Arvados™ Docs
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  1. Topics
    1. Arvados admin overview
  2. Users and Groups
    1. User management
    2. User management at the CLI
    3. Role group management at the CLI
    4. Reassign user data ownership
    5. Link user accounts
    6. Configuring federation
    7. Migrating users to federated accounts
    8. Changing upstream login providers
    9. Synchronizing from external sources
    10. Securing API access with scoped tokens
    11. Automatic logout and token expiration
  3. Monitoring
    1. Logging
    2. Metrics
    3. Health checks
    4. Diagnostics
    5. Management token
    6. User activity report
  4. Data Management
    1. Configuring collection versioning
    2. Configuring collection's managed properties
    3. Restricting upload or download
    4. Balancing Keep servers
    5. Preventing container reuse
    6. Logs table management
    7. Metadata vocabulary
    8. Configuring storage classes
    9. Recovering data
    10. Measuring deduplication
  5. Cloud
    1. Using Preemptible instances
    2. Testing cloud configuration
  6. Other
    1. Migrating from Docker 1.9
    2. Upgrading to Containers API

Diagnostics

The arvados-client diagnostics command exercises basic cluster functionality, and identifies some common installation and configuration problems. Especially after upgrading or reconfiguring Arvados or server/network infrastructure, it can be the quickest way to identify problems.

Using system privileges

On a server node, it is easiest to run the diagnostics command with system privileges. The word sudo here instructs the arvados-client command to load Controller.ExternalURL and SystemRootToken from /etc/arvados/config.yml and use those credentials to run tests with system privileges.

When run this way, diagnostics will also include health checks.

# arvados-client sudo diagnostics

Using regular user privileges

On any node (server node, shell node, or a workstation outside the system network), you can also run diagnostics by setting the usual ARVADOS_API_HOST and ARVADOS_API_TOKEN environment variables. Typically this is done with a regular user account.

$ export ARVADOS_API_HOST=zzzzz.arvadosapi.com
$ export ARVADOS_API_TOKEN=xxxxxxxxxx
$ arvados-client diagnostics

Internal/external client detection

The diagnostics output indicates whether its client connection is categorized by the server as internal or external. If you run diagnostics automatically with cron or a monitoring tool, you can use the -internal-client or -external-client flag to specify how you expect the client to be categorized, and the test will fail otherwise. Example:

# arvados-client sudo diagnostics -internal-client
[...]

--- cut here --- error summary ---

ERROR     60: checking internal/external client detection (11 ms): expecting internal=true external=false, but found internal=false external=true

Example output

# arvados-client sudo diagnostics
INFO       5: running health check (same as `arvados-server check`)
INFO      10: getting discovery document from https://zzzzz.arvadosapi.com/discovery/v1/apis/arvados/v1/rest
INFO      20: getting exported config from https://zzzzz.arvadosapi.com/arvados/v1/config
INFO      30: getting current user record
INFO      40: connecting to service endpoint https://keep.zzzzz.arvadosapi.com/
INFO      41: connecting to service endpoint https://*.collections.zzzzz.arvadosapi.com/
INFO      42: connecting to service endpoint https://download.zzzzz.arvadosapi.com/
INFO      43: connecting to service endpoint wss://ws.zzzzz.arvadosapi.com/websocket
INFO      44: connecting to service endpoint https://workbench.zzzzz.arvadosapi.com/
INFO      45: connecting to service endpoint https://workbench2.zzzzz.arvadosapi.com/
INFO      50: checking CORS headers at https://zzzzz.arvadosapi.com/
INFO      51: checking CORS headers at https://keep.zzzzz.arvadosapi.com/d41d8cd98f00b204e9800998ecf8427e+0
INFO      52: checking CORS headers at https://download.zzzzz.arvadosapi.com/
INFO      60: checking internal/external client detection
INFO      61: reading+writing via keep service at https://keep.zzzzz.arvadosapi.com:443/
INFO      80: finding/creating "scratch area for diagnostics" project
INFO      90: creating temporary collection
INFO     100: uploading file via webdav
INFO     110: checking WebDAV ExternalURL wildcard (https://*.collections.zzzzz.arvadosapi.com/)
INFO     120: downloading from webdav (https://d41d8cd98f00b204e9800998ecf8427e-0.collections.zzzzz.arvadosapi.com/foo)
INFO     121: downloading from webdav (https://d41d8cd98f00b204e9800998ecf8427e-0.collections.zzzzz.arvadosapi.com/sha256:feb5d9fea6a5e9606aa995e879d862b825965ba48de054caab5ef356dc6b3412.tar)
INFO     122: downloading from webdav (https://download.zzzzz.arvadosapi.com/c=d41d8cd98f00b204e9800998ecf8427e+0/_/foo)
INFO     123: downloading from webdav (https://download.zzzzz.arvadosapi.com/c=d41d8cd98f00b204e9800998ecf8427e+0/_/sha256:feb5d9fea6a5e9606aa995e879d862b825965ba48de054caab5ef356dc6b3412.tar)
INFO     124: downloading from webdav (https://a15a27cbc1c7d2d4a0d9e02529aaec7e-128.collections.zzzzz.arvadosapi.com/sha256:feb5d9fea6a5e9606aa995e879d862b825965ba48de054caab5ef356dc6b3412.tar)
INFO     125: downloading from webdav (https://download.zzzzz.arvadosapi.com/c=zzzzz-4zz18-twitqma8mbvwydy/_/sha256:feb5d9fea6a5e9606aa995e879d862b825965ba48de054caab5ef356dc6b3412.tar)
INFO     130: getting list of virtual machines
INFO     140: getting workbench1 webshell page
INFO     150: connecting to webshell service
INFO     160: running a container
INFO      ... container request submitted, waiting up to 10m for container to run
INFO    9990: deleting temporary collection
Previous: Health checks Next: Management token

The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.