Migrating from arvados-node-manager to arvados-dispatch-cloud¶

• Table of contents
• Migrating from arvados-node-manager to arvados-dispatch-cloud
  • Choose a node
  • Prepare key pair and worker VM image
  • Update cluster configuration file
  • Stop crunch-dispatch-slurm
  • Install arvados-dispatch-cloud
  • Verify the service is running
  • Verify the service is functional

Choose a node¶

The dispatch service can run on any host that can connect to the Arvados API service, the cloud provider's API, and the SSH service on cloud VMs. In the following example it runs on the same node as the API server and controller.

Prepare key pair and worker VM image¶

Generate an SSH private key with no passphrase. Save it in the cluster configuration file (see PrivateKey in the example below).

If you are using Azure, the dispatcher will create a login account and install your public key automatically, so you do not need to save the corresponding public key in an authorized_keys file in the VM image (or anywhere else, for that matter).

Prepare a worker VM image. It needs docker, arv-mount (python-arvados-fuse), and crunch-run ≥ 1.3.1.20190221194156.

Update cluster configuration file¶

In /etc/arvados/config.yml, add configuration items for the dispatch service.

Clusters:
  zzzzz:
    ManagementToken: "example-secret-management-token" 
    SystemRootToken: zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz    # a superuser token
    Services:
      Controller:
        ExternalURL: https://zzzzz.arvadosapi.com
    TLS:
      #Insecure: true                                    # uncomment to bypass TLS certificate verification
    CloudVMs:
      BootProbeCommand: "mount | grep /mnt/scratch" 
      MaxCloudOpsPerSecond: 10
      SSHPort: "2222" 
      SyncInterval: 1m
      TimeoutIdle: 2m
      TimeoutBooting: 10m
      TimeoutProbe: 5m
      TimeoutShutdown: 30s
      ImageID: "https://zzzzzzzz.blob.core.windows.net/system/Microsoft.Compute/Images/images/zzzzz-compute-osDisk.55555555-5555-5555-5555-555555555555.vhd" 
      Driver: azure
      DriverParameters:
        SubscriptionID: XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
        ClientID: XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
        ClientSecret: 2WyXt0XFbEtutnf2hp528t6Wk9S5bOHWkRaaWwavKQo=
        TenantID: XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
        CloudEnvironment: AzurePublicCloud
        ResourceGroup: zzzzz
        Location: centralus
        Network: zzzzz
        Subnet: zzzzz-subnet-private
        StorageAccount: example
        BlobContainer: vhds
        DeleteDanglingResourcesAfter: 20s
        AdminUsername: arvados
    Dispatch:
      PrivateKey: |
        -----BEGIN RSA PRIVATE KEY-----
        MIIEowIBAAKCAQEAqYm4XsQHm8sBSZFwUX5VeW1OkGsfoNzcGPG2nzzYRhNhClYZ
        0ABHhUk82HkaC/8l6d/jpYTf42HrK42nNQ0r0Yzs7qw8yZMQioK4Yk+kFyVLF78E
        GRG4pGAWXFs6pUchs/lm8fo9zcda4R3XeqgI+NO+nEERXmdRJa1FhI+Za3/S/+CV
        mg+6O00wZz2+vKmDPptGN4MCKmQOCKsMJts7wSZGyVcTtdNv7jjfr6yPAIOIL8X7
        ...
        JIBvlVfcHb1IHMA9YG7ZQjrMRmx2Xj3ce4RVPgUGHh8ra7gvLjd72/Tpf0doNClN
        ti/hAoGBAMW5D3LhU05LXWmOqpeT4VDgqk4MrTBcstVe7KdVjwzHrVHCAmI927vI
        pjpphWzpC9m3x4OsTNf8m+g6H7f3IiQS0aiFNtduXYlcuT5FHS2fSATTzg5PBon9
        1E6BudOve+WyFyBs7hFWAqWFBdWujAl4Qk5Ek09U2ilFEPE7RTgJ
        -----END RSA PRIVATE KEY-----
      StaleLockTimeout: 1m
      PollInterval: 10s
      ProbeInterval: 10s
      MaxProbesPerSecond: 10
      TimeoutSignal: 5s
      TimeoutTERM: 2m
    InstanceTypes:
      x1lg:
        ProviderType: x1.large
        VCPUs: 16
        RAM: 128GiB
        IncludedScratch: 128GiB
        Price: 1.23
    NodeProfiles:
      dispatcher:                       # references ARVADOS_NODE_PROFILE in environment file (see below).
        arvados-dispatch-cloud:
          Listen: ":9006" 

Create the host configuration file /etc/arvados/environment.

ARVADOS_NODE_PROFILE=dispatcher

Stop crunch-dispatch-slurm¶

Stop and disable the crunch-dispatch-slurm service, and uninstall the package to make sure it doesn't start after the next reboot/upgrade.

# systemctl stop crunch-dispatch-slurm
# systemctl disable crunch-dispatch-slurm
# apt-get remove crunch-dispatch-slurm

Containers that have already been locked and submitted to SLURM will make their way through the SLURM queue, but newly queued containers will be left for arvados-dispatch-cloud to run.

