feat: add Docker Compose SLURM environment for local job testing #73

Copilot · 2026-02-11T03:18:43Z

SLURM job scripts in research/ and scripts/ cannot be validated locally before cluster submission, causing slow iteration and wasted resources on configuration errors.

Implementation

Docker Compose setup (docker-compose.slurm.yml)

SLURM controller (slurmctld) and compute node (slurmd) containers
Project volume-mounted at /workspace for script access
GPU passthrough optional (commented by default, requires NVIDIA Docker runtime)

SLURM configuration (docker/slurm/slurm.conf)

Matches DRAC/Compute Canada partition structure: main (48h), long, long-cpu
Fair-share scheduling with priority policies per DRAC spec
Process tracking via pgid (cgroup unavailable in Docker)
Resources: 4 CPUs, 16GB RAM (configurable)

Example job scripts (docker/slurm/examples/)

Basic validation (job_hello.sh)
Environment setup testing (job_test_env.sh, job_test_ami_ml.sh)
GPU testing (job_gpu_test.sh)

CI integration (.github/workflows/test-slurm-jobs.yml)

Automated cluster build and test job execution

Usage

# Start cluster
docker compose -f docker-compose.slurm.yml up -d

# Submit jobs
docker exec -it ami-ml-slurmctld bash
cd /workspace
sbatch research/order_level_classifier/job_train_classifier.sh

# Monitor
sinfo    # cluster status
squeue   # job queue

See docker/slurm/README.md for adapting real job scripts (module loading, data paths, resource limits).

Limitations

Single compute node vs. multi-node cluster
No environment modules system (conda direct)
No HPC filesystem hierarchy (scratch/project)
No database accounting
Process isolation via pgid instead of cgroup

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

c1
- Triggering command: /usr/sbin/slurmctld /usr/sbin/slurmctld -D -vvv ln Root�� ARICA_TLS_ECC_Root_CA_2021.pem /etc/ssl/certs/HiPKI_Root_CA_-_Gs/,/_/g /usr/bin/ln /var/lib/dpkg/re/usr/bin/networkctl -liblua5.1-0_5.1list /usr/sbin/rm ln SM_S�� SERTrust_RSA_Certification_Autho-e /etc/ssl/certs/Security_Communics/,/_/g /usr/bin/ln -- -libpython3-dev_--norc b ln (dns block)
download.schedmd.com
- Triggering command: /usr/bin/wget wget REDACTED /usr/bin/dpkg-de.crt grep remi�� em rtificates/mozilla/Microsoft_RSAs/,/_/g /usr/bin/basename -pinentry-cursesbash p.ci (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

Configure Actions setup steps to set up my environment, which run before the firewall is enabled
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Original prompt

This section details on the original issue you should resolve

<issue_title>feat: add Docker Compose environment to simulate SLURM for local testing</issue_title>
<issue_description>## Context

Training jobs are submitted to HPC clusters via SLURM scripts in scripts/ and research/. There is no way to test these job scripts locally before scheduling real jobs, which makes iteration slow and wastes cluster resources on configuration errors.

Proposed Changes

Add a Docker Compose setup that simulates a minimal SLURM environment locally:

review the DRAC / Compute Canada SLURM documentation to match their config as closely as possible: https://docs.alliancecan.ca/wiki/Running_jobs see the bash scripts in the research/ folder of this repo for real examples of how the pipeline in this repo is scheduled in DRAC's SLURM. For example: research/order_level_classifier/job_train_classifier.sh

A container with a SLURM controller and single compute node (e.g., using giovtorres/slurm-docker-cluster or similar)

The project mounted as a volume so job scripts can be submitted with sbatch

GPU passthrough optional (for CPU-only smoke tests, training can run for 1-2 epochs)

A README explaining how to start the environment, submit jobs, and check output

Create a GitHub workflow to test SLURM jobs

This would allow developers to validate SLURM scripts, environment setup, and pipeline orchestration before submitting to the real cluster.

Related

research/order_level_classifier/job_*.sh — existing SLURM job scripts

scripts/train_species_classifier.sh — local equivalent (PR feat: add species classifier training pipeline #69)</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes feat: add Docker Compose environment to simulate SLURM for local testing #71

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

Co-authored-by: mihow <158175+mihow@users.noreply.github.com>

Copilot

Pull request overview

Adds a local Docker Compose–based SLURM “mini cluster” so developers can validate SLURM job scripts (from research/ and scripts/) before submitting to DRAC/Compute Canada, plus a CI workflow to smoke-test job submission.

