.gitpod.yml

image: gitpod/workspace-full

# Commands that will run on workspace start
tasks:
    - name: install dependencies
      command: |
        sudo apt-get update
        sudo apt-get install -y retry ansible
    - name: start mariadb
      command: |
        sudo docker run -p 3306:3306 -p 33060:33060 -e MYSQL_ROOT_PASSWORD=root mariadb:10.7
    - name: deploy slurm roles
      command: ansible-galaxy role install https://github.com/galaxyproject/ansible-slurm/archive/1.0.1.tar.gz
    - name: write slurm playbook
      command: |
        cat << EOF > slurm-playbook.yml
        - name: Slurm all in One
          hosts: localhost
          roles:
            - role: 1.0.1
              become: true
          vars:
              slurm_upgrade: true
              slurm_roles: ['controller', 'exec', 'dbd']
              slurm_config_dir: /etc/slurm
              slurm_config:
                  ClusterName: cluster
                  SlurmctldLogFile: /var/log/slurm/slurmctld.log
                  SlurmctldPidFile: /run/slurmctld.pid
                  SlurmdLogFile: /var/log/slurm/slurmd.log
                  SlurmdPidFile: /run/slurmd.pid
                  SlurmdSpoolDir: /tmp/slurmd # the default /var/lib/slurm/slurmd does not work because of noexec mounting in github actions
                  StateSaveLocation: /var/lib/slurm/slurmctld
                  AccountingStorageType: accounting_storage/slurmdbd
                  SelectType: select/cons_res
              slurmdbd_config:
                  StorageType: accounting_storage/mysql
                  PidFile: /run/slurmdbd.pid
                  LogFile: /var/log/slurm/slurmdbd.log
                  StoragePass: root
                  StorageUser: root
                  StorageHost: 127.0.0.1 # see https://stackoverflow.com/questions/58222386/github-actions-using-mysql-service-throws-access-denied-for-user-rootlocalh
                  StoragePort: 3306
                  DbdHost: localhost
              slurm_create_user: yes
              #slurm_munge_key: "../../../munge.key"
              slurm_nodes:
                  - name: localhost
                    State: UNKNOWN
                    Sockets: 1
                    CoresPerSocket: 2
                    RealMemory: 2000
              slurm_user:
                  comment: "Slurm Workload Manager"
                  gid: 1002
                  group: slurm
                  home: "/var/lib/slurm"
                  name: slurm
                  shell: "/bin/bash"
                  uid: 1002
        EOF

    - name: setup slurm
      command: |
        ansible-playbook slurm-playbook.yml || (journalctl -xe && exit 1)
    - name: add slurm account
      command: |
        sudo retry --until=success -- sacctmgr -i create account "Name=runner"
        sudo sacctmgr -i create user "Name=runner" "Account=runner"
    
    - name: test srun
      command: |
        srun -vvvv echo "hello world"
        sudo cat /var/log/slurm/slurmd.log

    - name: test sbatch
      command: |
        sbatch -vvvv -N 1 --mem 5 --wrap "echo 'hello world'"

    - name: setup snakemake
      command: |
        poetry install