Many software projects make use of CI/CD to automate certain jobs and integrate them into the development workflow with GitLab. Therefore, a runner is required to execute these jobs on a remote machine. In the following, it is described how such a runner can be set up on our systems to utilize the compute nodes for such CI jobs.
Setup of GitLab CI Runner with Jacamar CI
Jacamar CI is an HPC-focused CI/CD driver which allows scheduling of CI/CD jobs as jobs within a workload manager like Slurm. The advantage of running the CI/CD jobs directly on the cluster is the availability of all software and also the hardware (i.e. FPGAs) of the systems for these jobs.
For the setup, we need to install a GitLab runner that will continuously run in the user space. This runner will be registered in a GitLab project and execute incoming CI/CD jobs using Jacamar CI as a custom executor.
Log in to one of the cluster frontends and create a new folder for the CI (preferably on the parallel file system). Change into the created directory. This folder will - at the end of this guide - contain all required configuration files.
A good location is the directory assigned to your project in /scratch/....
1. Setup Environment with Modules
Jacamar CI and GitLab-Runner are available within our modules system. In order to load the modules you can use
module reset module load tools module load gitlab-runner module load jacamar
This loads the gitlab-runner and jacamar binaries in the latest versions into your environment. In the following setup you need the absolute paths of the binaries. These are
Path to Latest GitLab Binary
/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/gitlab-runner
Path to Latest Jacamar
/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar
2. Configuration of Jacamar CI Custom Executor
We need to create a configuration for Jacamar CI. Create a new file named jacamar-config.toml and insert the following content
[general] executor = "slurm" data_dir = "/scratch/PATH/TO/WORK/DIR/.../data"
You may adjust the path to the data directory accordingly. Note, that this data will only be temporal for the execution of a job. However, keep in mind the specified path should be accessible from all compute nodes.
3. Configuration of GitLab Runner
Now we need to setup CI/CD in your Gitlab project. Go to the settings of your project on Gitlab and enable the feature CI/CD in the General section under Visibility, project features, permissions.
In the now appearing CI/CD section (under Settings), go to Runners. There you will find a two step setup guide to connect a new runner to your project under the Specific Runner heading.
To execute these two steps run the Gitlab runner on Noctua
gitlab-runner register --config=jacamar-config.toml
Follow the steps. If you are asked for the executor type, choose custom.
4. Make GitLab Runner use Jacamar CI
Now we need to configure the GitLab runner to use our custom executor jacamar we configured in step 2.
Therefore, edit the configuration file gci-config.toml.
Below your runners definition, add the two following lines
pre_clone_script="module reset"
This will load the default modules of Noctua including Slurm, which is required for the custom executor.
Also, Jacamar CI requires at least git version +2.9. The pre-installed system version of git is sufficient.
To also allow artifact uploads to the GitLab server, gitlab-runner must be in the PATH variable. This requires setting the PATH variable in the environment settings of the configuration. Again, replace the /PATH/TO/WORK/DIR with the path to your working directory
environment = ["PATH=/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin:/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin"]
Now we need to configure Jacamar CI as a custom executor by editing the following fields in the configuration. /PATH/TO/WORK/DIR/ is the absolute path to the directory you have set up Jacamar CI and the GitLab runner.
[runners.custom] config_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" config_args = ["config","--no-auth", "--configuration", "/scratch/PATH/TO/WORK/DIR/jacamar-config.toml"] prepare_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" prepare_args = ["prepare", "--no-auth"] run_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" run_args = ["run", "--no-auth"] cleanup_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" cleanup_args = ["cleanup", "--no-auth", "--configuration", "/scratch/PATH/TO/WORK/DIR/jacamar-config.toml"]
The config should look similar to this when you are done
[general] executor = "slurm" data_dir = "/scratch/PATH/TO/WORK/DIR/.../data" concurrent = 1 check_interval = 0 [session_server] session_timeout = 1800 [[runners]] name = "Jacamar Test Runner" url = "https://git.uni-paderborn.de/" token = "TOKEN" executor = "custom" environment = ["PATH=/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin:/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin"] pre_clone_script="module reset" [runners.custom_build_dir] [runners.cache] [runners.cache.s3] [runners.cache.gcs] [runners.custom] config_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" config_args = ["config","--no-auth", "--configuration", "/scratch/PATH/TO/WORK/DIR/jacamar-config.toml"] prepare_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" prepare_args = ["prepare", "--no-auth"] run_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" run_args = ["run", "--no-auth"] cleanup_exec = "/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/jacamar" cleanup_args = ["cleanup", "--no-auth", "--configuration", "/scratch/PATH/TO/WORK/DIR/jacamar-config.toml"]
You may want to increase the value of concurrent to allow the GitLab runner to schedule multiple jobs at once. That's it. Now you only need to create a .gitlab-ci.yml file in your project and commit it to GitLab. GitLab will use your new runner for the jobs.
In the .gitlab-ci.yml you will need to specify the variable SCHEDULER_PARAMETERS to make it work with our Slurm installation. In this variable, you should specify your project account and the partition where the jobs should be executed.
Example
test:
stage: build
variables:
SCHEDULER_PARAMETERS: "-A PROJECT_ACCOUNT -p normal -t 0:05:00"
script:
- echo "Hello from " $(cat /etc/hostname)
Change the PROJECT_ACCOUNT to the name of your project (The name that you usually pass to sbatch via the -A option).
5. Execute GitLab Runner
The GitLab runner needs to be executed to fetch new CI jobs from GitLab. The best way is to use a systemd service which can restart the runner after a reboot of the frondend nodes.
Create a systemd user service file in your $HOME directory at .config/system/user/name.service which looks like the following example.
[Unit] Description=Jacamar User Service After=network.target [Service] ExecStart=/opt/software/pc2/EB-SW/software/gitlab-runner/latest/bin/gitlab-runner run --config=/PATH/TO/WORK/DIR/jacamar-config.toml WorkingDirectory=/scratch/PATH/TO/WORK/DIR/ [Install] WantedBy=default.target
The service can be enabled with systemd --user enable name.service and started with systemd --user start name.service. Use systemctl --user daemon-reload after changing the service file.
Now, schedule a pipeline in your GitLab project. The runner will fetch the created jobs and execute them on the specified partition.
Shared runners can only be created for the whole Gitlab instance. Group runner can be created for groups where the owner status is available. In every other case register a runner and create a service file for each repository.
Troubleshooting
Q: I have created a runner in my project but no pipelines are executed. What can be the problem?
A: If you have specified a tag when setting up the runner you will need to also use the tag in your CI jobs or allow the runner to also execute untagged jobs via the runner settings under Settings -> CI/CD -> Runners.
Q: Is it possible to use the runner for multiple projects?
A: Yes! In your GitLab project, go to Settings -> CI/CD -> Runners and click on the pencil next to your runner to edit its settings. Uncheck the option Lock to current projects. Now when enabling CI/CD in another project, you should be able to select the runner instead of creating a new one.
Q: My jobs are running successfully but fail on completion!
A: The runner is known to fail if a ~/.bash_logout exists in your home directory that contains a clear.