3 navsection: installguide
4 title: "Arvados upgrade notes"
8 Copyright (C) The Arvados Authors. All rights reserved.
10 SPDX-License-Identifier: CC-BY-SA-3.0
13 For Arvados administrators, this page will cover what you need to know and do in order to ensure a smooth upgrade of your Arvados installation. For general release notes covering features added and bugs fixed, see "Arvados releases":https://arvados.org/releases.
15 Upgrade instructions can be found at "Maintenance and upgrading":{{site.baseurl}}/admin/maintenance-and-upgrading.html#upgrading.
19 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. These notes are listed below, organized by release version. Scroll down to the version number you are upgrading to.
22 Note to developers: Add new items at the top. Include the date, issue number, commit, and considerations/instructions for those about to upgrade.
24 TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
28 <div class="releasenotes">
31 h2(#main). development main
33 "previous: Upgrading to 2.7.1":#v2_7_1
35 h3. Debian 10, Ubuntu 18.04, and CentOS 7 are no longer supported
37 Arvados 3.0 no longer supports some of the older distributions supported by Arvados 2.7: Debian 10 "buster," Ubuntu 18.04 "bionic," and CentOS 7. If you are running Arvados on any of these distributions, you must first upgrade to the next major release of your distribution before you upgrade to Arvados 3.0.
39 Arvados 2.7 supports Debian 11 "bullseye," Ubuntu 20.04 "focal," and CentOS 8. You can upgrade to one of those releases, then proceed to upgrade Arvados to 3.0.
41 h3. RVM is no longer supported
43 Some Arvados packages, most notably the Rails API server package @arvados-api-server@, would check whether RVM is installed on the system, and invoke Ruby commands through it if so. Arvados 3.0 no longer specially supports RVM. Instead, Arvados 3.0 supports all the different versions of Ruby that are packaged in our supported distributions, mitigating the need to support separate Ruby installations. Package scripts run plain @ruby@ and @gem@ commands and expect they come from a supported version.
45 If you have a custom install that requires a different version of Ruby than the one included with your distribution, you must configure your system to ensure package scripts find that version of @ruby@ before any others. For example, you might do this on Debian-based distributions by customizing apt's @DPkg::Path@ setting.
47 h3. S3 volume IAMRole configuration entry has been removed
49 The @Volumes.*.DriverParameters.IAMRole@ configuration entry for S3 volumes has been removed. You should remove it from your @/etc/arvados/config.yml@ file to avoid warnings when services start up. As before, if @AccessKeyID@ and @SecretAccessKey@ are blank, keepstore will retrieve IAM role credentials from instance metadata. Previously, documentation indicated that keepstore would refuse to use the IAM credentials if @IAMRole@ was specified and did not match the instance metadata, but that check has not been working for some time.
51 h3. Legacy container logging system has been removed
53 The following configuration keys are no longer supported. Remove them from your @/etc/arvados/config.yml@ file to avoid warnings when services start up.
54 * @Containers.Logging.LimitLogBytesPerJob@
55 * @Containers.Logging.LogBytesPerEvent@
56 * @Containers.Logging.LogPartialLineThrottlePeriod@
57 * @Containers.Logging.LogSecondsBetweenEvents@
58 * @Containers.Logging.LogThrottleBytes@
59 * @Containers.Logging.LogThrottleLines@
60 * @Containers.Logging.LogThrottlePeriod@
61 * @Containers.Logging.MaxAge@
62 * @Containers.Logging.SweepInterval@
64 Any container logging content remaining in the database from the legacy system will be deleted.
66 h3. Virtual environments inside distribution Python packages have moved
68 The distribution packages that we publish for Python packages include an entire virtualenv with all required libraries. In Arvados 3.0 these virtualenvs have moved from @/usr/share/python3/dist/PACKAGE_NAME@ to @/usr/lib/PACKAGE_NAME@ to prevent conflicts with distribution packages and better conform to filesystem standards.
70 If you only run the executables installed by these packages, you don't need to change anything. Those are still installed under @/usr/bin@ and will use the new location when you upgrade. If you have written your own scripts or tools that rely on these virtualenvs, you may need to update those with the new location. For example, if you have a shell script that activates the virtualenv by running:
72 <pre><code class="shell">source /usr/share/python3/dist/python3-arvados-python-client/bin/activate</code></pre>
74 You must update it to:
77 <pre><code class="shell">source <span class="userinput">/usr/lib/python3-arvados-python-client</span>/bin/activate</code></pre>
80 If you have a Python script with this shebang line:
82 <pre><code class="shell">#!/usr/share/python3/dist/python3-arvados-python-client/bin/python</code></pre>
84 You must update it to:
87 <pre><code class="shell">#!<span class="userinput">/usr/lib/python3-arvados-python-client</span>/bin/python</code></pre>
90 h3. WebDAV service uses @/var/cache@ for file content
92 @keep-web@ now stores copies of recently accessed data blocks in @/var/cache/arvados/keep@ instead of in memory. That directory will be created automatically. The default cache size is 10% of the filesystem size. Use the new @Collections.WebDAVCache.DiskCacheSize@ config to specify a different percentage or an absolute size.
94 If the previously supported @MaxBlockEntries@ config is present, remove it to avoid warning messages at startup.
96 h3. Check MaxGatewayTunnels config
98 If you use the LSF or Slurm dispatcher, ensure the new @API.MaxGatewayTunnels@ config entry is high enough to support the size of your cluster. See "LSF docs":{{site.baseurl}}/install/crunch2-lsf/install-dispatch.html#MaxGatewayTunnels or "Slurm docs":{{site.baseurl}}/install/crunch2-slurm/install-dispatch.html#MaxGatewayTunnels for details.
100 h2(#2_7_1). v2.7.1 (2023-12-12)
102 "previous: Upgrading to 2.7.0":#v2_7_0
104 h3. Remove Workbench1 packages after upgrading the salt installer
106 If you installed a previous version of Arvados with the Salt installer, and you upgrade your installer to upgrade the cluster, you should uninstall the @arvados-workbench@ package from the workbench instance afterwards.
108 h3. Remove Workbench1 packages and configuration
110 The Workbench1 application has been removed from the Arvados distribution. We recommend the following follow-up steps.
111 * Remove the Workbench1 package from any service node where it is installed (e.g., @apt remove arvados-workbench@).
112 * In your Nginx configuration, add your Workbench1 URL host (from @Services.Workbench1.ExternalURL@) to the @server_name@ directive in the Workbench2 section. For example: <notextile><pre>server {
114 server_name workbench.ClusterID.example.com workbench2.ClusterID.example.com;
117 * In your Nginx configuration, remove the @upstream@ and @server@ sections for Workbench1.
118 * Remove the @Services.Workbench1.InternalURLs@ section of your configuration file. (Do not remove @ExternalURL@.)
119 * Run @arvados-server config-check@ to identify any Workbench1-specific entries in your configuration file, and remove them.
121 h3. Check implications of Containers.MaximumPriceFactor 1.5
123 When scheduling a container, Arvados now considers using instance types other than the lowest-cost type consistent with the container's resource constraints. If a larger instance is already running and idle, or the cloud provider reports that the optimal instance type is not currently available, Arvados will select a larger instance type, provided the cost does not exceed 1.5x the optimal instance type cost.
125 This will typically reduce overall latency for containers and reduce instance booting/shutdown overhead, but may increase costs depending on workload and instance availability. To avoid this behavior, configure @Containers.MaximumPriceFactor: 1.0@.
127 h3. Synchronize keepstore and keep-balance upgrades
129 The internal communication between keepstore and keep-balance about read-only volumes has changed. After keep-balance is upgraded, old versions of keepstore will be treated as read-only. We recommend upgrading and restarting all keepstore services first, then upgrading and restarting keep-balance.
