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. Check MaxGatewayTunnels config
37 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.
39 h2(#2_7_1). v2.7.1 (2023-12-12)
41 "previous: Upgrading to 2.7.0":#v2_7_0
43 h3. Remove Workbench1 packages after upgrading the salt installer
45 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.
47 h3. Remove Workbench1 packages and configuration
49 The Workbench1 application has been removed from the Arvados distribution. We recommend the following follow-up steps.
50 * Remove the Workbench1 package from any service node where it is installed (e.g., @apt remove arvados-workbench@).
51 * 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 {
53 server_name workbench.ClusterID.example.com workbench2.ClusterID.example.com;
56 * In your Nginx configuration, remove the @upstream@ and @server@ sections for Workbench1.
57 * Remove the @Services.Workbench1.InternalURLs@ section of your configuration file. (Do not remove @ExternalURL@.)
58 * Run @arvados-server config-check@ to identify any Workbench1-specific entries in your configuration file, and remove them.
60 h3. Check implications of Containers.MaximumPriceFactor 1.5
62 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.
64 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@.
66 h3. Synchronize keepstore and keep-balance upgrades
68 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.
70 h3. Separate configs for MaxConcurrentRequests and MaxConcurrentRailsRequests
72 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.
74 A new configuration key @API.MaxConcurrentRailsRequests@ (default 8) limits the number of concurrent requests processed by a RailsAPI service process.
76 h2(#v2_7_0). v2.7.0 (2023-09-21)
78 "previous: Upgrading to 2.6.3":#v2_6_3
80 h3. New system for live container logs
82 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.
84 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.
86 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@).
88 h3. Workbench 1 deprecated
90 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.
92 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.
94 h3. Multi-node installer's domain name configuration changes
96 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.
97 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.
99 h3. Crunchstat log format change
101 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.
103 h3. arvados-login-sync configuration changes, including ignored groups
105 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@.
107 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.
109 h3. API clients can always retrieve their current token, regardless of scopes
111 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.
113 h3. Deprecated/legacy APIs slated for removal
115 The legacy APIs "humans":../api/methods/humans.html, "specimens":../api/methods/specimens.html, "traits":../api/methods/traits.html, "jobs":../api/methods/jobs.html, "job_tasks":../api/methods/job_tasks.html, "pipeline_instances":../api/methods/pipeline_instances.html, "pipeline_templates":../api/methods/pipeline_templates.html, "nodes":../api/methods/nodes.html, "repositories":../api/methods/repositories.html, and "keep_disks":../api/methods/keep_disks.html are deprecated and will be removed in a future major version of Arvados.
117 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.
119 h3. UseAWSS3v2Driver option removed
121 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.
123 h2(#v2_6_3). v2.6.3 (2023-06-06)
125 h3. Python SDK automatically retries failed requests much more
127 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.
129 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:
131 {% codeblock as python %}
133 arv_client = arvados.api('v1', num_retries=0, ...)
136 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.
138 h2(#v2_6_2). v2.6.2 (2023-05-22)
140 "previous: Upgrading to 2.6.1":#v2_6_1
142 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.
144 h2(#v2_6_1). v2.6.1 (2023-04-17)
146 "previous: Upgrading to 2.6.0":#v2_6_0
148 h3. Performance improvement for permission row de-duplication migration
150 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.
152 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.
154 h2(#v2_6_0). v2.6.0 (2023-04-06)
156 "previous: Upgrading to 2.5.0":#v2_5_0
158 h3. WebDAV InternalURLs must be reachable from controller nodes
160 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.
162 h3. Slow migration on upgrade
164 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.
166 h3. Default request concurrency, new limit on log requests
168 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.
170 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.
172 h3. New limit on concurrent workflows
174 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.
176 h3. Default limit for cloud VM instances
178 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.
180 Using the obsolete configuration entry @MaxCloudVMs@, which was previously accepted in config files but not obeyed, will now result in a deprecation warning.
182 h3. Default frequency for running keep-balance has changed
184 The frequency that @keep-balance@ will run (@Collections.BalancePeriod@) has been changed from every 10 minutes to every 6 hours.
