Migrating from arvados-node-manager to arvados-dispatch-cloud » History » Version 20

Tom Clegg, 03/26/2019 02:38 PM

1 5 Tom Clegg
h1. Migrating from arvados-node-manager to arvados-dispatch-cloud
2 1 Tom Clegg
3 1 Tom Clegg
{{toc}}
4 1 Tom Clegg
5 1 Tom Clegg
h2. Choose a node
6 1 Tom Clegg
7 1 Tom Clegg
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.
8 1 Tom Clegg
9 4 Tom Clegg
h2. Prepare key pair and worker VM image
10 4 Tom Clegg
11 9 Tom Clegg
Generate an SSH private key with no passphrase. Save it in the cluster configuration file (see @PrivateKey@ in the example below).
12 4 Tom Clegg
13 19 Tom Clegg
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).
14 4 Tom Clegg
15 14 Tom Clegg
Prepare a worker VM image. It needs docker, arv-mount (python-arvados-fuse), and crunch-run ≥ 1.3.1.20190221194156.
16 4 Tom Clegg
17 1 Tom Clegg
h2. Update cluster configuration file
18 1 Tom Clegg
19 1 Tom Clegg
In @/etc/arvados/config.yml@, add configuration items for the dispatch service.
20 1 Tom Clegg
21 1 Tom Clegg
<pre><code class="yaml">
22 1 Tom Clegg
Clusters:
23 8 Tom Clegg
  zzzzz:
24 18 Tom Clegg
    ManagementToken: "example-secret-management-token"
25 18 Tom Clegg
    SystemRootToken: zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz    # a superuser token
26 18 Tom Clegg
    Services:
27 18 Tom Clegg
      Controller:
28 18 Tom Clegg
        ExternalURL: https://zzzzz.arvadosapi.com
29 18 Tom Clegg
    TLS:
30 18 Tom Clegg
      #Insecure: true                                    # uncomment to bypass TLS certificate verification
31 1 Tom Clegg
    CloudVMs:
32 1 Tom Clegg
      BootProbeCommand: "mount | grep /mnt/scratch"
33 16 Tom Clegg
      MaxCloudOpsPerSecond: 10
34 1 Tom Clegg
      SSHPort: "2222"
35 1 Tom Clegg
      SyncInterval: 1m
36 1 Tom Clegg
      TimeoutIdle: 2m
37 1 Tom Clegg
      TimeoutBooting: 10m
38 1 Tom Clegg
      TimeoutProbe: 5m
39 1 Tom Clegg
      TimeoutShutdown: 30s
40 8 Tom Clegg
      ImageID: "https://zzzzzzzz.blob.core.windows.net/system/Microsoft.Compute/Images/images/zzzzz-compute-osDisk.55555555-5555-5555-5555-555555555555.vhd"
41 7 Ward Vandewege
      Driver: azure
42 1 Tom Clegg
      DriverParameters:
43 2 Tom Clegg
        SubscriptionID: XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
44 2 Tom Clegg
        ClientID: XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
45 1 Tom Clegg
        ClientSecret: 2WyXt0XFbEtutnf2hp528t6Wk9S5bOHWkRaaWwavKQo=
46 8 Tom Clegg
        TenantID: XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX
47 11 Tom Clegg
        CloudEnvironment: AzurePublicCloud
48 2 Tom Clegg
        ResourceGroup: zzzzz
49 2 Tom Clegg
        Location: centralus
50 3 Tom Clegg
        Network: zzzzz
51 2 Tom Clegg
        Subnet: zzzzz-subnet-private
52 3 Tom Clegg
        StorageAccount: example
53 2 Tom Clegg
        BlobContainer: vhds
54 11 Tom Clegg
        DeleteDanglingResourcesAfter: 20s
55 8 Tom Clegg
        AdminUsername: arvados
56 1 Tom Clegg
    Dispatch:
57 4 Tom Clegg
      PrivateKey: |
58 4 Tom Clegg
        -----BEGIN RSA PRIVATE KEY-----
59 4 Tom Clegg
        MIIEowIBAAKCAQEAqYm4XsQHm8sBSZFwUX5VeW1OkGsfoNzcGPG2nzzYRhNhClYZ
60 4 Tom Clegg
        0ABHhUk82HkaC/8l6d/jpYTf42HrK42nNQ0r0Yzs7qw8yZMQioK4Yk+kFyVLF78E
61 4 Tom Clegg
        GRG4pGAWXFs6pUchs/lm8fo9zcda4R3XeqgI+NO+nEERXmdRJa1FhI+Za3/S/+CV
62 4 Tom Clegg
        mg+6O00wZz2+vKmDPptGN4MCKmQOCKsMJts7wSZGyVcTtdNv7jjfr6yPAIOIL8X7
63 4 Tom Clegg
        ...
