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 (as of 2023-03-06)
33 "previous: Upgrading to 2.5.0":#v2_5_0
35 h3. Default request concurrency, new limit on log requests
37 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.
39 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.
41 h3. New limit on concurrent workflows
43 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.
45 h3. Default limit for cloud VM instances
47 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.
49 Using the obsolete configuration entry @MaxCloudVMs@, which was previously accepted in config files but not obeyed, will now result in a deprecation warning.
51 h3. Slow migration on upgrade
53 This upgrade includes a database schema update (changing an integer column in each table from 32-bit to 64-bit) that may be slow on a large installation. Expect the arvados-api-server package upgrade to take longer than usual.
55 h2(#v2_5_0). v2.5.0 (2022-12-22)
57 "previous: Upgrading to 2.4.4":#v2_4_4
59 h3. Dispatchers require PostgreSQL database access
61 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.
63 h3. Google or OpenID Connect login restricted to trusted clients
65 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.
67 h3. New keepstore S3 driver enabled by default
69 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.
71 h3. Old container logs are automatically deleted from PostgreSQL
73 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@.
75 h3. Fixed salt installer template file to support container shell access
77 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.
79 h3. Login-sync script requires configuration update on LoginCluster federations
81 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.
83 h3. Renamed keep-web metrics and WebDAV configs
85 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@.
87 The config entries @Collections.WebDAVCache.UUIDTTL@, @...MaxCollectionEntries@, and @...MaxUUIDEntries@ are no longer used, and should be removed from your config file.
89 h2(#v2_4_4). v2.4.4 (2022-11-18)
91 "previous: Upgrading to 2.4.3":#v2_4_3
93 This update only consists of improvements to @arvados-cwl-runner@. There are no changes to backend services.
95 h2(#v2_4_3). v2.4.3 (2022-09-21)
97 "previous: Upgrading to 2.4.2":#v2_4_2
99 h3. Fixed PAM authentication security vulnerability
101 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.
103 Other authentication methods (LDAP, OpenID Connect) are not affected by this flaw.
105 h2(#v2_4_2). v2.4.2 (2022-08-09)
107 "previous: Upgrading to 2.4.1":#v2_4_1
111 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.
113 This vulnerability is fixed in 2.4.2 ("#19316":https://dev.arvados.org/issues/19316).
115 It is likely that this vulnerability exists in all versions of Arvados up to 2.4.1.
117 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.
119 h3. CVE-2022-31163 and CVE-2022-32224
121 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.
123 h3. Disable Sharing URLs UI
125 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.
127 h2(#v2_4_1). v2.4.1 (2022-06-02)
129 "previous: Upgrading to 2.4.0":#v2_4_0
131 h3. Slurm dispatcher requires configuration update
133 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.
135 h3. New proxy parameters for arvados-controller
137 We now recommend disabling nginx proxy caching for arvados-controller, to avoid truncation of large responses.
139 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@).
142 proxy_max_temp_file_size 0;
143 proxy_request_buffering off;
145 proxy_http_version 1.1;
148 h3. Now recommending Singularity 3.9.9
150 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.
152 h3. Changes to @arvados-cwl-runner --create-workflow@ and @--update-workflow@
154 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@.
156 h2(#v2_4_0). v2.4.0 (2022-04-08)
158 "previous: Upgrading to 2.3.1":#v2_3_1
160 h3. Default result order changed
162 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.
164 h3. Ubuntu 18.04 Arvados Python packages now depend on python-3.8
166 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.
168 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.
170 h3. Minimum supported Ruby version is now 2.6
172 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.
174 h3. Anonymous token changes
176 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.
178 h3. Preemptible instance support changes
180 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.
182 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.
184 h3. Default LSF arguments have changed
186 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.
188 h3. Support for NVIDIA CUDA GPUs
190 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:
192 "Including GPU support in cloud compute node image":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html#nvidia
194 "Configure cloud dispatcher for GPU support":{{site.baseurl}}/install/crunch2-cloud/install-dispatch-cloud.html#GPUsupport
196 "LSF GPU configuration":{{site.baseurl}}/install/crunch2-lsf/install-dispatch.html
198 h3. Role groups are visible to all users by default
200 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.
202 h3. Previously trashed role groups will be deleted
204 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.