186 h2(#v2_5_0). v2.5.0 (2022-12-22)
188 "previous: Upgrading to 2.4.4":#v2_4_4
190 h3. Dispatchers require PostgreSQL database access
192 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.
194 h3. Google or OpenID Connect login restricted to trusted clients
196 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.
198 h3. New keepstore S3 driver enabled by default
200 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.
202 h3. Old container logs are automatically deleted from PostgreSQL
204 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@.
206 h3. Fixed salt installer template file to support container shell access
208 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.
210 h3. Login-sync script requires configuration update on LoginCluster federations
212 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.
214 h3. Renamed keep-web metrics and WebDAV configs
216 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@.
218 The config entries @Collections.WebDAVCache.UUIDTTL@, @...MaxCollectionEntries@, and @...MaxUUIDEntries@ are no longer used, and should be removed from your config file.
220 h2(#v2_4_4). v2.4.4 (2022-11-18)
222 "previous: Upgrading to 2.4.3":#v2_4_3
224 This update only consists of improvements to @arvados-cwl-runner@. There are no changes to backend services.
226 h2(#v2_4_3). v2.4.3 (2022-09-21)
228 "previous: Upgrading to 2.4.2":#v2_4_2
230 h3. Fixed PAM authentication security vulnerability
232 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.
234 Other authentication methods (LDAP, OpenID Connect) are not affected by this flaw.
236 h2(#v2_4_2). v2.4.2 (2022-08-09)
238 "previous: Upgrading to 2.4.1":#v2_4_1
242 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.
244 This vulnerability is fixed in 2.4.2 ("#19316":https://dev.arvados.org/issues/19316).
246 It is likely that this vulnerability exists in all versions of Arvados up to 2.4.1.
248 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.
250 h3. CVE-2022-31163 and CVE-2022-32224
252 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.
254 h3. Disable Sharing URLs UI
256 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.
258 h2(#v2_4_1). v2.4.1 (2022-06-02)
260 "previous: Upgrading to 2.4.0":#v2_4_0
262 h3. Slurm dispatcher requires configuration update
264 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.
266 h3. New proxy parameters for arvados-controller
268 We now recommend disabling nginx proxy caching for arvados-controller, to avoid truncation of large responses.
270 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@).
273 proxy_max_temp_file_size 0;
274 proxy_request_buffering off;
276 proxy_http_version 1.1;
279 h3. Now recommending Singularity 3.9.9
281 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.
283 h3. Changes to @arvados-cwl-runner --create-workflow@ and @--update-workflow@
285 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@.
287 h2(#v2_4_0). v2.4.0 (2022-04-08)
289 "previous: Upgrading to 2.3.1":#v2_3_1
291 h3. Default result order changed
293 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.
295 h3. Ubuntu 18.04 Arvados Python packages now depend on python-3.8
297 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.
299 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.
301 h3. Minimum supported Ruby version is now 2.6
303 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.
305 h3. Anonymous token changes
307 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.
309 h3. Preemptible instance support changes
311 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.
313 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.
315 h3. Default LSF arguments have changed
317 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.
319 h3. Support for NVIDIA CUDA GPUs
321 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:
323 "Including GPU support in cloud compute node image":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html#nvidia
325 "Configure cloud dispatcher for GPU support":{{site.baseurl}}/install/crunch2-cloud/install-dispatch-cloud.html#GPUsupport
327 "LSF GPU configuration":{{site.baseurl}}/install/crunch2-lsf/install-dispatch.html
329 h3. Role groups are visible to all users by default
331 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.
333 h3. Previously trashed role groups will be deleted
335 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.
337 h3. Dedicated keepstore process for each container
339 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.
340 * If you have containers that can effectively handle multiple I/O threads per VCPU, consider increasing the @Containers.LocalKeepBlobBuffersPerVCPU@ value.
341 * 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.
342 * 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.
344 h2(#v2_3_1). v2.3.1 (2021-11-24)
346 "previous: Upgrading to 2.3.0":#v2_3_0
348 h3. Users are visible to other users by default
350 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@.
352 h3. Backend support for vocabulary checking
354 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.
355 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.