Changes:

Introduces a SLURM controller + single compute node Compose stack with Ubuntu-based SLURM image and entrypoint wiring (munge + slurm daemons).
Adds SLURM configs and example job scripts (hello/env/ami-ml/GPU) to exercise common workflows.
Adds a GitHub Actions workflow to build the cluster and submit a basic test job.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
`docker-compose.slurm.yml`	Compose definition for controller/compute services, volumes, and optional GPU configuration.
`docker/slurm/Dockerfile`	Builds the SLURM image (Ubuntu + slurm + munge + miniconda + poetry) and installs configs/entrypoint.
`docker/slurm/entrypoint.sh`	Container entrypoint that starts munge and runs slurmctld/slurmd based on role env var.
`docker/slurm/slurm.conf`	SLURM cluster config (partitions, scheduling, accounting off, pgid proctrack, node resources).
`docker/slurm/cgroup.conf`	cgroup constraint config file (currently not aligned with pgid proctrack in `slurm.conf`).
`docker/slurm/gres.conf`	Example GPU GRES device mapping for node `c1`.
`docker/slurm/examples/job_hello.sh`	Minimal “hello world” SLURM job for basic submission validation.
`docker/slurm/examples/job_test_env.sh`	Example job intended to validate conda/poetry/workspace availability.
`docker/slurm/examples/job_test_ami_ml.sh`	Example job intended to validate installing/running ami-ml CLI entrypoints.
`docker/slurm/examples/job_gpu_test.sh`	Example job for verifying GPU passthrough and torch CUDA visibility.
`docker/slurm/README.md`	Documentation for running the local SLURM environment and troubleshooting/usage guidance.
`README.md`	Adds a repo-level pointer to the SLURM local testing docs and quick-start commands.
`.github/workflows/test-slurm-jobs.yml`	CI workflow that builds the image, starts the cluster, and submits smoke-test jobs.

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Copilot · 2026-02-11T03:55:23Z

docker/slurm/README.md

+# Check GPU availability
+scontrol show node c1 | grep Gres
+```
+


The GPU section suggests sbatch --gres=gpu:1 ..., but in the default config GresTypes=gpu is commented out and gres.conf isn't copied into the image by default. As written, GPU jobs are likely to stay pending or be rejected until those pieces are enabled. Consider adding explicit steps here (what to uncomment/copy in slurm.conf, Dockerfile, and/or compose) so users can actually get GRES working.

Suggested change

To make `--gres=gpu` work in this environment, you also need to:

- Ensure `GresTypes=gpu` is enabled in your `slurm.conf` (uncomment or add a line such as `GresTypes=gpu`).

- Provide a `gres.conf` file that defines the GPUs on the compute node and make it available inside the Slurm containers

(for example by adding `COPY gres.conf /etc/slurm/gres.conf` in the Slurm Dockerfile or by bind-mounting it via Docker Compose).