131 h3. Separate configs for MaxConcurrentRequests and MaxConcurrentRailsRequests
133 The default configuration value @API.MaxConcurrentRequests@ (the number of concurrent requests that will be processed by a single instance of an arvados service process) is raised from 8 to 64.
135 A new configuration key @API.MaxConcurrentRailsRequests@ (default 8) limits the number of concurrent requests processed by a RailsAPI service process.
137 h2(#v2_7_0). v2.7.0 (2023-09-21)
139 "previous: Upgrading to 2.6.3":#v2_6_3
141 h3. New system for live container logs
143 Starting with Arvados 2.7, a new system for fetching live container logs is in place. This system features significantly reduced database load compared to previous releases. When Workbench or another application needs to access the logs of a process (running or completed), they should use the "log endpoint of container_requests":{{ site.baseurl }}/api/methods/container_requests.html which forwards requests to the running container. This supersedes the previous system where compute processes would send all of their logs to the database, which produced significant load.
145 The legacy logging system is now disabled by default for all installations with the setting @Containers.Logging.LimitLogBytesForJob: 0@. If you have an existing Arvados installation where you have customized this value and do not need the legacy container logging system, we recommend removing @LimitLogBytesForJob@ from your configuration.
147 If you need to re-enable the legacy logging system, set @Containers.Logging.LimitLogBytesForJob@ to a positive value (the previous default was @Containers.Logging.LimitLogBytesForJob: 67108864@).
149 h3. Workbench 1 deprecated
151 The original Arvados Workbench application (referred to as "Workbench 1") is deprecated and will be removed in a future major version of Arvados. Users are advised to migrate to "Workbench 2". Starting with this release, new installations of Arvados will only set up Workbench 2 and no longer include Workbench 1 by default.
153 It is also important to note that Workbench 1 only supports the legacy logging system, which is now disabled by default. If you need to re-enable the legacy logging system, see above.
155 h3. Multi-node installer's domain name configuration changes
157 The @domain_name@ variable at @terraform/vpc/terraform.tfvars@ and @DOMAIN@ variable at @local.params@ changed their meaning. In previous versions they were used in combination with @cluster_name@ and @CLUSTER@ to build the cluster's domain name (e.g.: @cluster_name@.@domain_name@). To allow the use of any arbitrary cluster domain, now we don't enforce using the cluster prefix as part of the domain, so @domain_name@ and @DOMAIN@ need to hold the entire domain for the given cluster.
158 For example, if @cluster_name@ is set to @"xarv1"@ and @domain_name@ was previously set to @"example.com"@, it should now be set to @"xarv1.example.com"@ to keep using the same cluster domain.
160 h3. Crunchstat log format change
162 The reported number of CPUs available in a container is now formatted in @crunchstat.txt@ log files and @crunchstat-summary@ text reports as a floating-point number rather than an integer (@2.00 cpus@ rather than @2 cpus@). Programs that parse these files may need to be updated accordingly.
164 h3. arvados-login-sync configuration changes, including ignored groups
166 In the @Users@ section of your cluster configuration, there are now several options to control what system resources are or are not managed by @arvados-login-sync@. These options all have names that begin with @Sync@.
168 The defaults for all of these options match the previous behavior of @arvados-login-sync@ _except_ for @SyncIgnoredGroups@. This list names groups that @arvados-login-sync@ will never modify by adding or removing members. As a security precaution, the default list names security-sensitive system groups on Debian- and Red Hat-based distributions. If you are using Arvados to manage system group membership on shell nodes, especially @sudo@ or @wheel@, you may want to provide your own list. Set @SyncIgnoredGroups: []@ to restore the original behavior of ignoring no groups.
170 h3. API clients can always retrieve their current token, regardless of scopes
172 We have introduced a small exception to the previous behavior of "Arvados API token scopes":{{ site.baseurl }}/admin/scoped-tokens.html in this release. A valid token is now always allowed to issue a request to "@GET /arvados/v1/api_client_authorizations/current@":{{ site.baseurl }}/api/methods/api_client_authorizations.html#current regardless of its scopes. This allows clients to reliably determine whether a request failed because a token is invalid, or because the token is not permitted to perform a particular request. The API server itself needs to be able to do this to validate tokens issued by other clusters in a federation.
174 h3. Deprecated/legacy APIs slated for removal
176 The legacy APIs "humans":https://doc.arvados.org/v2.7/api/methods/humans.html, "specimens":https://doc.arvados.org/v2.7/api/methods/specimens.html, "traits":https://doc.arvados.org/v2.7/api/methods/traits.html, "jobs":https://doc.arvados.org/v2.7/api/methods/jobs.html, "job_tasks":https://doc.arvados.org/v2.7/api/methods/job_tasks.html, "pipeline_instances":https://doc.arvados.org/v2.7/api/methods/pipeline_instances.html, "pipeline_templates":https://doc.arvados.org/v2.7/api/methods/pipeline_templates.html, "nodes":https://doc.arvados.org/v2.7/api/methods/nodes.html, "repositories":https://doc.arvados.org/v2.7/api/methods/repositories.html, and "keep_disks":https://doc.arvados.org/v2.7/api/methods/keep_disks.html are deprecated and will be removed in a future major version of Arvados.
178 In addition, the @default_owner_uuid@, @api_client_id@, and @user_id@ fields of "api_client_authorizations":../api/methods/api_client_authorizations.html are deprecated and will be removed from @api_client_authorization@ responses in a future major version of Arvados. This should not affect clients as @default_owner_uuid@ was never implemented, and @api_client_id@ and @user_id@ returned internal ids that were not meaningful or usable with any other API call.
180 h3. UseAWSS3v2Driver option removed
182 The old "v1" S3 driver for keepstore has been removed. The new "v2" implementation, which has been the default since Arvados 2.5.0, is always used. The @Volumes.*.DriverParameters.UseAWSS3v2Driver@ configuration key is no longer recognized. If your config file uses it, remove it to avoid warning messages at startup.
184 h2(#v2_6_3). v2.6.3 (2023-06-06)
186 h3. Python SDK automatically retries failed requests much more
188 The Python SDK has always provided functionality to retry API requests that fail due to temporary problems like network failures, by passing @num_retries=N@ to a request's @execute()@ method. In this release, API client constructor functions like @arvados.api@ also accept a @num_retries@ argument. This value is stored on the client object and used as a floor for all API requests made with this client. This allows developers to set their preferred retry strategy once, without having to pass it to each @execute()@ call.
190 The default value for @num_retries@ in API constructor functions is 10. This means that an API request that repeatedly encounters temporary problems may spend up to about 35 minutes retrying in the worst case. We believe this is an appropriate default for most users, where eventual success is a much greater concern than responsiveness. If you have client applications where this is undesirable, update them to pass a lower @num_retries@ value to the constructor function. You can even pass @num_retries=0@ to have the API client act as it did before, like this:
192 {% codeblock as python %}
194 arv_client = arvados.api('v1', num_retries=0, ...)
197 The first time the Python SDK fetches an Arvados API discovery document, it will ensure that @googleapiclient.http@ logs are handled so you have a way to know about early problems that are being retried. If you prefer to handle these logs your own way, just ensure that the @googleapiclient.http@ logger (or a parent logger) has a handler installed before you call any Arvados API client constructor.
199 h2(#v2_6_2). v2.6.2 (2023-05-22)
201 "previous: Upgrading to 2.6.1":#v2_6_1
203 This version introduces a new API feature which is used by Workbench 2 to improve page loading performance. To avoid any errors using the new Workbench with an old API server, be sure to upgrade the API server before upgrading Workbench 2.