206 h3. Dedicated keepstore process for each container
208 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.
209 * If you have containers that can effectively handle multiple I/O threads per VCPU, consider increasing the @Containers.LocalKeepBlobBuffersPerVCPU@ value.
210 * 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.
211 * 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.
213 h2(#v2_3_1). v2.3.1 (2021-11-24)
215 "previous: Upgrading to 2.3.0":#v2_3_0
217 h3. Users are visible to other users by default
219 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@.
221 h3. Backend support for vocabulary checking
223 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.
224 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.
225 You can read more about how this feature works on the "admin page":{{site.baseurl}}/admin/metadata-vocabulary.html.
227 h2(#v2_3_0). v2.3.0 (2021-10-27)
229 "previous: Upgrading to 2.2.0":#v2_2_0
231 h3. Ubuntu 18.04 packages for arvados-api-server and arvados-workbench now conflict with ruby-bundler
233 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.
235 h3. Removed unused @update_uuid@ endpoint for users.
237 The @update_uuid@ endpoint was superseded by the "link accounts feature":{{site.baseurl}}/admin/link-accounts.html, so it's no longer available.
239 h3. Removed deprecated '@@' search operator
241 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.
243 h3. Storage classes must be defined explicitly
245 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.
247 h3. keep-balance requires access to PostgreSQL
249 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.)
251 h3. crunch-dispatch-local now requires config.yml
253 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.
255 h3. Multi-file docker image collections
257 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.
259 h2(#v2_2_0). v2.2.0 (2021-06-03)
261 "previous: Upgrading to 2.1.0":#v2_1_0
263 h3. New spelling of S3 credential configs
265 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.
267 h3. New proxy parameters for arvados-controller
269 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@).
272 proxy_set_header Upgrade $http_upgrade;
273 proxy_set_header Connection "upgrade";
276 h3. Changes on the collection's @preserve_version@ attribute semantics
278 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.
280 h3. System token requirements
282 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.
284 The @API.RailsSessionSecretToken@ configuration key has been removed. Delete this entry from your configuration file after upgrading.
286 h3. Centos7 Python 3 dependency upgraded to python3
288 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.
290 h3. ForceLegacyAPI14 option removed
292 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.
294 h2(#v2_1_0). v2.1.0 (2020-10-13)
296 "previous: Upgrading to 2.0.0":#v2_0_0
298 h3. LoginCluster conflicts with other Login providers
300 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.
302 h3. Minimum supported Python version is now 3.5
304 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:
307 apt remove python-arvados-fuse && apt install python3-arvados-fuse
308 apt remove python-arvados-python-client && apt install python3-arvados-python-client
309 apt remove python-arvados-cwl-runner && apt install python3-arvados-cwl-runner
310 apt remove python-crunchstat-summary && apt install python3-crunchstat-summary
311 apt remove python-cwltest && apt install python3-cwltest
317 yum remove python-arvados-fuse && yum install python3-arvados-fuse
318 yum remove python-arvados-python-client && yum install python3-arvados-python-client
319 yum remove python-arvados-cwl-runner && yum install python3-arvados-cwl-runner
320 yum remove python-crunchstat-summary && yum install python3-crunchstat-summary
321 yum remove python-cwltest && yum install python3-cwltest
324 h3. Minimum supported Ruby version is now 2.5
326 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.
328 h3. Removing libpam-arvados, replaced with libpam-arvados-go
330 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.
332 h3. Removing sso-provider
334 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.
336 After migrating your configuration, uninstall the @arvados-sso-provider@ package.
340 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.
342 h3. New permission system constraints
344 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.
346 # The @group_class@ field must be either @role@ or @project@. Invalid group_class are migrated to @role@.
347 # A @role@ cannot own things. Anything owned by a role is migrated to a @can_manage@ link and reassigned to the system user.
348 # Only @role@ and @user@ can have outgoing permission links. Permission links originating from projects are deleted by the migration.
349 # 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.
350 # A permission link can have the permission level (@name@) updated but not @head_uuid@, @tail_uuid@ or @link_class@.
352 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.
354 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.