356 You can read more about how this feature works on the "admin page":{{site.baseurl}}/admin/metadata-vocabulary.html.
358 h2(#v2_3_0). v2.3.0 (2021-10-27)
360 "previous: Upgrading to 2.2.0":#v2_2_0
362 h3. Ubuntu 18.04 packages for arvados-api-server and arvados-workbench now conflict with ruby-bundler
364 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.
366 h3. Removed unused @update_uuid@ endpoint for users.
368 The @update_uuid@ endpoint was superseded by the "link accounts feature":{{site.baseurl}}/admin/link-accounts.html, so it's no longer available.
370 h3. Removed deprecated '@@' search operator
372 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.
374 h3. Storage classes must be defined explicitly
376 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.
378 h3. keep-balance requires access to PostgreSQL
380 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.)
382 h3. crunch-dispatch-local now requires config.yml
384 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.
386 h3. Multi-file docker image collections
388 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.
390 h2(#v2_2_0). v2.2.0 (2021-06-03)
392 "previous: Upgrading to 2.1.0":#v2_1_0
394 h3. New spelling of S3 credential configs
396 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.
398 h3. New proxy parameters for arvados-controller
400 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@).
403 proxy_set_header Upgrade $http_upgrade;
404 proxy_set_header Connection "upgrade";
407 h3. Changes on the collection's @preserve_version@ attribute semantics
409 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.
411 h3. System token requirements
413 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.
415 The @API.RailsSessionSecretToken@ configuration key has been removed. Delete this entry from your configuration file after upgrading.
417 h3. Centos7 Python 3 dependency upgraded to python3
419 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.
421 h3. ForceLegacyAPI14 option removed
423 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.
425 h2(#v2_1_0). v2.1.0 (2020-10-13)
427 "previous: Upgrading to 2.0.0":#v2_0_0
429 h3. LoginCluster conflicts with other Login providers
431 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.
433 h3. Minimum supported Python version is now 3.5
435 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:
438 apt remove python-arvados-fuse && apt install python3-arvados-fuse
439 apt remove python-arvados-python-client && apt install python3-arvados-python-client
440 apt remove python-arvados-cwl-runner && apt install python3-arvados-cwl-runner
441 apt remove python-crunchstat-summary && apt install python3-crunchstat-summary
442 apt remove python-cwltest && apt install python3-cwltest
448 yum remove python-arvados-fuse && yum install python3-arvados-fuse
449 yum remove python-arvados-python-client && yum install python3-arvados-python-client
450 yum remove python-arvados-cwl-runner && yum install python3-arvados-cwl-runner
451 yum remove python-crunchstat-summary && yum install python3-crunchstat-summary
452 yum remove python-cwltest && yum install python3-cwltest
455 h3. Minimum supported Ruby version is now 2.5
457 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.
459 h3. Removing libpam-arvados, replaced with libpam-arvados-go
461 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.
463 h3. Removing sso-provider
465 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.
467 After migrating your configuration, uninstall the @arvados-sso-provider@ package.
471 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.
473 h3. New permission system constraints
475 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.
477 # The @group_class@ field must be either @role@ or @project@. Invalid group_class are migrated to @role@.
478 # A @role@ cannot own things. Anything owned by a role is migrated to a @can_manage@ link and reassigned to the system user.
479 # Only @role@ and @user@ can have outgoing permission links. Permission links originating from projects are deleted by the migration.
480 # 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.
481 # A permission link can have the permission level (@name@) updated but not @head_uuid@, @tail_uuid@ or @link_class@.
483 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.
485 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.
487 To determine which groups have invalid @group_class@ (these will be migrated to @role@ groups):
490 arv group list --filters '[["group_class", "not in", ["project", "role"]]]'
493 To list all @role@ groups, which will be reassigned to the system user (unless @owner_uuid@ is already the system user):
496 arv group list --filters '[["group_class", "=", "role"]]'
499 To list which @project@ groups have outgoing permission links (such links are now invalid and will be deleted by the migration):
502 for uuid in $(arv link list --filters '[["link_class", "=", "permission"], ["tail_uuid", "like", "%-j7d0g-%"]]' |
503 jq -r .items[].tail_uuid | sort | uniq) ; do
504 arv group list --filters '[["group_class", "=", "project"], ["uuid", "=", "'$uuid'"]]' | jq .items
508 h4. "Public favorites" moved to their own project
510 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.