205 h2(#v2_6_1). v2.6.1 (2023-04-17)
207 "previous: Upgrading to 2.6.0":#v2_6_0
209 h3. Performance improvement for permission row de-duplication migration
211 The migration which de-duplicates permission links has been optimized. We recommend upgrading from 2.5.0 directly to 2.6.1 in order to avoid the slow permission de-deplication migration in 2.6.0.
213 You should still plan for the arvados-api-server package upgrade to take longer than usual due to the database schema update changing the integer id column in each table from 32-bit to 64-bit.
215 h2(#v2_6_0). v2.6.0 (2023-04-06)
217 "previous: Upgrading to 2.5.0":#v2_5_0
219 h3. WebDAV InternalURLs must be reachable from controller nodes
221 Ensure your internal keep-web service addresses are listed in the @Services.WebDAV.InternalURLs@ section of your configuration file, and reachable from controller processes, as noted on the "updated install page":{{site.baseurl}}/admin/config-urls.html.
223 h3. Slow migration on upgrade
225 Important! This upgrade includes a database schema update changing the integer id column in each table from 32-bit to 64-bit. Because it touches every row in the table, on moderate to large sized installations *this may be very slow* (on the order of hours). Plan for the arvados-api-server package upgrade to take longer than usual.
227 h3. Default request concurrency, new limit on log requests
229 The configuration value @API.MaxConcurrentRequests@ (the number of concurrent requests that will be accepted by a single instance of arvados-controller) now has a default value of 64, instead of being unlimited.
231 New configuration value @API.LogCreateRequestFraction@ (default 0.50) limits requests that post live container logs to the API server, to avoid situations where log messages crowd out other more important requests.
233 h3. New limit on concurrent workflows
235 New configuration options @CloudVMs.SupervisorFraction@ (default 0.30) limits the number of concurrent workflow supervisors, to avoid situations where too many workflow runners crowds out actual workers.
237 h3. Default limit for cloud VM instances
239 There is a new configuration entry @CloudVMs.MaxInstances@ (default 64) that limits the number of VMs the cloud dispatcher will run at a time. This may need to be adjusted to suit your anticipated workload.
241 Using the obsolete configuration entry @MaxCloudVMs@, which was previously accepted in config files but not obeyed, will now result in a deprecation warning.
243 h3. Default frequency for running keep-balance has changed
245 The frequency that @keep-balance@ will run (@Collections.BalancePeriod@) has been changed from every 10 minutes to every 6 hours.
247 h2(#v2_5_0). v2.5.0 (2022-12-22)
249 "previous: Upgrading to 2.4.4":#v2_4_4
251 h3. Dispatchers require PostgreSQL database access
253 All dispatchers (cloud, LSF, and Slurm) now connect directly to the PostgreSQL database. Make sure these connections are supported by your network firewall rules, PostgreSQL connection settings, and PostgreSQL server configuration (in @pg_hba.conf@) as shown in the "PostgreSQL install instructions":{{site.baseurl}}/install/install-postgresql.html.
255 h3. Google or OpenID Connect login restricted to trusted clients
257 If you use OpenID Connect or Google login, and your cluster serves as the @LoginCluster@ in a federation _or_ your users log in from a web application other than the Workbench1 and Workbench2 @ExternalURL@ addresses in your configuration file, the additional web application URLs (e.g., the other clusters' Workbench addresses) must be listed explicitly in @Login.TrustedClients@, otherwise login will fail. Previously, login would succeed with a less-privileged token.
259 h3. New keepstore S3 driver enabled by default
261 A more actively maintained S3 client library is now enabled by default for keeepstore services. The previous driver is still available for use in case of unknown issues. To use the old driver, set @DriverParameters.UseAWSS3v2Driver@ to @false@ on the appropriate @Volumes@ config entries.
263 h3. Old container logs are automatically deleted from PostgreSQL
265 Cached copies of log entries from containers that finished more than 1 month ago are now deleted automatically (this only affects the "live" logs saved in the PostgreSQL database, not log collections saved in Keep). If you have an existing cron job that runs @rake db:delete_old_container_logs@, you can remove it. See configuration options @Containers.Logging.MaxAge@ and @Containers.Logging.SweepInterval@.
267 h3. Fixed salt installer template file to support container shell access
269 If you manage your cluster using the salt installer, you may want to update it to the latest version, use the appropriate @config_examples@ subdirectory and re-reploy with your custom @local.params@ file so that the @arvados-controller@'s @nginx@ configuration file gets fixed.
271 h3. Login-sync script requires configuration update on LoginCluster federations
273 If you have @arvados-login-sync@ running on a satellite cluster, please update the environment variable settings by removing the @LOGINCLUSTER_ARVADOS_API_*@ variables and setting @ARVADOS_API_TOKEN@ to a LoginCluster's admin token, as described on the "updated install page":{{site.baseurl}}/install/install-shell-server.html#arvados-login-sync.
275 h3. Renamed keep-web metrics and WebDAV configs
277 Metrics previously reported by keep-web (@arvados_keepweb_collectioncache_requests@, @..._hits@, @..._pdh_hits@, @..._api_calls@, @..._cached_manifests@, and @arvados_keepweb_sessions_cached_collection_bytes@) have been replaced with @arvados_keepweb_cached_session_bytes@.
279 The config entries @Collections.WebDAVCache.UUIDTTL@, @...MaxCollectionEntries@, and @...MaxUUIDEntries@ are no longer used, and should be removed from your config file.
281 h2(#v2_4_4). v2.4.4 (2022-11-18)
283 "previous: Upgrading to 2.4.3":#v2_4_3
285 This update only consists of improvements to @arvados-cwl-runner@. There are no changes to backend services.
287 h2(#v2_4_3). v2.4.3 (2022-09-21)
289 "previous: Upgrading to 2.4.2":#v2_4_2
291 h3. Fixed PAM authentication security vulnerability
293 In Arvados 2.4.2 and earlier, when using PAM authentication, if a user presented valid credentials but the account is disabled or otherwise not allowed to access the host, it would still be accepted for access to Arvados. From 2.4.3 onwards, Arvados now also checks that the account is permitted to access the host before completing the PAM login process.
295 Other authentication methods (LDAP, OpenID Connect) are not affected by this flaw.
297 h2(#v2_4_2). v2.4.2 (2022-08-09)
299 "previous: Upgrading to 2.4.1":#v2_4_1
303 GitHub Security Lab (GHSL) reported a remote code execution (RCE) vulnerability in the Arvados Workbench that allows authenticated attackers to execute arbitrary code via specially crafted JSON payloads.
305 This vulnerability is fixed in 2.4.2 ("#19316":https://dev.arvados.org/issues/19316).
307 It is likely that this vulnerability exists in all versions of Arvados up to 2.4.1.
309 This vulnerability is specific to the Ruby on Rails Workbench application ("Workbench 1"). We do not believe any other Arvados components, including the TypesScript browser-based Workbench application ("Workbench 2") or API Server, are vulnerable to this attack.
311 h3. CVE-2022-31163 and CVE-2022-32224
313 As a precaution, Arvados 2.4.2 has includes security updates for Ruby on Rails and the TZInfo Ruby gem. However, there are no known exploits in Arvados based on these CVEs.
315 h3. Disable Sharing URLs UI
317 There is now a configuration option @Workbench.DisableSharingURLsUI@ for admins to disable the user interface for "sharing link" feature (URLs which can be sent to users to access the data in a specific collection in Arvados without an Arvados account), for organizations where sharing links violate their data sharing policy.