356 To determine which groups have invalid @group_class@ (these will be migrated to @role@ groups):
359 arv group list --filters '[["group_class", "not in", ["project", "role"]]]'
362 To list all @role@ groups, which will be reassigned to the system user (unless @owner_uuid@ is already the system user):
365 arv group list --filters '[["group_class", "=", "role"]]'
368 To list which @project@ groups have outgoing permission links (such links are now invalid and will be deleted by the migration):
371 for uuid in $(arv link list --filters '[["link_class", "=", "permission"], ["tail_uuid", "like", "%-j7d0g-%"]]' |
372 jq -r .items[].tail_uuid | sort | uniq) ; do
373 arv group list --filters '[["group_class", "=", "project"], ["uuid", "=", "'$uuid'"]]' | jq .items
377 h4. "Public favorites" moved to their own project
379 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.
381 h2(#v2_0_0). v2.0.0 (2020-02-07)
383 "previous: Upgrading to 1.4.1":#v1_4_1
385 Arvados 2.0 is a major upgrade, with many changes. Please read these upgrade notes carefully before you begin.
387 h3. Migrating to centralized config.yml
389 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@.
391 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:
398 ExternalURL: "https://zzzzz.example.com"
401 h3. Keep-balance configuration migration
403 (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.
405 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.
407 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.
409 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.
411 h3. Arv-git-httpd configuration migration
413 (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.
415 h3. Keepstore and keep-web configuration migration
417 keepstore and keep-web no longer support configuration via (previously deprecated) command line configuration flags and environment variables.
419 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.
421 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.
423 h3. Keepproxy configuration migration
425 (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.
427 h3. Delete "keep_services" records
429 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.
431 <notextile><pre><code>$ export ARVADOS_API_HOST=...
432 $ export ARVADOS_API_TOKEN=...
433 $ arv --format=uuid keep_service list | xargs -n1 arv keep_service delete --uuid
434 </code></pre></notextile>
436 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.
438 h3. Enabling Postgres trigram indexes
440 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.
442 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:
444 <strong>Centos 7</strong>
446 <pre><code>~$ <span class="userinput">sudo yum install -y postgresql95-contrib</span>
447 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
451 <strong>RHEL 7</strong>
453 <pre><code>~$ <span class="userinput">sudo yum install -y rh-postgresql95-postgresql-contrib</span>
454 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
458 <strong>Debian or Ubuntu</strong>
460 <pre><code>~$ <span class="userinput">sudo apt-get install -y postgresql-contrib-9.5</span>
461 ~$ <span class="userinput">sudo -u postgres psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'</span>
465 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@.
469 Workbench 2 is now ready for regular use. Follow the instructions to "install workbench 2":../install/install-workbench2-app.html
471 h3. New property vocabulary format for Workbench2
473 (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.
475 h3. Cloud installations only: node manager replaced by arvados-dispatch-cloud
477 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
479 *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@.
482 <pre><code>~$ <span class="userinput">sudo systemctl --now disable crunch-dispatch-slurm</span>
483 ~$ <span class="userinput">sudo apt-get remove crunch-dispatch-slurm</span>
487 h3. Jobs API is read-only
489 (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.
491 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@.
493 h3. "/" prohibited in collection and project names
495 (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.
497 h3. No longer stripping ':' from strings in serialized database columns
499 (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.
501 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@.
503 h3. Scoped tokens should use PATCH for updates
505 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.
509 h2(#v1_4_1). v1.4.1 (2019-09-20)
511 "previous: Upgrading to 1.4.0":#v1_4_0
513 h3. Centos7 Python 3 dependency upgraded to rh-python36
515 The Python 3 dependency for Centos7 Arvados packages was upgraded from rh-python35 to rh-python36.
517 h2(#v1_4_0). v1.4.0 (2019-06-05)
519 "previous: Upgrading to 1.3.3":#v1_3_3
521 h3. Populating the new file_count and file_size_total columns on the collections table
523 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.
525 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.
527 h3. Stricter collection manifest validation on the API server
529 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.
