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title: "Upgrading Arvados and Release notes"
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Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
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What you need to know and do in order to upgrade your Arvados installation.
h2. General process
# Consult upgrade notes below to see if any manual configuration updates are necessary.
# Wait for the cluster to be idle and stop Arvados services.
# Install new packages using @apt-get upgrade@ or @yum upgrade@.
# Package installation scripts will perform any necessary data migrations.
# Restart Arvados services.
h2. 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.
{% comment %}
Note to developers: Add new items at the top. Include the date, issue number, commit, and considerations/instructions for those about to upgrade.
TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
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table(table table-bordered table-condensed).
|_. development|"master":#master|\3.|
|_. latest stable|"v1.4.0":#v1_4_0|\3.|
|_\5. past stable|
|"v1.3.3":#v1_3_3|"v1.3.0":#v1_3_0|\3.|
|"v1.2.1":#v1_2_1|"v1.2.0":#v1_2_0|\3.|
|"v1.1.4":#v1_1_4|"v1.1.3":#v1_1_3|"v1.1.2":#v1_1_2|"v1.1.1":#v1_1_1|"v1.1.0":#v1_1_0|
|\5. "older":#older|
h3(#master). development master (as of 2019-08-05)
h4. Keep-web dropped support on command line flags configuration
As we're migrating to a central cluster configuration file, the already deprecated way of getting configurations via environment variables and command line flags isn't valid anymore. Current keep-web supports both the now legacy @keep-web.yml@ config format (used by Arvados 1.4) and the new cluster config file format. Please check "keep-web's install guide":{{site.baseurl}}/install/install-keep-web.html for more details.
h4. No longer stripping ':' from strings in serialized database columns
(bug #15311) Strings read from serialized columns in the database with a leading ':' would have the ':' stripped after loading the record. This behavior existed due to legacy serialization behavior which stored Ruby symbols with a leading ':'. Unfortunately this corrupted fields where the leading ":" was intentional. This behavior has been removed.
You can test if any records in your database are affected by going to the API server directory and running @bundle exec rake symbols:check@. This will report which records contain fields with a leading ':' that would previously have been stripped. If there are records to be updated, you can update the database using @bundle exec rake symbols:stringify@.
h4. Enabling Postgres trigram indexes
Feature "#15106":https://dev.arvados.org/issues/15106 improves the speed and functionality of full text search by introducing trigram indexes on text searchable database columns via a migration. Prior to updating, you must first install the postgresql-contrib package on your system and subsequently run the CREATE EXTENSION pg_trgm
SQL command on the arvados_production database as a postgres superuser.
The "postgres-contrib package":https://www.postgresql.org/docs/10/contrib.html has been supported since PostgreSQL version 9.4. The version of the contrib package should match the version of your PostgreSQL installation. Using 9.5 as an example, the package can be installed and the extension enabled using the following:
Centos 7
~$ sudo yum install -y postgresql95-contrib
~$ su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"
~$ sudo yum install -y rh-postgresql95-postgresql-contrib
~$ su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"
~$ sudo apt-get install -y postgresql-contrib-9.5
~$ sudo -u postgres psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'
psql -d 'arvados_production' -c '\dx'
command will display the installed extensions for the arvados_production database. This list should now contain @pg_trgm@.
h4. Migrating to centralized config.yml
See "Migrating Configuration":config-migration.html for notes on migrating legacy per-component configuration files to the new centralized @/etc/arvados/config.yml@. To ensure a smooth transition, the per-component config files continue to be read, and take precedence over the centralized configuration.
h3(#v1_4_0). v1.4.0 (2019-06-05)
h4. Populating the new file_count and file_size_total columns on the collections table
As part of story "#14484":https://dev.arvados.org/issues/14484, two new columns were added to the collections table in a database migration. If your installation has a large collections table, this migration may take some time. We've seen it take ~5 minutes on an installation with 250k collections, but your mileage may vary.
The new columns are initialized with a zero value. In order to populate them, it is necessary to run a script called populate-file-info-columns-in-collections.rb
from the scripts directory of the API server. This can be done out of band, ideally directly after the API server has been upgraded to v1.4.0.
h4. Stricter collection manifest validation on the API server
As a consequence of "#14482":https://dev.arvados.org/issues/14482, the Ruby SDK does a more rigorous collection manifest validation. Collections created after 2015-05 are unlikely to be invalid, however you may check for invalid manifests using the script below.