64 4 Tom Clegg
        JIBvlVfcHb1IHMA9YG7ZQjrMRmx2Xj3ce4RVPgUGHh8ra7gvLjd72/Tpf0doNClN
65 4 Tom Clegg
        ti/hAoGBAMW5D3LhU05LXWmOqpeT4VDgqk4MrTBcstVe7KdVjwzHrVHCAmI927vI
66 4 Tom Clegg
        pjpphWzpC9m3x4OsTNf8m+g6H7f3IiQS0aiFNtduXYlcuT5FHS2fSATTzg5PBon9
67 4 Tom Clegg
        1E6BudOve+WyFyBs7hFWAqWFBdWujAl4Qk5Ek09U2ilFEPE7RTgJ
68 4 Tom Clegg
        -----END RSA PRIVATE KEY-----
69 1 Tom Clegg
      StaleLockTimeout: 1m
70 1 Tom Clegg
      PollInterval: 10s
71 1 Tom Clegg
      ProbeInterval: 10s
72 1 Tom Clegg
      MaxProbesPerSecond: 10
73 16 Tom Clegg
      TimeoutSignal: 5s
74 16 Tom Clegg
      TimeoutTERM: 2m
75 1 Tom Clegg
    InstanceTypes:
76 1 Tom Clegg
      x1lg:
77 1 Tom Clegg
        ProviderType: x1.large
78 15 Tom Clegg
        VCPUs: 16
79 15 Tom Clegg
        RAM: 128GiB
80 1 Tom Clegg
        IncludedScratch: 128GiB
81 1 Tom Clegg
        Price: 1.23
82 1 Tom Clegg
    NodeProfiles:
83 8 Tom Clegg
      dispatcher:                       # references ARVADOS_NODE_PROFILE in environment file (see below).
84 1 Tom Clegg
        arvados-dispatch-cloud:
85 10 Ward Vandewege
          Listen: ":9006"
86 1 Tom Clegg
</code></pre>
87 1 Tom Clegg
88 1 Tom Clegg
Create the host configuration file @/etc/arvados/environment@.
89 1 Tom Clegg
90 1 Tom Clegg
<pre>
91 8 Tom Clegg
ARVADOS_NODE_PROFILE=dispatcher
92 1 Tom Clegg
</pre>
93 1 Tom Clegg
94 1 Tom Clegg
h2. Stop crunch-dispatch-slurm
95 1 Tom Clegg
96 1 Tom Clegg
Stop and disable the crunch-dispatch-slurm service, and uninstall the package to make sure it doesn't start after the next reboot/upgrade.
97 1 Tom Clegg
98 1 Tom Clegg
<pre>
99 1 Tom Clegg
# systemctl stop crunch-dispatch-slurm
100 1 Tom Clegg
# systemctl disable crunch-dispatch-slurm
101 1 Tom Clegg
# apt-get remove crunch-dispatch-slurm
102 1 Tom Clegg
</pre>
103 1 Tom Clegg
104 5 Tom Clegg
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.