319 h2(#v2_4_1). v2.4.1 (2022-06-02)
321 "previous: Upgrading to 2.4.0":#v2_4_0
323 h3. Slurm dispatcher requires configuration update
325 If you use the Slurm dispatcher (@crunch-dispatch-slurm@) you must add a @Services.DispatchSLURM.InternalURLs@ section to your configuration file, as shown on the "updated install page":{{site.baseurl}}/install/crunch2-slurm/install-dispatch.html.
327 h3. New proxy parameters for arvados-controller
329 We now recommend disabling nginx proxy caching for arvados-controller, to avoid truncation of large responses.
331 In your Nginx configuration file (@/etc/nginx/conf.d/arvados-api-and-controller.conf@), add the following lines to the @location /@ block with @http://controller@ (see "Update nginx configuration":{{site.baseurl}}/install/install-api-server.html#update-nginx for an example) and reload/restart Nginx (@sudo nginx -s reload@).
334 proxy_max_temp_file_size 0;
335 proxy_request_buffering off;
337 proxy_http_version 1.1;
340 h3. Now recommending Singularity 3.9.9
342 The compute image "build script":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html now installs Singularity 3.9.9 instead of 3.7.4. The newer version includes a bugfix that should resolve "intermittent loopback device errors":https://dev.arvados.org/issues/18489 when running containers.
344 h3. Changes to @arvados-cwl-runner --create-workflow@ and @--update-workflow@
346 When using @arvados-cwl-runner --create-workflow@ or @--update-workflow@, by default it will now make a copy of all collection and Docker image dependencies in the target project. Running workflows retains the old behavior (use the dependencies wherever they are found). The can be controlled explicit with @--copy-deps@ and @--no-copy-deps@.
348 h2(#v2_4_0). v2.4.0 (2022-04-08)
350 "previous: Upgrading to 2.3.1":#v2_3_1
352 h3. Default result order changed
354 When requesting a list of objects without an explicit @order@ parameter, the default order has changed from @modified_at desc, uuid asc@ to @modified_at desc, uuid desc@. This means that if two objects have identical @modified_at@ timestamps, the tiebreaker will now be based on @uuid@ in decending order where previously it would be ascending order. The practical effect of this should be minor; with microsecond precision it is unusual to have two records with exactly the same timestamp, and order-sensitive queries should already provide an explicit @order@ parameter.
356 h3. Ubuntu 18.04 Arvados Python packages now depend on python-3.8
358 Ubuntu 18.04 ships with Python 3.6 as the default version of Python 3. Ubuntu also ships a version of Python 3.8, and the Arvados Python packages (@python3-arvados-cwl-runner@, @python3-arvados-fuse@, @python3-arvados-python-client@, @python3-arvados-user-activity@ and @python3-crunchstat-summary@) now depend on the @python-3.8@ system package.
360 This means that they are now installed under @/usr/share/python3.8@ (before, the path was @/usr/share/python3@). If you rely on the @python3@ executable from the packages (e.g. to load a virtualenv), you may need to update the path to that executable.
362 h3. Minimum supported Ruby version is now 2.6
364 The minimum supported Ruby version is now 2.6. If you are running Arvados on Debian 10 or Ubuntu 18.04, you may need to switch to using RVM or upgrade your OS. See "Install Ruby and Bundler":../install/ruby.html for more information.
366 h3. Anonymous token changes
368 The anonymous token configured in @Users.AnonymousUserToken@ must now be 32 characters or longer. This was already the suggestion in the documentation, now it is enforced. The @script/get_anonymous_user_token.rb@ script that was needed to register the anonymous user token in the database has been removed. Registration of the anonymous token is no longer necessary.
370 h3. Preemptible instance support changes
372 The @Containers.UsePreemptibleInstances@ option has been renamed to @Containers.AlwaysUsePreemptibleInstances@ and has the same behavior when @true@ and one or more preemptible instances are configured. However, a value of @false@ no longer disables support for preemptible instances, instead users can now enable use of preemptible instances at the level of an individual workflow or workflow step.
374 In addition, there is a new configuration option @Containers.PreemptiblePriceFactor@ will automatically add a preemptible instance type corresponding to each regular instance type. See "Using Preemptible instances":spot-instances.html for details.
376 h3. Default LSF arguments have changed
378 If you use LSF and your configuration specifies @Containers.LSF.BsubArgumentsList@, you should update it to include the new arguments (@"-R", "select[mem>=%MMB]", ...@, see "configuration reference":{{site.baseurl}}/admin/config.html). Otherwise, containers that are too big to run on any LSF host will remain in the LSF queue instead of being cancelled.
380 h3. Support for NVIDIA CUDA GPUs
382 Arvados now supports requesting NVIDIA CUDA GPUs for cloud and LSF (Slurm is currently not supported). To be able to request GPU nodes, some additional configuration is needed:
384 "Including GPU support in cloud compute node image":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html#nvidia
386 "Configure cloud dispatcher for GPU support":{{site.baseurl}}/install/crunch2-cloud/install-dispatch-cloud.html#GPUsupport
388 "LSF GPU configuration":{{site.baseurl}}/install/crunch2-lsf/install-dispatch.html
390 h3. Role groups are visible to all users by default
392 The permission model has changed such that all role groups are visible to all active users. This enables users to share objects with groups they don't belong to. To preserve the previous behavior, where role groups are only visible to members and admins, add @RoleGroupsVisibleToAll: false@ to the @Users@ section of your configuration file.
394 h3. Previously trashed role groups will be deleted
396 Due to a bug in previous versions, the @DELETE@ operation on a role group caused the group to be flagged as trash in the database, but continue to grant permissions regardless. After upgrading, any role groups that had been trashed this way will be deleted. This might surprise some users if they were relying on permissions that were still in effect due to this bug. Future @DELETE@ operations on a role group will immediately delete the group and revoke the associated permissions.
398 h3. Dedicated keepstore process for each container
400 When Arvados runs a container via @arvados-dispatch-cloud@, the @crunch-run@ supervisor process now brings up its own keepstore server to handle I/O for mounted collections, outputs, and logs. With the default configuration, the keepstore process allocates one 64 MiB block buffer per VCPU requested by the container. For most workloads this will increase throughput, reduce total network traffic, and make it possible to run more containers at once without provisioning additional keepstore nodes to handle the I/O load.
401 * If you have containers that can effectively handle multiple I/O threads per VCPU, consider increasing the @Containers.LocalKeepBlobBuffersPerVCPU@ value.
402 * If you already have a robust permanent keepstore infrastructure, you can set @Containers.LocalKeepBlobBuffersPerVCPU@ to 0 to disable this feature and preserve the previous behavior of sending container I/O traffic to your separately provisioned keepstore servers.
403 * This feature is enabled only if no volumes use @AccessViaHosts@, and no volumes have underlying @Replication@ less than @Collections.DefaultReplication@. If the feature is configured but cannot be enabled due to an incompatible volume configuration, this will be noted in the @crunch-run.txt@ file in the container log.
405 h2(#v2_3_1). v2.3.1 (2021-11-24)
407 "previous: Upgrading to 2.3.0":#v2_3_0
409 h3. Users are visible to other users by default
411 When a new user is set up (either via @AutoSetupNewUsers@ config or via Workbench admin interface) the user immediately becomes visible to other users. To revert to the previous behavior, where the administrator must add two users to the same group using the Workbench admin interface in order for the users to see each other, change the new @Users.ActivatedUsersAreVisibleToOthers@ config to @false@.
413 h3. Backend support for vocabulary checking
415 If your installation uses the vocabulary feature on Workbench2, you will need to update the cluster configuration by moving the vocabulary definition file to the node where @controller@ runs, and set the @API.VocabularyPath@ configuration parameter to the local path where the file was placed.