- Include an entry for the compute node in `gres.conf`, for example:

```conf

NodeName=c1 Name=gpu File=/dev/nvidia0

Restart the Slurm Docker stack after changing configuration files, e.g.:

docker compose down docker compose up -d

Copilot · 2026-02-11T03:55:23Z

docker/slurm/examples/job_test_env.sh

+conda --version
+
+# Create and activate a test environment
+echo "Creating test conda environment..."


conda activate test-env will fail in a non-interactive script unless the conda shell hook is initialized (e.g., eval "$(/opt/miniconda3/bin/conda shell.bash hook)" or sourcing conda.sh). Add the conda init step before calling conda activate, similar to job_test_ami_ml.sh.

Suggested change

echo "Creating test conda environment..."

echo "Creating test conda environment..."

# Initialize conda for this non-interactive shell

eval "$(conda shell.bash hook)"

Copilot · 2026-02-11T03:55:24Z

docker/slurm/README.md

+
+- **Authentication**: MUNGE for inter-process communication
+- **Scheduling**: Backfill scheduler with fair-share policies
+- **Resource Management**: Cgroup-based process tracking and resource constraints


The README claims "Cgroup-based process tracking and resource constraints", but docker/slurm/slurm.conf explicitly configures ProctrackType=proctrack/pgid and comments out TaskPlugin=task/cgroup for Docker compatibility. Update the README to match the actual configuration (or enable cgroup tracking and document the required Docker/cgroup setup).

Suggested change

- **Resource Management**: Cgroup-based process tracking and resource constraints

- **Resource Management**: Process tracking via Linux process groups (`ProctrackType=proctrack/pgid`); cgroup-based tracking is disabled in this Docker setup for compatibility.

Copilot · 2026-02-11T03:55:24Z

docker/slurm/README.md

+1. **Scale**: Single node vs. multi-node cluster
+2. **Modules**: No `module load` environment modules (uses conda directly)
+3. **Storage**: No scratch/project filesystem hierarchy
+4. **Accounting**: No database accounting (uses flat file)


This says accounting "uses flat file", but the shipped slurm.conf sets AccountingStorageType=accounting_storage/none (no accounting storage). Either update the README wording or change the SLURM config to match what's documented.

Suggested change

4. **Accounting**: No database accounting (uses flat file)

4. **Accounting**: Disabled (no accounting storage; `AccountingStorageType=accounting_storage/none`)

Copilot · 2026-02-11T03:55:24Z

.github/workflows/test-slurm-jobs.yml

+          docker-compose -f docker-compose.slurm.yml build
+
+      - name: Start SLURM cluster
+        run: |
+          docker-compose -f docker-compose.slurm.yml up -d


The workflow uses the legacy docker-compose binary. On GitHub-hosted runners (and many local setups) only the Compose v2 plugin (docker compose) is guaranteed to be present; docker-compose may be missing. Consider switching these commands to docker compose ... for more reliable CI execution.

Suggested change

docker-compose -f docker-compose.slurm.yml build

- name: Start SLURM cluster

run: |

docker-compose -f docker-compose.slurm.yml up -d

docker compose -f docker-compose.slurm.yml build

- name: Start SLURM cluster

run: |

docker compose -f docker-compose.slurm.yml up -d

Copilot · 2026-02-11T03:55:25Z

README.md

+Quick start:
+```bash
+# Build and start the SLURM cluster
+docker-compose -f docker-compose.slurm.yml up -d


The docs use the legacy docker-compose binary. Consider using the Compose v2 plugin syntax (docker compose -f docker-compose.slurm.yml ...) to match modern Docker installs where docker-compose may not be available.

Suggested change

docker-compose -f docker-compose.slurm.yml up -d

docker compose -f docker-compose.slurm.yml up -d

Copilot · 2026-02-11T03:55:25Z

docker/slurm/examples/job_test_ami_ml.sh

+eval "$(/opt/miniconda3/bin/conda shell.bash hook)"
+conda activate ami-ml || {
+    echo "Creating ami-ml environment..."
+    conda create -n ami-ml python=3.9 -y
+    conda activate ami-ml
+
+    # Install dependencies with Poetry
+    poetry install
+}
+
+# Load environment variables
+if [ -f .env ]; then
+    set -o allexport
+    source .env
+    set +o allexport
+    echo "Loaded environment variables from .env"
+else
+    echo "Warning: .env file not found"
+fi
+
+# Test that ami-ml commands are available
+echo "Testing ami-ml commands..."
+ami-classification --help || echo "ami-classification command not available"
+ami-dataset --help || echo "ami-dataset command not available"


poetry install will, by default, create an isolated virtualenv and install ami-dataset/ami-classification entrypoints there. Since the script later calls ami-classification/ami-dataset directly (not via poetry run), these commands are likely to be missing even after install. Either run the checks via poetry run ... or configure Poetry to install into the active conda env (e.g., disable Poetry venv creation) and consider failing the job when the commands aren't found so this script actually validates the setup.

Copilot · 2026-02-11T03:55:25Z

.github/workflows/test-slurm-jobs.yml

+          # Wait for job to complete (with timeout)
+          timeout=60
+          elapsed=0
+          while [ $elapsed -lt $timeout ]; do