531 You could set up a new rvm gemset and install the specific arvados gem for testing, like so:
534 <pre><code>~$ <span class="userinput">rvm gemset create rubysdk-test</span>
535 ~$ <span class="userinput">rvm gemset use rubysdk-test</span>
536 ~$ <span class="userinput">gem install arvados -v 1.3.1.20190301212059</span>
540 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:
542 {% codeblock as ruby %}
544 require 'arvados/keep'
553 req = api.collection.index(
554 :select => [:uuid, :created_at, :manifest_text],
555 :include_trash => true, :include_old_versions => true,
556 :limit => batch_size, :offset => offset)
558 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
562 req[:items].each do |col|
564 Keep::Manifest.validate! col[:manifest_text]
565 rescue Exception => e
566 puts "Collection #{col[:uuid]} manifest not valid"
567 invalid << {uuid: col[:uuid], error: e, created_at: col[:created_at]}
570 puts "Checked #{offset} / #{req[:items_available]} - Invalid: #{invalid.size}"
571 offset += req[:limit]
572 break if offset > req[:items_available]
576 puts "No invalid collection manifests found"
578 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
582 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.
584 h3. Python packaging change
586 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.
588 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.).
590 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.
592 This can be done by activating the virtualenv outside of the script:
595 <pre>~$ <code class="userinput">source /usr/share/python2.7/dist/python-arvados-python-client/bin/activate</code>
596 (python-arvados-python-client) ~$ <code class="userinput">path-to-the-python-script</code>
600 Or alternatively, by updating the shebang line at the start of the script to:
604 #!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
608 h3. python-arvados-cwl-runner deb/rpm package now conflicts with python-cwltool deb/rpm package
610 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.
612 h3. Centos7 Python 3 dependency upgraded to rh-python35
614 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.
616 h3. Centos7 package for libpam-arvados depends on the python-pam package, which is available from EPEL
618 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.
620 h3. New configuration
622 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.
624 h2(#v1_3_3). v1.3.3 (2019-05-14)
626 "previous: Upgrading to 1.3.0":#v1_3_0
628 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.
630 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.
632 h2(#v1_3_0). v1.3.0 (2018-12-05)
634 "previous: Upgrading to 1.2":#v1_2_0
636 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.
638 The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present.
640 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.
642 h2(#v1_2_1). v1.2.1 (2018-11-26)
644 There are no special upgrade notes for this release.
646 h2(#v1_2_0). v1.2.0 (2018-09-05)
648 "previous: Upgrading to 1.1.2 or 1.1.3":#v1_1_2
650 h3. Regenerate Postgres table statistics
652 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:
660 tables=`echo "\dt" | psql arvados_production | grep public|awk -e '{print $3}'`
663 echo "echo 'analyze $t' | psql arvados_production"
664 time echo "analyze $t" | psql arvados_production
668 If you also need to do the vacuum, you could adapt the script to run 'vacuum analyze' instead of 'analyze'.
670 h3. New component: arvados-controller
672 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.
674 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.
676 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.
678 h2(#v1_1_4). v1.1.4 (2018-04-10)
680 "previous: Upgrading to 1.1.3":#v1_1_3
682 h3. arvados-cwl-runner regressions (2018-04-05)
684 <strong>Secondary files missing from toplevel workflow inputs</strong>
686 This only affects workflows that rely on implicit discovery of secondaryFiles.
688 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.
690 As an example, the following workflow will fail because the @toplevel_input@ does not declare the @secondaryFiles@ that are expected by @step_input@:
701 step_input: toplevel_input
705 class: CommandLineTool
715 When run, this produces an error like this:
718 cwltool ERROR: [step step1] Cannot make job: Missing required secondary file 'hello.txt.idx' from file object: {
719 "basename": "hello.txt",
721 "location": "keep:ade9d0e032044bd7f58daaecc0d06bc6+51/hello.txt",
729 To fix this error, add the appropriate @secondaryFiles@ section to @toplevel_input@
732 <pre><code>class: Workflow
735 <span class="userinput">toplevel_input:
743 step_input: toplevel_input
747 class: CommandLineTool
758 This bug has been fixed in Arvados release v1.2.0.
760 <strong>Secondary files on default file inputs</strong>
762 @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:
765 class: CommandLineTool
778 When run, this produces an error like this:
781 2018-05-03 10:58:47 cwltool ERROR: Unhandled error, try again with --debug for more information:
782 [Errno 2] File not found: u'hello.txt.idx'
785 To fix this, manually upload the primary and secondary files to keep and explicitly declare @secondaryFiles@ on the default primary file:
788 <pre><code>class: CommandLineTool
794 <span class="userinput">default:
796 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
799 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt.idx</span>
805 This bug has been fixed in Arvados release v1.2.0.
807 h2(#v1_1_3). v1.1.3 (2018-02-08)
809 There are no special upgrade notes for this release.
811 h2(#v1_1_2). v1.1.2 (2017-12-22)
813 "previous: Upgrading to 1.1.0 or 1.1.1":#v1_1_0
815 h3. The minimum version for Postgres is now 9.4 (2017-12-08)
817 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.