416 This will enable the vocabulary checking cluster-wide, including Workbench2. The @Workbench.VocabularyURL@ configuration parameter is deprecated and will be removed in a future release.
417 You can read more about how this feature works on the "admin page":{{site.baseurl}}/admin/metadata-vocabulary.html.
419 h2(#v2_3_0). v2.3.0 (2021-10-27)
421 "previous: Upgrading to 2.2.0":#v2_2_0
423 h3. Ubuntu 18.04 packages for arvados-api-server and arvados-workbench now conflict with ruby-bundler
425 Ubuntu 18.04 ships with Bundler version 1.16.1, which is no longer compatible with the Gemfiles in the Arvados packages (made with Bundler 2.2.19). The Ubuntu 18.04 packages for arvados-api-server and arvados-workbench now conflict with the ruby-bundler package to work around this issue. The post-install scripts for arvados-api-server and arvados-workbench install the proper version of Bundler as a gem.
427 h3. Removed unused @update_uuid@ endpoint for users.
429 The @update_uuid@ endpoint was superseded by the "link accounts feature":{{site.baseurl}}/admin/link-accounts.html, so it's no longer available.
431 h3. Removed deprecated '@@' search operator
433 The '@@' full text search operator, previously deprecated, has been removed. To perform a string search across multiple columns, use the 'ilike' operator on 'any' column as described in the "available list method filter section":{{site.baseurl}}/api/methods.html#substringsearchfilter of the API documentation.
435 h3. Storage classes must be defined explicitly
437 If your configuration uses the StorageClasses attribute on any Keep volumes, you must add a new @StorageClasses@ section that lists all of your storage classes. Refer to the updated documentation about "configuring storage classes":{{site.baseurl}}/admin/storage-classes.html for details.
439 h3. keep-balance requires access to PostgreSQL
441 Make sure the keep-balance process can connect to your PostgreSQL server using the settings in your config file. (In previous versions, keep-balance accessed the database through controller instead of connecting to the database server directly.)
443 h3. crunch-dispatch-local now requires config.yml
445 The @crunch-dispatch-local@ dispatcher now reads the API host and token from the system wide @/etc/arvados/config.yml@ . It will fail to start that file is not found or not readable.
447 h3. Multi-file docker image collections
449 Typically a docker image collection contains a single @.tar@ file at the top level. Handling of atypical cases has changed. If a docker image collection contains files with extensions other than @.tar@, they will be ignored (previously they could cause errors). If a docker image collection contains multiple @.tar@ files, it will cause an error at runtime, "cannot choose from multiple tar files in image collection" (previously one of the @.tar@ files was selected). Subdirectories are ignored. The @arv keep docker@ command always creates a collection with a single @.tar@ file, and never uses subdirectories, so this change will not affect most users.
451 h2(#v2_2_0). v2.2.0 (2021-06-03)
453 "previous: Upgrading to 2.1.0":#v2_1_0
455 h3. New spelling of S3 credential configs
457 If you use the S3 driver for Keep volumes and specify credentials in your configuration file (as opposed to using an IAM role), you should change the spelling of the @AccessKey@ and @SecretKey@ config keys to @AccessKeyID@ and @SecretAccessKey@. If you don't update them, the previous spellings will still be accepted, but warnings will be logged at server startup.
459 h3. New proxy parameters for arvados-controller
461 In your Nginx configuration file (@/etc/nginx/conf.d/arvados-api-and-controller.conf@), add the following lines to the @location /@ block with @http://controller@ (see "Update nginx configuration":{{site.baseurl}}/install/install-api-server.html#update-nginx for an example) and reload/restart Nginx (@sudo nginx -s reload@).
464 proxy_set_header Upgrade $http_upgrade;
465 proxy_set_header Connection "upgrade";
468 h3. Changes on the collection's @preserve_version@ attribute semantics
470 The @preserve_version@ attribute on collections was originally designed to allow clients to persist a preexisting collection version. This forced clients to make 2 requests if the intention is to "make this set of changes in a new version that will be kept", so we have changed the semantics to do just that: When passing @preserve_version=true@ along with other collection updates, the current version is persisted and also the newly created one will be persisted on the next update.
472 h3. System token requirements
474 System services now log a warning at startup if any of the system tokens (@ManagementToken@, @SystemRootToken@, and @Collections.BlobSigningKey@) are less than 32 characters, or contain characters other than a-z, A-Z, and 0-9. After upgrading, run @arvados-server config-check@ and update your configuration file if needed to resolve any warnings.
476 The @API.RailsSessionSecretToken@ configuration key has been removed. Delete this entry from your configuration file after upgrading.
478 h3. Centos7 Python 3 dependency upgraded to python3
480 Now that Python 3 is part of the base repository in CentOS 7, the Python 3 dependency for Centos7 Arvados packages was changed from SCL rh-python36 to python3.
482 h3. ForceLegacyAPI14 option removed
484 The ForceLegacyAPI14 configuration option has been removed. In the unlikely event it is mentioned in your config file, remove it to avoid "deprecated/unknown config" warning logs.
486 h2(#v2_1_0). v2.1.0 (2020-10-13)
488 "previous: Upgrading to 2.0.0":#v2_0_0
490 h3. LoginCluster conflicts with other Login providers
492 A satellite cluster that delegates its user login to a central user database must only have `Login.LoginCluster` set, or it will return an error. This is a change in behavior, previously it would return an error if another login provider was _not_ configured, even though the provider would never be used.
494 h3. Minimum supported Python version is now 3.5
496 We no longer publish Python 2 based distribution packages for our Python components. There are equivalent packages based on Python 3, but their names are slightly different. If you were using the Python 2 based packages, you can install the Python 3 based package for a drop in replacement. On Debian and Ubuntu:
499 apt remove python-arvados-fuse && apt install python3-arvados-fuse
500 apt remove python-arvados-python-client && apt install python3-arvados-python-client
501 apt remove python-arvados-cwl-runner && apt install python3-arvados-cwl-runner
502 apt remove python-crunchstat-summary && apt install python3-crunchstat-summary
503 apt remove python-cwltest && apt install python3-cwltest
509 yum remove python-arvados-fuse && yum install python3-arvados-fuse
510 yum remove python-arvados-python-client && yum install python3-arvados-python-client
511 yum remove python-arvados-cwl-runner && yum install python3-arvados-cwl-runner
512 yum remove python-crunchstat-summary && yum install python3-crunchstat-summary
513 yum remove python-cwltest && yum install python3-cwltest
516 h3. Minimum supported Ruby version is now 2.5
518 The minimum supported Ruby version is now 2.5. If you are running Arvados on Debian 9 or Ubuntu 16.04, you may need to switch to using RVM or upgrade your OS. See "Install Ruby and Bundler":../install/ruby.html for more information.
520 h3. Removing libpam-arvados, replaced with libpam-arvados-go
522 The Python-based PAM package has been replaced with a version written in Go. See "using PAM for authentication":{{site.baseurl}}/install/setup-login.html#pam for details.
524 h3. Removing sso-provider
526 The SSO (single sign-on) component is deprecated and will not be supported in future releases. Existing configurations will continue to work in this release, but you should switch to one of the built-in authentication mechanisms as soon as possible. See "setting up web based login":{{site.baseurl}}/install/setup-login.html for details.
528 After migrating your configuration, uninstall the @arvados-sso-provider@ package.
532 Keepstore now uses "V4 signatures":https://docs.aws.amazon.com/AmazonS3/latest/API/sig-v4-authenticating-requests.html by default for S3 requests. If you are using Amazon S3, no action is needed; all regions support V4 signatures. If you are using a different S3-compatible service that does not support V4 signatures, add @V2Signature: true@ to your volume driver parameters to preserve the old behavior. See "configuring S3 object storage":{{site.baseurl}}/install/configure-s3-object-storage.html.