You could set up a new rvm gemset and install the specific arvados gem for testing, like so:
~$ rvm gemset create rubysdk-test
~$ rvm gemset use rubysdk-test
~$ gem install arvados -v 1.3.1.20190301212059
~$
source /usr/share/python2.7/dist/python-arvados-python-client/bin/activate
(python-arvados-python-client) ~$ path-to-the-python-script
#!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
#!/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 doneIf you also need to do the vacuum, you could adapt the script to run 'vacuum analyze' instead of 'analyze'. h4. New component: arvados-controller Commit "db5107dca":https://dev.arvados.org/projects/arvados/repository/revisions/db5107dca adds a new system service, arvados-controller. More detail is available in story "#13496":https://dev.arvados.org/issues/13497. To add the Arvados Controller to your system please refer to the "installation instructions":../install/install-controller.html 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. h3(#v1_1_4). v1.1.4 (2018-04-10) h4. 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: echoWhen 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
class: CommandLineTool inputs: step_input: type: File secondaryFiles: - .idx default: class: File location: hello.txt outputs: [] baseCommand: echoWhen 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
[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.) h4. New websockets component (2017-03-23) As part of story "#10766":https://dev.arvados.org/issues/10766, commit "e8cc0d7":https://dev.arvados.org/projects/arvados/repository/revisions/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/pumaExample, with systemd:
$ systemctl disable puma $ systemctl stop pumah4. Change of database encoding for hashes and arrays (2017-03-06) As part of story "#11168":https://dev.arvados.org/issues/11168, commit "660a614":https://dev.arvados.org/projects/arvados/repository/revisions/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. h4. Docker image format compatibility check (2017-02-03) As part of story "#10969":https://dev.arvados.org/issues/10969, commit "74a9dec":https://dev.arvados.org/projects/arvados/repository/revisions/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":https://dev.arvados.org/issues/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.*
h4. Debian and RPM packages now have systemd unit files (2016-09-27)
Several Debian and RPM packages -- keep-balance ("d9eec0b":https://dev.arvados.org/projects/arvados/repository/revisions/d9eec0b), keep-web ("3399e63":https://dev.arvados.org/projects/arvados/repository/revisions/3399e63), keepproxy ("6de67b6":https://dev.arvados.org/projects/arvados/repository/revisions/6de67b6), and arvados-git-httpd ("9e27ddf":https://dev.arvados.org/projects/arvados/repository/revisions/9e27ddf) -- now enable their respective components using systemd. These components prefer YAML configuration files over command line flags ("3bbe1cd":https://dev.arvados.org/projects/arvados/repository/revisions/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:
*# Bring down the runit service: "sv down /etc/sv/keep-web"
*# Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml -- see "keep-web -help")
*# Ensure the service is running correctly under systemd: "systemctl status keep-web" / "journalctl -u keep-web"
*# 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
h4. Installation paths for Python modules and script changed (2016-05-31)
Commits "ae72b172c8":https://dev.arvados.org/projects/arvados/repository/revisions/ae72b172c8 and "3aae316c25":https://dev.arvados.org/projects/arvados/repository/revisions/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":https://dev.arvados.org/issues/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.
h4. Crunchrunner package is required on compute and shell nodes (2016-04-25)
Commit "eebcb5e":https://dev.arvados.org/projects/arvados/repository/revisions/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@
h4. Keep permission signature algorithm change (2016-04-21)
Commit "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/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.
h4. Workbench's "Getting Started" popup disabled by default (2015-01-05)
Commit "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/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.
h4. Crunch jobs now have access to Keep-backed writable scratch storage (2015-12-03)
Commit "5590c9ac":https://dev.arvados.org/projects/arvados/repository/revisions/5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see "#7751":https://dev.arvados.org/issues/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":https://dev.arvados.org/projects/arvados/repository/revisions/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.
h4. Recommended configuration change for keep-web (2015-11-11)
Commit "1e2ace5":https://dev.arvados.org/projects/arvados/repository/revisions/1e2ace5 changes recommended config for keep-web (see "#5824":https://dev.arvados.org/issues/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":http://doc.arvados.org/install/install-keep-web.html
h4. Stopped containers are now automatically removed on compute nodes (2015-11-04)
Commit "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/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":http://doc.arvados.org/install/install-compute-node.html to learn how to turn this off before upgrading.
h4. New keep-web service (2015-11-04)
Commit "21006cf":https://dev.arvados.org/projects/arvados/repository/revisions/21006cf adds a new keep-web service (see "#5824":https://dev.arvados.org/issues/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).