512 h2(#v2_0_0). v2.0.0 (2020-02-07)
514 "previous: Upgrading to 1.4.1":#v1_4_1
516 Arvados 2.0 is a major upgrade, with many changes. Please read these upgrade notes carefully before you begin.
518 h3. Migrating to centralized config.yml
520 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@.
522 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:
529 ExternalURL: "https://zzzzz.example.com"
532 h3. Keep-balance configuration migration
534 (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.
536 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.
538 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.
540 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.
542 h3. Arv-git-httpd configuration migration
544 (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.
546 h3. Keepstore and keep-web configuration migration
548 keepstore and keep-web no longer support configuration via (previously deprecated) command line configuration flags and environment variables.
550 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.
552 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.
554 h3. Keepproxy configuration migration
556 (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.
558 h3. Delete "keep_services" records
560 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.
562 <notextile><pre><code>$ export ARVADOS_API_HOST=...
563 $ export ARVADOS_API_TOKEN=...
564 $ arv --format=uuid keep_service list | xargs -n1 arv keep_service delete --uuid
565 </code></pre></notextile>
567 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.
569 h3. Enabling Postgres trigram indexes
571 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.
573 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:
575 <strong>Centos 7</strong>
577 <pre><code>~$ <span class="userinput">sudo yum install -y postgresql95-contrib</span>
578 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
582 <strong>RHEL 7</strong>
584 <pre><code>~$ <span class="userinput">sudo yum install -y rh-postgresql95-postgresql-contrib</span>
585 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
589 <strong>Debian or Ubuntu</strong>
591 <pre><code>~$ <span class="userinput">sudo apt-get install -y postgresql-contrib-9.5</span>
592 ~$ <span class="userinput">sudo -u postgres psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'</span>
596 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@.
600 Workbench 2 is now ready for regular use. Follow the instructions to "install workbench 2":../install/install-workbench2-app.html
602 h3. New property vocabulary format for Workbench2
604 (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.
606 h3. Cloud installations only: node manager replaced by arvados-dispatch-cloud
608 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
610 *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@.
613 <pre><code>~$ <span class="userinput">sudo systemctl --now disable crunch-dispatch-slurm</span>
614 ~$ <span class="userinput">sudo apt-get remove crunch-dispatch-slurm</span>
618 h3. Jobs API is read-only
620 (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.
622 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@.
624 h3. "/" prohibited in collection and project names
626 (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.
628 h3. No longer stripping ':' from strings in serialized database columns
630 (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.
632 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@.
634 h3. Scoped tokens should use PATCH for updates
636 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.
640 h2(#v1_4_1). v1.4.1 (2019-09-20)
642 "previous: Upgrading to 1.4.0":#v1_4_0
644 h3. Centos7 Python 3 dependency upgraded to rh-python36
646 The Python 3 dependency for Centos7 Arvados packages was upgraded from rh-python35 to rh-python36.
648 h2(#v1_4_0). v1.4.0 (2019-06-05)
650 "previous: Upgrading to 1.3.3":#v1_3_3
652 h3. Populating the new file_count and file_size_total columns on the collections table
654 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.
656 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.
658 h3. Stricter collection manifest validation on the API server
660 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.
662 You could set up a new rvm gemset and install the specific arvados gem for testing, like so:
665 <pre><code>~$ <span class="userinput">rvm gemset create rubysdk-test</span>
666 ~$ <span class="userinput">rvm gemset use rubysdk-test</span>
667 ~$ <span class="userinput">gem install arvados -v 1.3.1.20190301212059</span>
671 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:
673 {% codeblock as ruby %}
675 require 'arvados/keep'
684 req = api.collection.index(
685 :select => [:uuid, :created_at, :manifest_text],
686 :include_trash => true, :include_old_versions => true,
687 :limit => batch_size, :offset => offset)
689 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
693 req[:items].each do |col|
695 Keep::Manifest.validate! col[:manifest_text]
696 rescue Exception => e
697 puts "Collection #{col[:uuid]} manifest not valid"
698 invalid << {uuid: col[:uuid], error: e, created_at: col[:created_at]}
701 puts "Checked #{offset} / #{req[:items_available]} - Invalid: #{invalid.size}"
702 offset += req[:limit]
703 break if offset > req[:items_available]
707 puts "No invalid collection manifests found"
709 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
713 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.
