Arvados

h1. Migrating from arvados-node-manager to arvados-dispatch-cloud

{{toc}}

h2. 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.

h2. 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 or EC2, 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.

h2. Update cluster configuration file

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

<pre><code class="yaml">

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"

</code></pre>

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

<pre>

ARVADOS_NODE_PROFILE=dispatcher

</pre>

h2. 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.

<pre>

# systemctl stop crunch-dispatch-slurm

# systemctl disable crunch-dispatch-slurm

# apt-get remove crunch-dispatch-slurm

</pre>

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.

h2. Install arvados-dispatch-cloud

<pre>

# apt-get install arvados-dispatch-cloud

</pre>

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:

<pre>

[Service]

Environment=ARVADOS_API_HOST=zzzzz.arvadosapi.com

Environment=ARVADOS_API_TOKEN=zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz

</pre>

h2. Verify the service is running

<pre>

$ token="example-secret-management-token"

$ curl -H "Authorization: Bearer $token" http://localhost:9005/metrics

</pre>

h2. Verify the service is functional

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

<pre>

# journalctl -ocat -fu arvados-dispatch-cloud

</pre>

Example logs:

<pre>

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"}

</pre>