Migrating from arvados-node-manager to arvados-dispatch-cloud » History » Version 12

Version 11 (Tom Clegg, 02/15/2019 09:19 PM) → Version 12/22 (Tom Clegg, 02/18/2019 06:37 PM)

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, 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. The version of crunch-run must be new enough to include commit:2873d55ea (TODO: when merged/published, give minimum package version instead of commit).

h2. Update cluster configuration file

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

<pre><code class="yaml">
Clusters:
zzzzz:
CloudVMs:
BootProbeCommand: "mount | grep /mnt/scratch"
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
InstanceTypes:
x1lg:
ProviderType: x1.large
VCPUs: 16
RAM: 128G
Scratch: 128G
Price: 1.23
ManagementToken: "example-secret-management-token"
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>

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>