534 h3. New permission system constraints
536 Some constraints on the permission system have been added, in particular @role@ and @project@ group types now have distinct behavior. These constraints were already de-facto imposed by the Workbench UI, so on most installations the only effect of this migration will be to reassign @role@ groups to the system user and create a @can_manage@ permission link for the previous owner.
538 # The @group_class@ field must be either @role@ or @project@. Invalid group_class are migrated to @role@.
539 # A @role@ cannot own things. Anything owned by a role is migrated to a @can_manage@ link and reassigned to the system user.
540 # Only @role@ and @user@ can have outgoing permission links. Permission links originating from projects are deleted by the migration.
541 # A @role@ is always owned by the system_user. When a group is created, it creates a @can_manage@ link for the object that would have been assigned to @owner_uuid@. Migration adds @can_manage@ links and reassigns roles to the system user. This also has the effect of requiring that all @role@ groups have unique names on the system. If there is a name collision during migration, roles will be renamed to ensure they are unique.
542 # A permission link can have the permission level (@name@) updated but not @head_uuid@, @tail_uuid@ or @link_class@.
544 The @arvados-sync-groups@ tool has been updated to reflect these constraints, so it is important to use the version of @arvados-sync-groups@ that matches the API server version.
546 Before upgrading, use the following commands to find out which groups and permissions in your database will be automatically modified or deleted during the upgrade.
548 To determine which groups have invalid @group_class@ (these will be migrated to @role@ groups):
551 arv group list --filters '[["group_class", "not in", ["project", "role"]]]'
554 To list all @role@ groups, which will be reassigned to the system user (unless @owner_uuid@ is already the system user):
557 arv group list --filters '[["group_class", "=", "role"]]'
560 To list which @project@ groups have outgoing permission links (such links are now invalid and will be deleted by the migration):
563 for uuid in $(arv link list --filters '[["link_class", "=", "permission"], ["tail_uuid", "like", "%-j7d0g-%"]]' |
564 jq -r .items[].tail_uuid | sort | uniq) ; do
565 arv group list --filters '[["group_class", "=", "project"], ["uuid", "=", "'$uuid'"]]' | jq .items
569 h4. "Public favorites" moved to their own project
571 As a side effect of new permission system constraints, "star" links (indicating shortcuts in Workbench) that were previously owned by "All users" (which is now a "role" and cannot own things) will be migrated to a new system project called "Public favorites" which is readable by the "Anonymous users" role.
573 h2(#v2_0_0). v2.0.0 (2020-02-07)
575 "previous: Upgrading to 1.4.1":#v1_4_1
577 Arvados 2.0 is a major upgrade, with many changes. Please read these upgrade notes carefully before you begin.
579 h3. Migrating to centralized config.yml
581 See "Migrating Configuration":https://doc.arvados.org/v2.1/admin/config-migration.html for notes on migrating legacy per-component configuration files to the new centralized @/etc/arvados/config.yml@.
583 To ensure a smooth transition, the per-component config files continue to be read, and take precedence over the centralized configuration. Your cluster should continue to function after upgrade but before doing the full configuration migration. However, several services (keepstore, keep-web, keepproxy) require a minimal `/etc/arvados/config.yml` to start:
590 ExternalURL: "https://zzzzz.example.com"
593 h3. Keep-balance configuration migration
595 (feature "#14714":https://dev.arvados.org/issues/14714 ) The keep-balance service can now be configured using the centralized configuration file at @/etc/arvados/config.yml@. The following command line and configuration options have changed.
597 You can no longer specify types of keep services to balance via the @KeepServiceTypes@ config option in the legacy config at @/etc/arvados/keep-balance/keep-balance.yml@. If you are still using the legacy config and @KeepServiceTypes@ has a value other than "disk", keep-balance will produce an error.
599 You can no longer specify individual keep services to balance via the @config.KeepServiceList@ command line option or @KeepServiceList@ legacy config option. Instead, keep-balance will operate on all keepstore servers with @service_type:disk@ as reported by the @arv keep_service list@ command. If you are still using the legacy config, @KeepServiceList@ should be removed or keep-balance will produce an error.
601 Please see the "config migration guide":https://doc.arvados.org/v2.1/admin/config-migration.html and "keep-balance install guide":{{site.baseurl}}/install/install-keep-balance.html for more details.
603 h3. Arv-git-httpd configuration migration
605 (feature "#14712":https://dev.arvados.org/issues/14712 ) The arv-git-httpd package can now be configured using the centralized configuration file at @/etc/arvados/config.yml@. Configuration via individual command line arguments is no longer available. Please see "arv-git-httpd's config migration guide":https://doc.arvados.org/v2.1/admin/config-migration.html#arv-git-httpd for more details.
607 h3. Keepstore and keep-web configuration migration
609 keepstore and keep-web no longer support configuration via (previously deprecated) command line configuration flags and environment variables.
611 keep-web now supports the 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.
613 keepstore now supports the legacy @keepstore.yml@ config format (used by Arvados 1.4) and the new cluster config file format. Please check the "keepstore config migration notes":https://doc.arvados.org/v2.1/admin/config-migration.html#keepstore and "keepstore install guide":{{site.baseurl}}/install/install-keepstore.html for more details.
615 h3. Keepproxy configuration migration
617 (feature "#14715":https://dev.arvados.org/issues/14715 ) Keepproxy can now be configured using the centralized config at @/etc/arvados/config.yml@. Configuration via individual command line arguments is no longer available and the @DisableGet@, @DisablePut@, and @PIDFile@ configuration options are no longer supported. If you are still using the legacy config and @DisableGet@ or @DisablePut@ are set to true or @PIDFile@ has a value, keepproxy will produce an error and fail to start. Please see "keepproxy's config migration guide":https://doc.arvados.org/v2.1/admin/config-migration.html#keepproxy for more details.
619 h3. Delete "keep_services" records
621 After all keepproxy and keepstore configurations have been migrated to the centralized configuration file, all keep_services records you added manually during installation should be removed. System logs from keepstore and keepproxy at startup, as well as the output of @arvados-server config-check@, will remind you to do this.
623 <notextile><pre><code>$ export ARVADOS_API_HOST=...
624 $ export ARVADOS_API_TOKEN=...
625 $ arv --format=uuid keep_service list | xargs -n1 arv keep_service delete --uuid
626 </code></pre></notextile>
628 Once these old records are removed, @arv keep_service list@ will instead return the services listed under Services/Keepstore/InternalURLs and Services/Keepproxy/ExternalURL in your centralized configuration file.
630 h3. Enabling Postgres trigram indexes
632 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 <code class="userprint">CREATE EXTENSION pg_trgm</code> SQL command on the arvados_production database as a postgres superuser.
634 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:
636 <strong>Centos 7</strong>
638 <pre><code>~$ <span class="userinput">sudo yum install -y postgresql95-contrib</span>
639 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
643 <strong>RHEL 7</strong>
645 <pre><code>~$ <span class="userinput">sudo yum install -y rh-postgresql95-postgresql-contrib</span>
646 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
650 <strong>Debian or Ubuntu</strong>
652 <pre><code>~$ <span class="userinput">sudo apt-get install -y postgresql-contrib-9.5</span>
653 ~$ <span class="userinput">sudo -u postgres psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'</span>
657 Subsequently, the <code class="userinput">psql -d 'arvados_production' -c '\dx'</code> command will display the installed extensions for the arvados_production database. This list should now contain @pg_trgm@.
