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">
32 h2(#main). development main (as of 2022-10-14)
34 "previous: Upgrading to 2.4.3":#v2_4_3
36 h3. Old container logs are automatically deleted from PostgreSQL
38 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@.
40 h3. Fixed salt installer template file to support container shell access
42 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.
44 h3. Login-sync script requires configuration update on LoginCluster federations
46 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.
48 h3. Renamed keep-web metrics and WebDAV configs
50 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@.
52 The config entries @Collections.WebDAVCache.UUIDTTL@, @...MaxCollectionEntries@, and @...MaxUUIDEntries@ are no longer used, and should be removed from your config file.
54 h2(#v2_4_3). v2.4.3 (2022-09-21)
56 "previous: Upgrading to 2.4.2":#v2_4_2
58 h3. Fixed PAM authentication security vulnerability
60 In Arvados 2.4.2 and earlier, when using PAM authentication, if a user
61 presented valid credentials but the account is disabled or otherwise
62 not allowed to access the host, it would still be accepted for access
63 to Arvados. From 2.4.3 onwards, Arvados now also checks that the
64 account is permitted to access the host before completing the PAM login
67 Other authentication methods (LDAP, OpenID Connect) are not affected
70 h2(#v2_4_2). v2.4.2 (2022-08-09)
72 "previous: Upgrading to 2.4.1":#v2_4_1
76 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.
78 This vulnerability is fixed in 2.4.2 ("#19316":https://dev.arvados.org/issues/19316).
80 It is likely that this vulnerability exists in all versions of Arvados up to 2.4.1.
82 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.
84 h3. CVE-2022-31163 and CVE-2022-32224
86 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.
88 h3. Disable Sharing URLs UI
90 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.
92 h2(#v2_4_1). v2.4.1 (2022-06-02)
94 "previous: Upgrading to 2.4.0":#v2_4_0
96 h3. Slurm dispatcher requires configuration update
98 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.
100 h3. New proxy parameters for arvados-controller
102 We now recommend disabling nginx proxy caching for arvados-controller, to avoid truncation of large responses.
104 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@).
107 proxy_max_temp_file_size 0;
108 proxy_request_buffering off;
110 proxy_http_version 1.1;
113 h3. Now recommending Singularity 3.9.9
115 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.
117 h3. Changes to @arvados-cwl-runner --create-workflow@ and @--update-workflow@
119 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@.
121 h2(#v2_4_0). v2.4.0 (2022-04-08)
123 "previous: Upgrading to 2.3.1":#v2_3_1
125 h3. Default result order changed
127 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.
129 h3. Ubuntu 18.04 Arvados Python packages now depend on python-3.8
131 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.
133 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.
135 h3. Minimum supported Ruby version is now 2.6
137 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.
139 h3. Anonymous token changes
141 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.
143 h3. Preemptible instance support changes
145 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.
147 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.
149 h3. Default LSF arguments have changed
151 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.
153 h3. Support for NVIDIA CUDA GPUs
155 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:
157 "Including GPU support in cloud compute node image":{{site.baseurl}}/install/crunch2-cloud/install-compute-node.html#nvidia
159 "Configure cloud dispatcher for GPU support":{{site.baseurl}}/install/crunch2-cloud/install-dispatch-cloud.html#GPUsupport
161 "LSF GPU configuration":{{site.baseurl}}/install/crunch2-lsf/install-dispatch.html
163 h3. Role groups are visible to all users by default
165 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.
167 h3. Previously trashed role groups will be deleted
169 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.
171 h3. Dedicated keepstore process for each container
173 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.
174 * If you have containers that can effectively handle multiple I/O threads per VCPU, consider increasing the @Containers.LocalKeepBlobBuffersPerVCPU@ value.
175 * 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.
176 * 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.
178 h2(#v2_3_1). v2.3.1 (2021-11-24)
180 "previous: Upgrading to 2.3.0":#v2_3_0
182 h3. Users are visible to other users by default
184 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@.
186 h3. Backend support for vocabulary checking
188 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.
189 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.
