What you need to know and do in order to upgrade your Arvados installation.
apt-get upgrade or yum upgrade.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.
The Python 3 dependency for Centos7 Arvados packages was upgraded from rh-python35 to rh-python36.
As part of story #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.
As a consequence of #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
Next, you can run the following script using admin credentials, it will scan the whole collection database and report any collection that didn’t pass the check:
require 'arvados' require 'arvados/keep' api = Arvados.new offset = 0 batch_size = 100 invalid = [] while true begin req = api.collection.index( :select => [:uuid, :created_at, :manifest_text], :include_trash => true, :include_old_versions => true, :limit => batch_size, :offset => offset) rescue invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" } raise end req[:items].each do |col| begin Keep::Manifest.validate! col[:manifest_text] rescue Exception => e puts "Collection #{col[:uuid]} manifest not valid" invalid << {uuid: col[:uuid], error: e, created_at: col[:created_at]} end end puts "Checked #{offset} / #{req[:items_available]} - Invalid: #{invalid.size}" offset += req[:limit] break if offset > req[:items_available] end if invalid.empty? puts "No invalid collection manifests found" else invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" } end
The script will return a final report enumerating any invalid collection by UUID, with its creation date and error message so you can take the proper correction measures, if needed.
As part of story #9945, the distribution packaging (deb/rpm) of our Python packages has changed. These packages now include a built-in virtualenv to reduce dependencies on system packages. We have also stopped packaging and publishing backports for all the Python dependencies of our packages, as they are no longer needed.
One practical consequence of this change is that the use of the Arvados Python SDK (aka “import arvados”) will require a tweak if the SDK was installed from a distribution package. It now requires the loading of the virtualenv environment from our packages. The Install documentation for the Arvados Python SDK reflects this change. This does not affect the use of the command line tools (e.g. arv-get, etc.).
Python scripts that rely on the distribution Arvados Python SDK packages to import the Arvados SDK will need to be tweaked to load the correct Python environment.
This can be done by activating the virtualenv outside of the script:
~$source /usr/share/python2.7/dist/python-arvados-python-client/bin/activate(python-arvados-python-client) ~$path-to-the-python-script
Or alternatively, by updating the shebang line at the start of the script to:
#!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
As part of story #9945, the distribution packaging (deb/rpm) of our Python packages has changed. The python-arvados-cwl-runner package now includes a version of cwltool. If present, the python-cwltool and cwltool distribution packages will need to be uninstalled before the python-arvados-cwl-runner deb or rpm package can be installed.
As part of story #9945, the Python 3 dependency for Centos7 Arvados packages was upgraded from SCL python33 to rh-python35.
As part of story #9945, it was discovered that the Centos7 package for libpam-arvados was missing a dependency on the python-pam package, which is available from the EPEL repository. The dependency has been added to the libpam-arvados package. This means that going forward, the EPEL repository will need to be enabled to install libpam-arvados on Centos7.
Arvados is migrating to a centralized configuration file for all components. During the migration, legacy configuration files will continue to be loaded. See Migrating Configuration for details.
This release corrects a potential data loss issue, if you are running Arvados 1.3.0 or 1.3.1 we strongly recommended disabling keep-balance until you can upgrade to 1.3.3 or 1.4.0. With keep-balance disabled, there is no chance of data loss.
We’ve put together a wiki page which outlines how to recover blocks which have been put in the trash, but not yet deleted, as well as how to identify any collections which have missing blocks so that they can be regenerated. The keep-balance component has been enhanced to provide a list of missing blocks and affected collections and we’ve provided a utility script which can be used to identify the workflows that generated those collections and who ran those workflows, so that they can be rerun.
This release includes several database migrations, which will be executed automatically as part of the API server upgrade. On large Arvados installations, these migrations will take a while. We’ve seen the upgrade take 30 minutes or more on installations with a lot of collections.
The arvados-controller component now requires the /etc/arvados/config.yml file to be present. See the arvados-controller installation instructions.
Support for the deprecated “jobs” API is broken in this release. Users who rely on it should not upgrade. This will be fixed in an upcoming 1.3.1 patch release, however users are encouraged to migrate as support for the “jobs” API will be dropped in an upcoming release. Users who are already using the “containers” API are not affected.
There are no special upgrade notes for this release.
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’.
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.
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.
There are no special upgrade notes for this release.
As part of story #11908, commit 8f987a9271 introduces a dependency on Postgres 9.4. Previously, Arvados required Postgres 9.3.
pg_dumprh-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/psqlThere are no special upgrade notes for this release.
As part of story #12032, commit 68bdf4cbb1 introduces a dependency on Postgres 9.3. Previously, Arvados required Postgres 9.1.
pg_dumprh-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/psqlAs part of story #11807, commit 55aafbb converts old “jobs” database records from YAML to JSON, making the upgrade process slower than usual.
As part of story #9005, commit cb230b0 reduces service discovery overhead in keep-web requests.
As part of story #11349, commit 2c094e2 adds a “management” http server to nodemanager.
[Manage](see example configuration files in source:services/nodemanager/doc or https://doc.arvados.org/install/install-nodemanager.html for more info)
address = 127.0.0.1
port = 8989
http://{address}:{port}/status.json with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)As part of story #10766, commit e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.
Example, with systemd:
$ sudo sv down /etc/sv/puma
$ sudo rm -r /etc/sv/puma
$ systemctl disable puma
$ systemctl stop puma
As part of story #11168, commit 660a614 uses JSON instead of YAML to encode hashes and arrays in the database.
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.
/etc/arvados/api/application.yml): docker_image_formats: ["v1"]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.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).
"sudo systemctl enable keep-web; sudo systemctl start keep-web"."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"Commits ae72b172c8 and 3aae316c25 change the filesystem location where Python modules and scripts are installed.
/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.Commit eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.
sudo apt-get install crunchrunnersudo yum install crunchrunnerCommit 3c88abd changes the Keep permission signature algorithm.
Commit e1276d6e disables Workbench’s “Getting Started” popup by default.
enable_getting_started_popup: true in Workbench’s application.yml configuration.Commit 5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see #7751)
Commit 1e2ace5 changes recommended config for keep-web (see #5824)
-attachment-only-host download.uuid_prefix.arvadosapi.comkeep_web_download_urlCommit 1d1c6de removes stopped containers (see #7444)
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.Commit 21006cf adds a new keep-web service (see #5824).
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Apache License, Version 2.0.