+            status=$(docker exec ami-ml-slurmctld squeue -j $JOB_ID -h -o "%T" 2>/dev/null || echo "COMPLETED")
+            if [ "$status" = "COMPLETED" ] || [ -z "$status" ]; then
+              echo "Job $JOB_ID completed"
+              break
+            fi
+            echo "Job $JOB_ID status: $status (waiting...)"
+            sleep 5
+            elapsed=$((elapsed + 5))
+          done
+
+          # Display job output
+          docker exec ami-ml-slurmctld bash -c "cd /workspace && cat test_simple_*.out"
+


In the polling loop, if the job never completes within the timeout, the script exits the loop and continues without failing explicitly. Add a check after the loop to fail the step when elapsed >= timeout (and/or when the final state is not COMPLETED), so CI deterministically reports a failure instead of hanging or passing with partial output.

Copilot · 2026-02-11T03:55:25Z

docker-compose.slurm.yml

+    # Uncomment the deploy section below to enable GPU support
+    # Requires NVIDIA Docker runtime to be installed
+    # deploy:
+    #   resources:
+    #     reservations:
+    #       devices:
+    #         - driver: nvidia
+    #           count: all
+    #           capabilities: [gpu]
+


The commented GPU passthrough example uses the deploy: section. For docker compose up (non-Swarm), deploy is typically ignored, so uncommenting this may not actually provide GPUs to the container. Prefer the Compose v2 GPU mechanism (e.g., gpus: all / device requests) and document the exact command/runtime requirement.

Suggested change

# Uncomment the deploy section below to enable GPU support

# Requires NVIDIA Docker runtime to be installed

# deploy:

# resources:

# reservations:

# devices:

# - driver: nvidia

# count: all

# capabilities: [gpu]

# Uncomment the line below to enable GPU support with Docker Compose v2

# Requires NVIDIA Container Toolkit / runtime to be installed and configured

# Run with: docker compose -f docker-compose.slurm.yml up

# gpus: all

Copilot · 2026-02-11T03:55:26Z

docker/slurm/README.md

+```bash
+# From the repository root
+docker-compose -f docker-compose.slurm.yml build
+docker-compose -f docker-compose.slurm.yml up -d
+```


These instructions use docker-compose. If the project wants to be compatible with Docker Compose v2-only installs, consider updating the docs to use docker compose ... (or note that either works if a compatibility shim is installed).

Initial plan

271f81f

Copilot AI assigned Copilot and mihow Feb 11, 2026

Copilot started work on behalf of mihow February 11, 2026 03:19 View session

Copilot AI and others added 5 commits February 11, 2026 03:23

Add Docker Compose SLURM environment with configuration and examples

e50bf0d

Co-authored-by: mihow <158175+mihow@users.noreply.github.com>

Fix SLURM Docker environment configuration and test successfully

4e57e70

Co-authored-by: mihow <158175+mihow@users.noreply.github.com>

Update GitHub workflow for SLURM testing with simplified tests

121ffd6

Co-authored-by: mihow <158175+mihow@users.noreply.github.com>

Fix documentation to match actual SLURM configuration resources

1a55b70

Co-authored-by: mihow <158175+mihow@users.noreply.github.com>

Add explicit permissions to GitHub Actions workflow for security

9ecc9c4

Co-authored-by: mihow <158175+mihow@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add Docker Compose environment to simulate SLURM for local testing~~ feat: add Docker Compose SLURM environment for local job testing Feb 11, 2026

Copilot AI requested a review from mihow February 11, 2026 03:35

Copilot finished work on behalf of mihow February 11, 2026 03:35

mihow requested review from Copilot and removed request for mihow February 11, 2026 03:48

Copilot started reviewing on behalf of mihow February 11, 2026 03:48 View session

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feat: add Docker Compose SLURM environment for local job testing #73

feat: add Docker Compose SLURM environment for local job testing #73

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+To make `--gres=gpu` work in this environment, you also need to:
+- Ensure `GresTypes=gpu` is enabled in your `slurm.conf` (uncomment or add a line such as `GresTypes=gpu`).
+- Provide a `gres.conf` file that defines the GPUs on the compute node and make it available inside the Slurm containers
+  (for example by adding `COPY gres.conf /etc/slurm/gres.conf` in the Slurm Dockerfile or by bind-mounting it via Docker Compose).
+- Include an entry for the compute node in `gres.conf`, for example:
+  ```conf
+  NodeName=c1 Name=gpu File=/dev/nvidia0

	- Resource Management: Cgroup-based process tracking and resource constraints
	- Resource Management: Process tracking via Linux process groups (`ProctrackType=proctrack/pgid`); cgroup-based tracking is disabled in this Docker setup for compatibility.

	4. Accounting: No database accounting (uses flat file)
	4. Accounting: Disabled (no accounting storage; `AccountingStorageType=accounting_storage/none`)

	docker-compose -f docker-compose.slurm.yml up -d
	docker compose -f docker-compose.slurm.yml up -d

feat: add Docker Compose SLURM environment for local job testing #73

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I tried to connect to the following addresses, but was blocked by firewall rules:

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