715 h3. Python packaging change
717 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.
719 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.).
721 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.
723 This can be done by activating the virtualenv outside of the script:
726 <pre>~$ <code class="userinput">source /usr/share/python2.7/dist/python-arvados-python-client/bin/activate</code>
727 (python-arvados-python-client) ~$ <code class="userinput">path-to-the-python-script</code>
731 Or alternatively, by updating the shebang line at the start of the script to:
735 #!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
739 h3. python-arvados-cwl-runner deb/rpm package now conflicts with python-cwltool deb/rpm package
741 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.
743 h3. Centos7 Python 3 dependency upgraded to rh-python35
745 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.
747 h3. Centos7 package for libpam-arvados depends on the python-pam package, which is available from EPEL
749 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.
751 h3. New configuration
753 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.
755 h2(#v1_3_3). v1.3.3 (2019-05-14)
757 "previous: Upgrading to 1.3.0":#v1_3_0
759 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.
761 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.
763 h2(#v1_3_0). v1.3.0 (2018-12-05)
765 "previous: Upgrading to 1.2":#v1_2_0
767 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.
769 The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present.
771 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.
773 h2(#v1_2_1). v1.2.1 (2018-11-26)
775 There are no special upgrade notes for this release.
777 h2(#v1_2_0). v1.2.0 (2018-09-05)
779 "previous: Upgrading to 1.1.2 or 1.1.3":#v1_1_2
781 h3. Regenerate Postgres table statistics
783 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:
791 tables=`echo "\dt" | psql arvados_production | grep public|awk -e '{print $3}'`
794 echo "echo 'analyze $t' | psql arvados_production"
795 time echo "analyze $t" | psql arvados_production
799 If you also need to do the vacuum, you could adapt the script to run 'vacuum analyze' instead of 'analyze'.
801 h3. New component: arvados-controller
803 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.
805 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.
807 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.
809 h2(#v1_1_4). v1.1.4 (2018-04-10)
811 "previous: Upgrading to 1.1.3":#v1_1_3
813 h3. arvados-cwl-runner regressions (2018-04-05)
815 <strong>Secondary files missing from toplevel workflow inputs</strong>
817 This only affects workflows that rely on implicit discovery of secondaryFiles.
819 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.
821 As an example, the following workflow will fail because the @toplevel_input@ does not declare the @secondaryFiles@ that are expected by @step_input@:
832 step_input: toplevel_input
836 class: CommandLineTool
846 When run, this produces an error like this:
849 cwltool ERROR: [step step1] Cannot make job: Missing required secondary file 'hello.txt.idx' from file object: {
850 "basename": "hello.txt",
852 "location": "keep:ade9d0e032044bd7f58daaecc0d06bc6+51/hello.txt",
860 To fix this error, add the appropriate @secondaryFiles@ section to @toplevel_input@
863 <pre><code>class: Workflow
866 <span class="userinput">toplevel_input:
874 step_input: toplevel_input
878 class: CommandLineTool
889 This bug has been fixed in Arvados release v1.2.0.
891 <strong>Secondary files on default file inputs</strong>
893 @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:
896 class: CommandLineTool
909 When run, this produces an error like this:
912 2018-05-03 10:58:47 cwltool ERROR: Unhandled error, try again with --debug for more information:
913 [Errno 2] File not found: u'hello.txt.idx'
916 To fix this, manually upload the primary and secondary files to keep and explicitly declare @secondaryFiles@ on the default primary file:
919 <pre><code>class: CommandLineTool
925 <span class="userinput">default:
927 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
930 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt.idx</span>
936 This bug has been fixed in Arvados release v1.2.0.
938 h2(#v1_1_3). v1.1.3 (2018-02-08)
940 There are no special upgrade notes for this release.
942 h2(#v1_1_2). v1.1.2 (2017-12-22)
944 "previous: Upgrading to 1.1.0 or 1.1.1":#v1_1_0
946 h3. The minimum version for Postgres is now 9.4 (2017-12-08)
948 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.