661 Workbench 2 is now ready for regular use. Follow the instructions to "install workbench 2":../install/install-workbench2-app.html
663 h3. New property vocabulary format for Workbench2
665 (feature "#14151":https://dev.arvados.org/issues/14151) Workbench2 supports a new vocabulary format and it isn't compatible with the previous one, please read the "metadata vocabulary format admin page":{{site.baseurl}}/admin/metadata-vocabulary.html for more information.
667 h3. Cloud installations only: node manager replaced by arvados-dispatch-cloud
669 Node manager is deprecated and replaced by @arvados-dispatch-cloud@. No automated config migration is available. Follow the instructions to "install the cloud dispatcher":../install/crunch2-cloud/install-dispatch-cloud.html
671 *Only one dispatch process should be running at a time.* If you are migrating a system that currently runs Node manager and @crunch-dispatch-slurm@, it is safest to remove the @crunch-dispatch-slurm@ service entirely before installing @arvados-dispatch-cloud@.
674 <pre><code>~$ <span class="userinput">sudo systemctl --now disable crunch-dispatch-slurm</span>
675 ~$ <span class="userinput">sudo apt-get remove crunch-dispatch-slurm</span>
679 h3. Jobs API is read-only
681 (task "#15133":https://dev.arvados.org/issues/15133 ) The legacy 'jobs' API is now read-only. It has been superceded since Arvados 1.1 by containers / container_requests (aka crunch v2). Arvados installations since the end of 2017 (v1.1.0) have probably only used containers, and are unaffected by this change.
683 So that older Arvados sites don't lose access to legacy records, the API has been converted to read-only. Creating and updating jobs (and related types job_task, pipeline_template and pipeline_instance) is disabled and much of the business logic related has been removed, along with various other code specific to the jobs API. Specifically, the following programs associated with the jobs API have been removed: @crunch-dispatch.rb@, @crunch-job@, @crunchrunner@, @arv-run-pipeline-instance@, @arv-run@.
685 h3. "/" prohibited in collection and project names
687 (issue "#15836":https://dev.arvados.org/issues/15836) By default, Arvados now rejects new names containing the @/@ character when creating or renaming collections and projects. Previously, these names were permitted, but the resulting objects were invisible in the WebDAV "home" tree. If you prefer, you can restore the previous behavior, and optionally configure a substitution string to make the affected objects accessible via WebDAV. See @ForwardSlashNameSubstitution@ in the "configuration reference":config.html.
689 h3. No longer stripping ':' from strings in serialized database columns
691 (bug "#15311":https://dev.arvados.org/issues/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.
693 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@.
695 h3. Scoped tokens should use PATCH for updates
697 The API server accepts both PUT and PATCH for updates, but they will be normalized to PATCH by arvados-controller. Scoped tokens should be updated accordingly.
701 h2(#v1_4_1). v1.4.1 (2019-09-20)
703 "previous: Upgrading to 1.4.0":#v1_4_0
705 h3. Centos7 Python 3 dependency upgraded to rh-python36
707 The Python 3 dependency for Centos7 Arvados packages was upgraded from rh-python35 to rh-python36.
709 h2(#v1_4_0). v1.4.0 (2019-06-05)
711 "previous: Upgrading to 1.3.3":#v1_3_3
713 h3. Populating the new file_count and file_size_total columns on the collections table
715 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.
717 The new columns are initialized with a zero value. In order to populate them, it is necessary to run a script called <code class="userinput">populate-file-info-columns-in-collections.rb</code> 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.
719 h3. Stricter collection manifest validation on the API server
721 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.
723 You could set up a new rvm gemset and install the specific arvados gem for testing, like so:
726 <pre><code>~$ <span class="userinput">rvm gemset create rubysdk-test</span>
727 ~$ <span class="userinput">rvm gemset use rubysdk-test</span>
728 ~$ <span class="userinput">gem install arvados -v 1.3.1.20190301212059</span>
732 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:
734 {% codeblock as ruby %}
736 require 'arvados/keep'
745 req = api.collection.index(
746 :select => [:uuid, :created_at, :manifest_text],
747 :include_trash => true, :include_old_versions => true,
748 :limit => batch_size, :offset => offset)
750 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
754 req[:items].each do |col|
756 Keep::Manifest.validate! col[:manifest_text]
757 rescue Exception => e
758 puts "Collection #{col[:uuid]} manifest not valid"
759 invalid << {uuid: col[:uuid], error: e, created_at: col[:created_at]}
762 puts "Checked #{offset} / #{req[:items_available]} - Invalid: #{invalid.size}"
763 offset += req[:limit]
764 break if offset > req[:items_available]
768 puts "No invalid collection manifests found"
770 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
774 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.
776 h3. Python packaging change
778 As part of story "#9945":https://dev.arvados.org/issues/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.
780 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":{{ site.baseurl }}/sdk/python/sdk-python.html reflects this change. This does not affect the use of the command line tools (e.g. arv-get, etc.).
782 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.
784 This can be done by activating the virtualenv outside of the script:
787 <pre>~$ <code class="userinput">source /usr/share/python2.7/dist/python-arvados-python-client/bin/activate</code>
788 (python-arvados-python-client) ~$ <code class="userinput">path-to-the-python-script</code>
792 Or alternatively, by updating the shebang line at the start of the script to:
796 #!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
800 h3. python-arvados-cwl-runner deb/rpm package now conflicts with python-cwltool deb/rpm package
802 As part of story "#9945":https://dev.arvados.org/issues/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.
804 h3. Centos7 Python 3 dependency upgraded to rh-python35
806 As part of story "#9945":https://dev.arvados.org/issues/9945, the Python 3 dependency for Centos7 Arvados packages was upgraded from SCL python33 to rh-python35.
808 h3. Centos7 package for libpam-arvados depends on the python-pam package, which is available from EPEL
810 As part of story "#9945":https://dev.arvados.org/issues/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.
812 h3. New configuration
814 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":https://doc.arvados.org/v2.1/admin/config-migration.html for details.
816 h2(#v1_3_3). v1.3.3 (2019-05-14)
818 "previous: Upgrading to 1.3.0":#v1_3_0
820 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.
822 We've put together a "wiki page":https://dev.arvados.org/projects/arvados/wiki/Recovering_lost_data 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":https://github.com/arvados/arvados/blob/main/tools/keep-xref/keep-xref.py which can be used to identify the workflows that generated those collections and who ran those workflows, so that they can be rerun.
824 h2(#v1_3_0). v1.3.0 (2018-12-05)
826 "previous: Upgrading to 1.2":#v1_2_0
828 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.
830 The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present.
832 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":upgrade-crunch2.html as support for the "jobs" API will be dropped in an upcoming release. Users who are already using the "containers" API are not affected.
834 h2(#v1_2_1). v1.2.1 (2018-11-26)
836 There are no special upgrade notes for this release.
838 h2(#v1_2_0). v1.2.0 (2018-09-05)
840 "previous: Upgrading to 1.1.2 or 1.1.3":#v1_1_2
842 h3. Regenerate Postgres table statistics
844 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:
852 tables=`echo "\dt" | psql arvados_production | grep public|awk -e '{print $3}'`
855 echo "echo 'analyze $t' | psql arvados_production"
856 time echo "analyze $t" | psql arvados_production
860 If you also need to do the vacuum, you could adapt the script to run 'vacuum analyze' instead of 'analyze'.
862 h3. New component: arvados-controller
864 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.
866 To add the Arvados Controller to your system please refer to the "installation instructions":../install/install-api-server.html after upgrading your system to 1.2.0.
868 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.
