Upgrading Arvados and Release notes

What you need to know and do in order to upgrade your Arvados installation.

General process

  1. Wait for the cluster to be idle and stop Arvados services.
  2. Install new packages using apt-get upgrade or yum upgrade.
  3. Package installation scripts will perform any necessary data migrations.
  4. Consult upgrade notes below to see if any manual configuration updates are necessary.
  5. Restart Arvados services.

Upgrade notes

Some versions introduce changes that require special attention when upgrading: e.g., there is a new service to install, or there is a change to the default configuration that you might need to override in order to preserve the old behavior.

v1.2.0 (2018-09-05)

Regenerate Postgres table statistics

It is recommended to regenerate the table statistics for Postgres after upgrading to v1.2.0. If autovacuum is enabled on your installation, this script would do the trick:

#!/bin/bash

set -e
set -u

tables=`echo "\dt" | psql arvados_production | grep public|awk -e '{print $3}'`

for t in $tables; do
    echo "echo 'analyze $t' | psql arvados_production"
    time echo "analyze $t" | psql arvados_production
done

If you also need to do the vacuum, you could adapt the script to run ‘vacuum analyze’ instead of ‘analyze’.

New component: arvados-controller

Commit db5107dca adds a new system service, arvados-controller. More detail is available in story #13496.

To add the Arvados Controller to your system please refer to the installation instructions after upgrading your system to 1.2.0.

Verify your setup by confirming that API calls appear in the controller’s logs (e.g., journalctl -fu arvados-controller) while loading a workbench page.

v1.1.4 (2018-04-10)

arvados-cwl-runner regressions (2018-04-05)

Secondary files missing from toplevel workflow inputs

This only affects workflows that rely on implicit discovery of secondaryFiles.

If a workflow input does not declare secondaryFiles corresponding to the secondaryFiles of workflow steps which use the input, the workflow would inconsistently succeed or fail depending on whether the input values were specified as local files or referenced an existing collection (and whether the existing collection contained the secondary files or not). To ensure consistent behavior, the workflow is now required to declare in the top level workflow inputs any secondaryFiles that are expected by workflow steps.

As an example, the following workflow will fail because the toplevel_input does not declare the secondaryFiles that are expected by step_input:

class: Workflow
cwlVersion: v1.0
inputs:
  toplevel_input: File
outputs: []
steps:
  step1:
    in:
      step_input: toplevel_input
    out: []
    run:
      id: sub
      class: CommandLineTool
      inputs:
        step_input:
          type: File
          secondaryFiles:
            - .idx
      outputs: []
      baseCommand: echo

When run, this produces an error like this:

cwltool ERROR: [step step1] Cannot make job: Missing required secondary file 'hello.txt.idx' from file object: {
    "basename": "hello.txt",
    "class": "File",
    "location": "keep:ade9d0e032044bd7f58daaecc0d06bc6+51/hello.txt",
    "size": 0,
    "nameroot": "hello",
    "nameext": ".txt",
    "secondaryFiles": []
}

To fix this error, add the appropriate secondaryFiles section to toplevel_input

class: Workflow
cwlVersion: v1.0
inputs:
  toplevel_input:
    type: File
    secondaryFiles:
      - .idx
outputs: []
steps:
  step1:
    in:
      step_input: toplevel_input
    out: []
    run:
      id: sub
      class: CommandLineTool
      inputs:
        step_input:
          type: File
          secondaryFiles:
            - .idx
      outputs: []
      baseCommand: echo

This bug has been fixed in Arvados release v1.2.0.

Secondary files on default file inputs

File inputs that have default values and also expect secondaryFiles and will fail to upload default secondaryFiles. As an example, the following case will fail:

class: CommandLineTool
inputs:
  step_input:
    type: File
    secondaryFiles:
      - .idx
    default:
      class: File
      location: hello.txt
outputs: []
baseCommand: echo

When run, this produces an error like this:

2018-05-03 10:58:47 cwltool ERROR: Unhandled error, try again with --debug for more information:
  [Errno 2] File not found: u'hello.txt.idx'

To fix this, manually upload the primary and secondary files to keep and explicitly declare secondaryFiles on the default primary file:

class: CommandLineTool
inputs:
  step_input:
    type: File
    secondaryFiles:
      - .idx
    default:
      class: File
      location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
      secondaryFiles:
       - class: File
         location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt.idx
outputs: []
baseCommand: echo

This bug has been fixed in Arvados release v1.2.0.

v1.1.3 (2018-02-08)

There are no special upgrade notes for this release.

v1.1.2 (2017-12-22)

The minimum version for Postgres is now 9.4 (2017-12-08)

As part of story #11908, commit 8f987a9271 introduces a dependency on Postgres 9.4. Previously, Arvados required Postgres 9.3.

  • Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
  • Ubuntu 16.04 (pg 9.5) does not require an upgrade
  • Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
  • CentOS 7 and RHEL7 (pg 9.2) require upgrade to Postgres 9.4. It is necessary to migrate of the contents of your database: https://www.postgresql.org/docs/9.0/static/migration.html
    1. Create a database backup using pg_dump
    2. Install the rh-postgresql94 backport package from either Software Collections: http://doc.arvados.org/install/install-postgresql.html or the Postgres developers: https://www.postgresql.org/download/linux/redhat/
    3. Restore from the backup using psql

v1.1.1 (2017-11-30)

There are no special upgrade notes for this release.

v1.1.0 (2017-10-24)

The minimum version for Postgres is now 9.3 (2017-09-25)

As part of story #12032, commit 68bdf4cbb1 introduces a dependency on Postgres 9.3. Previously, Arvados required Postgres 9.1.

  • Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
  • Ubuntu 16.04 (pg 9.5) does not require an upgrade
  • Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
  • CentOS 7 and RHEL7 (pg 9.2) should upgrade to Postgres 9.4. It is necessary to migrate of the contents of your database: https://www.postgresql.org/docs/9.0/static/migration.html
    1. Create a database backup using pg_dump
    2. Install the rh-postgresql94 backport package from either Software Collections: http://doc.arvados.org/install/install-postgresql.html or the Postgres developers: https://www.postgresql.org/download/linux/redhat/
    3. Restore from the backup using psql

Older versions

Upgrade slower than usual (2017-06-30)

As part of story #11807, commit 55aafbb converts old “jobs” database records from YAML to JSON, making the upgrade process slower than usual.

  • The migration can take some time if your database contains a substantial number of YAML-serialized rows (i.e., you installed Arvados before March 3, 2017 660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
  • The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
  • Expect it to take about 1 minute per 20K jobs that have ever been created/run.

Service discovery overhead change in keep-web (2017-06-05)

As part of story #9005, commit cb230b0 reduces service discovery overhead in keep-web requests.

  • When upgrading keep-web or keepproxy to/past this version, make sure to update API server as well. Otherwise, a bad token in a request can cause keep-web to fail future requests until either keep-web restarts or API server gets upgraded.

Node manager now has an http endpoint for management (2017-04-12)

As part of story #11349, commit 2c094e2 adds a “management” http server to nodemanager.

  • To enable it, add to your configuration file:
    [Manage]
    address = 127.0.0.1
    port = 8989
    (see example configuration files in source:services/nodemanager/doc or https://doc.arvados.org/install/install-nodemanager.html for more info)
  • The server responds to http://{address}:{port}/status.json with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)

New websockets component (2017-03-23)

As part of story #10766, commit e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.

  • See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
  • Remove the old puma server after the upgrade is complete. Example, with runit:

    $ sudo sv down /etc/sv/puma
    $ sudo rm -r /etc/sv/puma
    Example, with systemd:

    $ systemctl disable puma
    $ systemctl stop puma

Change of database encoding for hashes and arrays (2017-03-06)

As part of story #11168, commit 660a614 uses JSON instead of YAML to encode hashes and arrays in the database.

  • Aside from a slight performance improvement, this should have no externally visible effect.
  • Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
  • After upgrading, make sure to restart puma and crunch-dispatch-* processes.

Docker image format compatibility check (2017-02-03)

As part of story #10969, commit 74a9dec introduces a Docker image format compatibility check: the arv keep docker command prevents users from inadvertently saving docker images that compute nodes won’t be able to run.

  • If your compute nodes run a version of docker older than 1.10 you must override the default by adding to your API server configuration (/etc/arvados/api/application.yml):
    docker_image_formats: ["v1"]
  • Refer to the comments above docker_image_formats in /var/www/arvados-api/current/config/application.default.yml or source:services/api/config/application.default.yml or issue #10969 for more detail.
  • NOTE: This does not include any support for migrating existing Docker images from v1 to v2 format. This will come later: for now, sites running Docker 1.9 or earlier should still avoid upgrading Docker further than 1.9.

Debian and RPM packages now have systemd unit files (2016-09-27)

Several Debian and RPM packages — keep-balance (d9eec0b), keep-web (3399e63), keepproxy (6de67b6), and arvados-git-httpd (9e27ddf) — now enable their respective components using systemd. These components prefer YAML configuration files over command line flags (3bbe1cd).

