0.0s
 => [frontend base 1/2] FROM docker.io/oven/bun:1@sha256:eb409bed239c3adff079a6b71283f151e802d66b99f643ba7a71e1be7d3da513                                                                                                                                                                                                                 0.0s
 => CACHED [frontend base 2/2] WORKDIR /app                                                                                                                                                                                                                                                                                               0.0s
 => CACHED [frontend install 1/2] COPY package.json bun.lockb /temp/dev/                                                                                                                                                                                                                                                                  0.0s
 => CACHED [frontend install 2/2] RUN cd /temp/dev/ &&     bun install --frozen-lockfile                                                                                                                                                                                                                                                  0.0s
 => CACHED [frontend dev 1/2] COPY --from=install /temp/dev/node_modules node_modules                                                                                                                                                                                                                                                     0.0s
 => [frontend dev 2/2] COPY . .                                                                                                                                                                                                                                                                                                           0.1s
 => [frontend] exporting to image                                                                                                                                                                                                                                                                                                         0.0s
 => => exporting layers                                                                                                                                                                                                                                                                                                                   0.0s
 => => preparing layers for inline cache                                                                                                                                                                                                                                                                                                  0.0s
 => => writing image sha256:85eaeadc9d5b95f71c4531cda338cee6855eeaa1d2a892a13ff68994c8bf3119                                                                                                                                                                                                                                              0.0s
 => => naming to us-central1-docker.pkg.dev/cuhealthai-foundations/jravilab-public/molevolvr-frontend:dev                                                                                                                                                                                                                                 0.0s
 => [frontend] resolving provenance for metadata file                                                                                                                                                                                                                                                                                     0.0s
Running: docker compose -f docker-compose.yml -f docker-compose.slurm.yml -f docker-compose.dev.yml up -d
[+] Running 7/7
 ✔ Container molevolvr20-dev-db-1      Started                                                                                                                                                                                                                                                                                            0.7s
 ✘ Container molevolvr20-db-1          Error                                                                                                                                                                                                                                                                                              1.2s
 ✔ Container molevolvr20-worker-1      Started                                                                                                                                                                                                                                                                                            0.7s
 ✔ Container molevolvr20-master-1      Started                                                                                                                                                                                                                                                                                            0.7s
 ✔ Container molevolvr20-backend-1     Recreated                                                                                                                                                                                                                                                                                          0.2s
 ✔ Container molevolvr20-frontend-1    Recreated                                                                                                                                                                                                                                                                                          0.1s
 ✔ Container molevolvr20-accounting-1  Started                                                                                                                                                                                                                                                                                            0.0s
dependency failed to start: container molevolvr20-db-1 exited (1)

Attached image is docker desktop showing the services that successfully started, other services restarting indefinitely, and other services that fail to start at all:

[AleruDivine]

@vincerubinetti

[falquaddoomi]

Hi @AleruDivine, thanks for the report and for including so much context!

Could I ask you to run ./run_stack.sh logs -f db and include the results here?

[AleruDivine]

@falquaddoomi here's the output

[falquaddoomi]

Hey @AleruDivine, it looks like you didn't fill in a random password for the POSTGRES_PASSWORD in your copied .env file. You'll also want to specify random passwords for any other variable in that file that's currently blank, e.g. MARIADB_ROOT_PASSWORD and MARIADB_PASSWORD. The values don't matter; you can specify anything you like as long as it's not blank.

If you do that, then try to re-run the stack, it should come up, but let me know if you run into further issues.

[AleruDivine]

Yes, I had just realized. My apologies! It works now

[AleruDivine]

Thanks for all the help @falquaddoomi