870 h2(#v1_1_4). v1.1.4 (2018-04-10)
872 "previous: Upgrading to 1.1.3":#v1_1_3
874 h3. arvados-cwl-runner regressions (2018-04-05)
876 <strong>Secondary files missing from toplevel workflow inputs</strong>
878 This only affects workflows that rely on implicit discovery of secondaryFiles.
880 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.
882 As an example, the following workflow will fail because the @toplevel_input@ does not declare the @secondaryFiles@ that are expected by @step_input@:
893 step_input: toplevel_input
897 class: CommandLineTool
907 When run, this produces an error like this:
910 cwltool ERROR: [step step1] Cannot make job: Missing required secondary file 'hello.txt.idx' from file object: {
911 "basename": "hello.txt",
913 "location": "keep:ade9d0e032044bd7f58daaecc0d06bc6+51/hello.txt",
921 To fix this error, add the appropriate @secondaryFiles@ section to @toplevel_input@
924 <pre><code>class: Workflow
927 <span class="userinput">toplevel_input:
935 step_input: toplevel_input
939 class: CommandLineTool
950 This bug has been fixed in Arvados release v1.2.0.
952 <strong>Secondary files on default file inputs</strong>
954 @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:
957 class: CommandLineTool
970 When run, this produces an error like this:
973 2018-05-03 10:58:47 cwltool ERROR: Unhandled error, try again with --debug for more information:
974 [Errno 2] File not found: u'hello.txt.idx'
977 To fix this, manually upload the primary and secondary files to keep and explicitly declare @secondaryFiles@ on the default primary file:
980 <pre><code>class: CommandLineTool
986 <span class="userinput">default:
988 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
991 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt.idx</span>
997 This bug has been fixed in Arvados release v1.2.0.
999 h2(#v1_1_3). v1.1.3 (2018-02-08)
1001 There are no special upgrade notes for this release.
1003 h2(#v1_1_2). v1.1.2 (2017-12-22)
1005 "previous: Upgrading to 1.1.0 or 1.1.1":#v1_1_0
1007 h3. The minimum version for Postgres is now 9.4 (2017-12-08)
1009 As part of story "#11908":https://dev.arvados.org/issues/11908, commit "8f987a9271":https://dev.arvados.org/projects/arvados/repository/revisions/8f987a9271 introduces a dependency on Postgres 9.4. Previously, Arvados required Postgres 9.3.
1011 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
1012 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
1013 * Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
1014 * 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
1015 *# Create a database backup using @pg_dump@
1016 *# 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/
1017 *# Restore from the backup using @psql@
1019 h2(#v1_1_1). v1.1.1 (2017-11-30)
1021 There are no special upgrade notes for this release.
1023 h2(#v1_1_0). v1.1.0 (2017-10-24)
1025 h3. The minimum version for Postgres is now 9.3 (2017-09-25)
1027 As part of story "#12032":https://dev.arvados.org/issues/12032, commit "68bdf4cbb1":https://dev.arvados.org/projects/arvados/repository/revisions/68bdf4cbb1 introduces a dependency on Postgres 9.3. Previously, Arvados required Postgres 9.1.
1029 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
1030 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
1031 * Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
1032 * 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
1033 *# Create a database backup using @pg_dump@
1034 *# 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/
1035 *# Restore from the backup using @psql@
1037 h2(#older). Older versions
1039 h3. Upgrade slower than usual (2017-06-30)
1041 As part of story "#11807":https://dev.arvados.org/issues/11807, commit "55aafbb":https://dev.arvados.org/projects/arvados/repository/revisions/55aafbb converts old "jobs" database records from YAML to JSON, making the upgrade process slower than usual.
1043 * 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":https://dev.arvados.org/projects/arvados/repository/revisions/660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
1044 * The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
1045 * Expect it to take about 1 minute per 20K jobs that have ever been created/run.
1047 h3. Service discovery overhead change in keep-web (2017-06-05)
1049 As part of story "#9005":https://dev.arvados.org/issues/9005, commit "cb230b0":https://dev.arvados.org/projects/arvados/repository/revisions/cb230b0 reduces service discovery overhead in keep-web requests.
1051 * 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.
1053 h3. Node manager now has an http endpoint for management (2017-04-12)
1055 As part of story "#11349":https://dev.arvados.org/issues/11349, commit "2c094e2":https://dev.arvados.org/projects/arvados/repository/revisions/2c094e2 adds a "management" http server to nodemanager.
1057 * To enable it, add to your configuration file: <pre>[Manage]
1060 * The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
1062 h3. New websockets component (2017-03-23)
1064 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.
1065 * See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
1066 * Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
1067 $ sudo sv down /etc/sv/puma
1068 $ sudo rm -r /etc/sv/puma
1069 </pre> Example, with systemd: <pre>
1070 $ systemctl disable puma
1071 $ systemctl stop puma
1074 h3. Change of database encoding for hashes and arrays (2017-03-06)
1076 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.
1078 * Aside from a slight performance improvement, this should have no externally visible effect.
1079 * Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
1080 * After upgrading, make sure to restart puma and crunch-dispatch-* processes.
1082 h3. Docker image format compatibility check (2017-02-03)
1084 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.
1085 * 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@): <pre><code class="yaml">docker_image_formats: ["v1"]</code></pre>
1086 * 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.
1087 * *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.*
1089 h3. Debian and RPM packages now have systemd unit files (2016-09-27)
1091 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).
1093 * On Debian-based systems using systemd, services are enabled automatically when packages are installed.
1094 * On RedHat-based systems using systemd, unit files are installed but services must be enabled explicitly: e.g., <code>"sudo systemctl enable keep-web; sudo systemctl start keep-web"</code>.
1095 * The new systemd-supervised services will not start up successfully until configuration files are installed in /etc/arvados/: e.g., <code>"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"</code>
1096 * To migrate from runit to systemd after installing the new packages, we recommend the following procedure:
1097 *# Bring down the runit service: "sv down /etc/sv/keep-web"
1098 *# Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml -- see "keep-web -help")
1099 *# Ensure the service is running correctly under systemd: "systemctl status keep-web" / "journalctl -u keep-web"
1100 *# Remove the runit service so it doesn't start at next boot
1101 * Affected services:
1102 ** keep-balance - /etc/arvados/keep-balance/keep-balance.yml
1103 ** keep-web - /etc/arvados/keep-web/keep-web.yml
1104 ** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
1105 ** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
1107 h3. Installation paths for Python modules and script changed (2016-05-31)
1109 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.
1111 * 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.
1112 * 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.
1114 h3. Crunchrunner package is required on compute and shell nodes (2016-04-25)
1116 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.
1118 * On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
1119 * On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
1121 h3. Keep permission signature algorithm change (2016-04-21)
1123 Commit "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/3c88abd changes the Keep permission signature algorithm.
1125 * 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.
1126 * Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
1128 h3. Workbench's "Getting Started" popup disabled by default (2015-01-05)
1130 Commit "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/e1276d6e disables Workbench's "Getting Started" popup by default.
1132 * If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
1134 h3. Crunch jobs now have access to Keep-backed writable scratch storage (2015-12-03)
1136 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)
1138 * 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
1139 * 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.
1141 h3. Recommended configuration change for keep-web (2015-11-11)
1143 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)
1145 * proxy/dns/ssl config should be updated to route "https://download.ClusterID.example.com/" requests to keep-web (alongside the existing "collections" routing)
1146 * keep-web command line adds @-attachment-only-host download.ClusterID.example.com@
1147 * Workbench config adds @keep_web_download_url@
1148 * More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
1150 h3. Stopped containers are now automatically removed on compute nodes (2015-11-04)
1152 Commit "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/7444)
1154 * 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.
1156 h3. New keep-web service (2015-11-04)
1158 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).
1160 * 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).