Install arvados-dispatch-cloud¶

# apt-get install arvados-dispatch-cloud

For now, ARVADOS_API_HOST and ARVADOS_API_TOKEN environment variables must be provided (future versions will get these values from the config file). You can use systemctl edit to do this through systemd:

[Service]
Environment=ARVADOS_API_HOST=zzzzz.arvadosapi.com
Environment=ARVADOS_API_TOKEN=zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz

Verify the service is running¶

$ token="example-secret-management-token" 
$ curl -H "Authorization: Bearer $token" http://localhost:9005/metrics

Verify the service is functional¶

Watch the dispatcher's logs while you run an Arvados container:

# journalctl -ocat -fu arvados-dispatch-cloud

Example logs:

Starting Arvados dispatch cloud...
{"Listen":"[::]:9006","PID":46639,"Service":"arvados-dispatch-cloud","level":"info","msg":"listening","time":"2019-02-18T18:10:33.550358536Z"}
Started Arvados dispatch cloud.
{"PID":46639,"level":"info","msg":"FixStaleLocks starting.","time":"2019-02-18T18:10:33.706568502Z"}
{"PID":46639,"level":"info","msg":"FixStaleLocks finished (34.717µs), starting scheduling.","time":"2019-02-18T18:10:33.706606521Z"}
{"N":0,"PID":46639,"level":"info","msg":"loaded initial instance list","time":"2019-02-18T18:10:33.982989844Z"}
{"ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","InstanceType":"Standard_D1_v2","PID":46639,"Priority":1124349393114703,"State":"Queued","level":"info","msg":"added container to queue","time":"2019-02-18T18:15:33.620474859Z"}
{"ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","InstanceType":"Standard_D1_v2","PID":46639,"level":"info","msg":"creating new instance","time":"2019-02-18T18:15:33.711915757Z"}
{"Address":"10.25.64.8","IdleBehavior":"run","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"State":"unknown","level":"info","msg":"instance appeared in cloud","time":"2019-02-18T18:16:34.512277597Z"}
{"Address":"10.25.64.8","Command":"sudo crunch-run --list","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"error":"dial tcp 10.25.64.8:2222: connect: connection refused","level":"warning","msg":"probe failed","stderr":"","stdout":"","time":"2019-02-18T18:16:43.386626115Z"}
{"Address":"10.25.64.8","Command":"sudo crunch-run --list","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"error":"dial tcp 10.25.64.8:2222: connect: connection refused","level":"warning","msg":"probe failed","stderr":"","stdout":"","time":"2019-02-18T18:16:53.381814784Z"}
{"Address":"10.25.64.8","Command":"sudo crunch-run --list","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"error":"Process exited with status 1","level":"warning","msg":"probe failed","stderr":"","stdout":"","time":"2019-02-18T18:17:04.897049820Z"}
{"Address":"10.25.64.8","Command":"/bin/ls /arvados-compute-node-boot.complete  \u003e/dev/null 2\u003e\u00261 \u0026\u0026 sudo wget --quiet https://c97qk.arvadosapi.com/crunch-run --output-document=/usr/bin/crunch-run","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"level":"info","msg":"boot probe succeeded","stderr":"","stdout":"","time":"2019-02-18T18:17:33.866226306Z"}
{"Address":"10.25.64.8","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"ProbeStart":"2019-02-18T18:17:33.357445643Z","level":"info","msg":"instance booted; will try probeRunning","time":"2019-02-18T18:17:33.866286736Z"}
{"Address":"10.25.64.8","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"ProbeStart":"2019-02-18T18:17:33.357445643Z","RunningContainers":0,"State":"idle","level":"info","msg":"probes succeeded, instance is in service","time":"2019-02-18T18:17:33.886177977Z"}
{"Address":"10.25.64.8","ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"Priority":1124349393114703,"level":"info","msg":"crunch-run process started","time":"2019-02-18T18:17:33.903776572Z"}
{"Address":"10.25.64.8","ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"ProbeStart":"2019-02-18T18:19:03.315677365Z","level":"info","msg":"crunch-run process ended","time":"2019-02-18T18:19:03.334773308Z"}
{"ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","PID":46639,"State":"Complete","level":"info","msg":"dropped container from queue","time":"2019-02-18T18:19:13.500015828Z"}
{"Address":"10.25.64.8","Age":129980928971,"IdleBehavior":"run","Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","InstanceType":"Standard_D1_v2","PID":46639,"State":"idle","level":"info","msg":"shutdown idle worker","time":"2019-02-18T18:21:13.255492437Z"}
{"PID":46639,"level":"info","msg":"Will delete compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-nic because it is older than 20s","time":"2019-02-18T18:22:35.044805153Z"}
{"Instance":"/subscriptions/zzzzzzzz-zzzz-zzzz-zzzz-zzzzzzzzzzzz/resourceGroups/c97qk/providers/Microsoft.Compute/virtualMachines/compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq","PID":46639,"WorkerState":"shutdown","level":"info","msg":"instance disappeared in cloud","time":"2019-02-18T18:22:35.086986833Z"}
{"PID":46639,"level":"info","msg":"Deleted NIC compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-nic","time":"2019-02-18T18:22:45.273921501Z"}
{"PID":46639,"level":"info","msg":"Blob compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-os.vhd is unlocked and not modified for 209.176892224 seconds, will delete","time":"2019-02-18T18:25:33.188314532Z"}
{"PID":46639,"level":"info","msg":"Deleted blob compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-os.vhd","time":"2019-02-18T18:25:33.194356552Z"}