819 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
820 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
821 * Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
822 * 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
823 *# Create a database backup using @pg_dump@
824 *# 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/
825 *# Restore from the backup using @psql@
827 h2(#v1_1_1). v1.1.1 (2017-11-30)
829 There are no special upgrade notes for this release.
831 h2(#v1_1_0). v1.1.0 (2017-10-24)
833 h3. The minimum version for Postgres is now 9.3 (2017-09-25)
835 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.
837 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
838 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
839 * Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
840 * 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
841 *# Create a database backup using @pg_dump@
842 *# 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/
843 *# Restore from the backup using @psql@
845 h2(#older). Older versions
847 h3. Upgrade slower than usual (2017-06-30)
849 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.
851 * 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.
852 * The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
853 * Expect it to take about 1 minute per 20K jobs that have ever been created/run.
855 h3. Service discovery overhead change in keep-web (2017-06-05)
857 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.
859 * 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.
861 h3. Node manager now has an http endpoint for management (2017-04-12)
863 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.
865 * To enable it, add to your configuration file: <pre>[Manage]
868 * The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
870 h3. New websockets component (2017-03-23)
872 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.
873 * See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
874 * Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
875 $ sudo sv down /etc/sv/puma
876 $ sudo rm -r /etc/sv/puma
877 </pre> Example, with systemd: <pre>
878 $ systemctl disable puma
879 $ systemctl stop puma
882 h3. Change of database encoding for hashes and arrays (2017-03-06)
884 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.
886 * Aside from a slight performance improvement, this should have no externally visible effect.
887 * Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
888 * After upgrading, make sure to restart puma and crunch-dispatch-* processes.
890 h3. Docker image format compatibility check (2017-02-03)
892 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.
893 * 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>
894 * 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.
895 * *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.*
897 h3. Debian and RPM packages now have systemd unit files (2016-09-27)
899 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).
901 * On Debian-based systems using systemd, services are enabled automatically when packages are installed.
902 * 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>.
903 * 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>
904 * To migrate from runit to systemd after installing the new packages, we recommend the following procedure:
905 *# Bring down the runit service: "sv down /etc/sv/keep-web"
906 *# Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml -- see "keep-web -help")
907 *# Ensure the service is running correctly under systemd: "systemctl status keep-web" / "journalctl -u keep-web"
908 *# Remove the runit service so it doesn't start at next boot
910 ** keep-balance - /etc/arvados/keep-balance/keep-balance.yml
911 ** keep-web - /etc/arvados/keep-web/keep-web.yml
912 ** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
913 ** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
915 h3. Installation paths for Python modules and script changed (2016-05-31)
917 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.
919 * 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.
920 * 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.
922 h3. Crunchrunner package is required on compute and shell nodes (2016-04-25)
924 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.
926 * On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
927 * On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
929 h3. Keep permission signature algorithm change (2016-04-21)
931 Commit "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/3c88abd changes the Keep permission signature algorithm.
933 * 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.
934 * Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
936 h3. Workbench's "Getting Started" popup disabled by default (2015-01-05)
938 Commit "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/e1276d6e disables Workbench's "Getting Started" popup by default.
940 * If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
942 h3. Crunch jobs now have access to Keep-backed writable scratch storage (2015-12-03)
944 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)
946 * 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
947 * 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.
949 h3. Recommended configuration change for keep-web (2015-11-11)
951 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)
953 * proxy/dns/ssl config should be updated to route "https://download.ClusterID.example.com/" requests to keep-web (alongside the existing "collections" routing)
954 * keep-web command line adds @-attachment-only-host download.ClusterID.example.com@
955 * Workbench config adds @keep_web_download_url@
956 * More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
958 h3. Stopped containers are now automatically removed on compute nodes (2015-11-04)
960 Commit "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/7444)
962 * 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.
964 h3. New keep-web service (2015-11-04)
966 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).
968 * 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).