  • On Debian-based systems using systemd, services are enabled automatically when packages are installed.
  • On RedHat-based systems using systemd, unit files are installed but services must be enabled explicitly: e.g., "sudo systemctl enable keep-web; sudo systemctl start keep-web".
  • The new systemd-supervised services will not start up successfully until configuration files are installed in /etc/arvados/: e.g., "Sep 26 18:23:55 62751f5bb946 keep-web[74]: 2016/09/26 18:23:55 open /etc/arvados/keep-web/keep-web.yml: no such file or directory"
  • To migrate from runit to systemd after installing the new packages, we recommend the following procedure:
    1. Bring down the runit service: “sv down /etc/sv/keep-web”
    2. Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml — see “keep-web -help”)
    3. Ensure the service is running correctly under systemd: “systemctl status keep-web” / “journalctl -u keep-web”
    4. Remove the runit service so it doesn’t start at next boot
  • Affected services:
    • keep-balance – /etc/arvados/keep-balance/keep-balance.yml
    • keep-web – /etc/arvados/keep-web/keep-web.yml
    • keepproxy – /etc/arvados/keepproxy/keepproxy.yml
    • arvados-git-httpd – /etc/arvados/arv-git-httpd/arv-git-httpd.yml

Installation paths for Python modules and script changed (2016-05-31)

Commits ae72b172c8 and 3aae316c25 change the filesystem location where Python modules and scripts are installed.

  • Previous packages installed these files to the distribution’s preferred path under /usr/local (or the equivalent location in a Software Collection). Now they get installed to a path under /usr. This improves compatibility with other Python packages provided by the distribution. See #9242 for more background.
  • If you simply import Python modules from scripts, or call Python tools relying on $PATH, you don’t need to make any changes. If you have hardcoded full paths to some of these files (e.g., in symbolic links or configuration files), you will need to update those paths after this upgrade.

Crunchrunner package is required on compute and shell nodes (2016-04-25)

Commit eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.

  • On each Debian-based compute node and shell node, run: sudo apt-get install crunchrunner
  • On each Red Hat-based compute node and shell node, run: sudo yum install crunchrunner

Keep permission signature algorithm change (2016-04-21)

Commit 3c88abd changes the Keep permission signature algorithm.

  • All software components that generate signatures must be upgraded together. These are: keepstore, API server, keep-block-check, and keep-rsync. For example, if keepstore < 0.1.20160421183420 but API server >= 0.1.20160421183420, clients will not be able to read or write data in Keep.
  • Jobs and client operations that are in progress during the upgrade (including arv-put’s “resume cache”) will fail.

Workbench’s “Getting Started” popup disabled by default (2015-01-05)

Commit e1276d6e disables Workbench’s “Getting Started” popup by default.

  • If you want new users to continue seeing this popup, set enable_getting_started_popup: true in Workbench’s application.yml configuration.

Crunch jobs now have access to Keep-backed writable scratch storage (2015-12-03)

Commit 5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see #7751)

  • All compute nodes must be upgraded to arvados-fuse >= 0.1.2015112518060 because crunch-job uses some new arv-mount flags (—mount-tmp, —mount-by-pdh) introduced in merge 346a558
  • Jobs will fail if the API server (in particular crunch-job from the arvados-cli gem) is upgraded without upgrading arvados-fuse on compute nodes.

Recommended configuration change for keep-web (2015-11-11)

Commit 1e2ace5 changes recommended config for keep-web (see #5824)

  • proxy/dns/ssl config should be updated to route “https://download.uuid_prefix.arvadosapi.com/” requests to keep-web (alongside the existing “collections” routing)
  • keep-web command line adds -attachment-only-host download.uuid_prefix.arvadosapi.com
  • Workbench config adds keep_web_download_url
  • More info on the (still beta/non-TOC-linked) keep-web doc page

Stopped containers are now automatically removed on compute nodes (2015-11-04)

Commit 1d1c6de removes stopped containers (see #7444)

  • arvados-docker-cleaner removes all docker containers as soon as they exit, effectively making docker run default to --rm. If you run arvados-docker-cleaner on a host that does anything other than run crunch-jobs, and you still want to be able to use docker start, read the new doc page to learn how to turn this off before upgrading.

New keep-web service (2015-11-04)

Commit 21006cf adds a new keep-web service (see #5824).

  • Nothing relies on keep-web yet, but early adopters can install it now by following http://doc.arvados.org/install/install-keep-web.html (it is not yet linked in the TOC).

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