950 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
951 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
952 * Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
953 * 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
954 *# Create a database backup using @pg_dump@
955 *# 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/
956 *# Restore from the backup using @psql@
958 h2(#v1_1_1). v1.1.1 (2017-11-30)
960 There are no special upgrade notes for this release.
962 h2(#v1_1_0). v1.1.0 (2017-10-24)
964 h3. The minimum version for Postgres is now 9.3 (2017-09-25)
966 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.
968 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
969 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
970 * Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
971 * 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
972 *# Create a database backup using @pg_dump@
973 *# 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/
974 *# Restore from the backup using @psql@
976 h2(#older). Older versions
978 h3. Upgrade slower than usual (2017-06-30)
980 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.
982 * 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.
983 * The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
984 * Expect it to take about 1 minute per 20K jobs that have ever been created/run.
986 h3. Service discovery overhead change in keep-web (2017-06-05)
988 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.
990 * 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.
992 h3. Node manager now has an http endpoint for management (2017-04-12)
994 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.
996 * To enable it, add to your configuration file: <pre>[Manage]
999 * The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
1001 h3. New websockets component (2017-03-23)
1003 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.
1004 * See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
1005 * Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
1006 $ sudo sv down /etc/sv/puma
1007 $ sudo rm -r /etc/sv/puma
1008 </pre> Example, with systemd: <pre>
1009 $ systemctl disable puma
1010 $ systemctl stop puma
1013 h3. Change of database encoding for hashes and arrays (2017-03-06)
1015 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.
1017 * Aside from a slight performance improvement, this should have no externally visible effect.
1018 * Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
1019 * After upgrading, make sure to restart puma and crunch-dispatch-* processes.
1021 h3. Docker image format compatibility check (2017-02-03)
1023 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.
1024 * 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>
1025 * 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.
1026 * *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.*
1028 h3. Debian and RPM packages now have systemd unit files (2016-09-27)
1030 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).
1032 * On Debian-based systems using systemd, services are enabled automatically when packages are installed.
1033 * 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>.
1034 * 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>
1035 * To migrate from runit to systemd after installing the new packages, we recommend the following procedure:
1036 *# Bring down the runit service: "sv down /etc/sv/keep-web"
1037 *# Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml -- see "keep-web -help")
1038 *# Ensure the service is running correctly under systemd: "systemctl status keep-web" / "journalctl -u keep-web"
1039 *# Remove the runit service so it doesn't start at next boot
1040 * Affected services:
1041 ** keep-balance - /etc/arvados/keep-balance/keep-balance.yml
1042 ** keep-web - /etc/arvados/keep-web/keep-web.yml
1043 ** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
1044 ** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
1046 h3. Installation paths for Python modules and script changed (2016-05-31)
1048 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.
1050 * 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.
1051 * 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.
1053 h3. Crunchrunner package is required on compute and shell nodes (2016-04-25)
1055 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.
1057 * On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
1058 * On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
1060 h3. Keep permission signature algorithm change (2016-04-21)
1062 Commit "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/3c88abd changes the Keep permission signature algorithm.
1064 * 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.
1065 * Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
1067 h3. Workbench's "Getting Started" popup disabled by default (2015-01-05)
1069 Commit "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/e1276d6e disables Workbench's "Getting Started" popup by default.
1071 * If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
1073 h3. Crunch jobs now have access to Keep-backed writable scratch storage (2015-12-03)
1075 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)
1077 * 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
1078 * 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.
1080 h3. Recommended configuration change for keep-web (2015-11-11)
1082 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)
1084 * proxy/dns/ssl config should be updated to route "https://download.ClusterID.example.com/" requests to keep-web (alongside the existing "collections" routing)
1085 * keep-web command line adds @-attachment-only-host download.ClusterID.example.com@
1086 * Workbench config adds @keep_web_download_url@
1087 * More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
1089 h3. Stopped containers are now automatically removed on compute nodes (2015-11-04)
1091 Commit "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/7444)
1093 * 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.
1095 h3. New keep-web service (2015-11-04)
1097 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).
1099 * 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).