105 1 Tom Clegg
106 5 Tom Clegg
h2. Install arvados-dispatch-cloud
107 1 Tom Clegg
108 1 Tom Clegg
<pre>
109 5 Tom Clegg
# apt-get install arvados-dispatch-cloud
110 1 Tom Clegg
</pre>
111 1 Tom Clegg
112 13 Tom Clegg
113 1 Tom Clegg
h2. Verify the service is running
114 1 Tom Clegg
115 1 Tom Clegg
<pre>
116 1 Tom Clegg
$ token="example-secret-management-token"
117 1 Tom Clegg
$ curl -H "Authorization: Bearer $token" http://localhost:9005/metrics
118 1 Tom Clegg
</pre>
119 1 Tom Clegg
120 1 Tom Clegg
h2. Verify the service is functional
121 5 Tom Clegg
122 5 Tom Clegg
Watch the dispatcher's logs while you run an Arvados container:
123 5 Tom Clegg
124 5 Tom Clegg
<pre>
125 5 Tom Clegg
# journalctl -ocat -fu arvados-dispatch-cloud
126 5 Tom Clegg
</pre>
127 12 Tom Clegg
128 12 Tom Clegg
Example logs:
129 12 Tom Clegg
130 12 Tom Clegg
<pre>
131 12 Tom Clegg
Starting Arvados dispatch cloud...
132 12 Tom Clegg
{"Listen":"[::]:9006","PID":46639,"Service":"arvados-dispatch-cloud","level":"info","msg":"listening","time":"2019-02-18T18:10:33.550358536Z"}
133 12 Tom Clegg
Started Arvados dispatch cloud.
134 12 Tom Clegg
{"PID":46639,"level":"info","msg":"FixStaleLocks starting.","time":"2019-02-18T18:10:33.706568502Z"}
135 12 Tom Clegg
{"PID":46639,"level":"info","msg":"FixStaleLocks finished (34.717µs), starting scheduling.","time":"2019-02-18T18:10:33.706606521Z"}
136 12 Tom Clegg
{"N":0,"PID":46639,"level":"info","msg":"loaded initial instance list","time":"2019-02-18T18:10:33.982989844Z"}
137 12 Tom Clegg
{"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"}
138 12 Tom Clegg
{"ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","InstanceType":"Standard_D1_v2","PID":46639,"level":"info","msg":"creating new instance","time":"2019-02-18T18:15:33.711915757Z"}
139 12 Tom Clegg
{"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"}
140 12 Tom Clegg
{"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"}
141 12 Tom Clegg
{"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"}
142 12 Tom Clegg
{"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"}
143 12 Tom Clegg
{"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"}
144 12 Tom Clegg
{"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"}
145 12 Tom Clegg
{"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"}
146 12 Tom Clegg
{"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"}
147 12 Tom Clegg
{"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"}
148 12 Tom Clegg
{"ContainerUUID":"c97qk-dz642-qxo0qjp93y2k4ht","PID":46639,"State":"Complete","level":"info","msg":"dropped container from queue","time":"2019-02-18T18:19:13.500015828Z"}
149 12 Tom Clegg
{"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"}
150 12 Tom Clegg
{"PID":46639,"level":"info","msg":"Will delete compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-nic because it is older than 20s","time":"2019-02-18T18:22:35.044805153Z"}
151 12 Tom Clegg
{"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"}
152 12 Tom Clegg
{"PID":46639,"level":"info","msg":"Deleted NIC compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-nic","time":"2019-02-18T18:22:45.273921501Z"}
153 12 Tom Clegg
{"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"}
154 12 Tom Clegg
{"PID":46639,"level":"info","msg":"Deleted blob compute-5656b5905b6e0c2d20ae4145148c6b31-7qs8dk3yfw0hteq-os.vhd","time":"2019-02-18T18:25:33.194356552Z"}
155 12 Tom Clegg
</pre>