190 You can read more about how this feature works on the "admin page":{{site.baseurl}}/admin/metadata-vocabulary.html.
192 h2(#v2_3_0). v2.3.0 (2021-10-27)
194 "previous: Upgrading to 2.2.0":#v2_2_0
196 h3. Ubuntu 18.04 packages for arvados-api-server and arvados-workbench now conflict with ruby-bundler
198 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.
200 h3. Removed unused @update_uuid@ endpoint for users.
202 The @update_uuid@ endpoint was superseded by the "link accounts feature":{{site.baseurl}}/admin/link-accounts.html, so it's no longer available.
204 h3. Removed deprecated '@@' search operator
206 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.
208 h3. Storage classes must be defined explicitly
210 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.
212 h3. keep-balance requires access to PostgreSQL
214 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.)
216 h3. crunch-dispatch-local now requires config.yml
218 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.
220 h3. Multi-file docker image collections
222 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.
224 h2(#v2_2_0). v2.2.0 (2021-06-03)
226 "previous: Upgrading to 2.1.0":#v2_1_0
228 h3. New spelling of S3 credential configs
230 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.
232 h3. New proxy parameters for arvados-controller
234 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@).
237 proxy_set_header Upgrade $http_upgrade;
238 proxy_set_header Connection "upgrade";
241 h3. Changes on the collection's @preserve_version@ attribute semantics
243 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.
245 h3. System token requirements
247 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.
249 The @API.RailsSessionSecretToken@ configuration key has been removed. Delete this entry from your configuration file after upgrading.
251 h3. Centos7 Python 3 dependency upgraded to python3
253 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.
255 h3. ForceLegacyAPI14 option removed
257 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.
259 h2(#v2_1_0). v2.1.0 (2020-10-13)
261 "previous: Upgrading to 2.0.0":#v2_0_0
263 h3. LoginCluster conflicts with other Login providers
265 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.
267 h3. Minimum supported Python version is now 3.5
269 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:
272 apt remove python-arvados-fuse && apt install python3-arvados-fuse
273 apt remove python-arvados-python-client && apt install python3-arvados-python-client
274 apt remove python-arvados-cwl-runner && apt install python3-arvados-cwl-runner
275 apt remove python-crunchstat-summary && apt install python3-crunchstat-summary
276 apt remove python-cwltest && apt install python3-cwltest
282 yum remove python-arvados-fuse && yum install python3-arvados-fuse
283 yum remove python-arvados-python-client && yum install python3-arvados-python-client
284 yum remove python-arvados-cwl-runner && yum install python3-arvados-cwl-runner
285 yum remove python-crunchstat-summary && yum install python3-crunchstat-summary
286 yum remove python-cwltest && yum install python3-cwltest
289 h3. Minimum supported Ruby version is now 2.5
291 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.
293 h3. Removing libpam-arvados, replaced with libpam-arvados-go
295 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.
297 h3. Removing sso-provider
299 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.
301 After migrating your configuration, uninstall the @arvados-sso-provider@ package.
305 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.
307 h3. New permission system constraints
309 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.
311 # The @group_class@ field must be either @role@ or @project@. Invalid group_class are migrated to @role@.
312 # A @role@ cannot own things. Anything owned by a role is migrated to a @can_manage@ link and reassigned to the system user.
313 # Only @role@ and @user@ can have outgoing permission links. Permission links originating from projects are deleted by the migration.
314 # 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.
315 # A permission link can have the permission level (@name@) updated but not @head_uuid@, @tail_uuid@ or @link_class@.
317 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.
319 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.
321 To determine which groups have invalid @group_class@ (these will be migrated to @role@ groups):
324 arv group list --filters '[["group_class", "not in", ["project", "role"]]]'
327 To list all @role@ groups, which will be reassigned to the system user (unless @owner_uuid@ is already the system user):
330 arv group list --filters '[["group_class", "=", "role"]]'
333 To list which @project@ groups have outgoing permission links (such links are now invalid and will be deleted by the migration):
336 for uuid in $(arv link list --filters '[["link_class", "=", "permission"], ["tail_uuid", "like", "%-j7d0g-%"]]' |
337 jq -r .items[].tail_uuid | sort | uniq) ; do
338 arv group list --filters '[["group_class", "=", "project"], ["uuid", "=", "'$uuid'"]]' | jq .items
342 h4. "Public favorites" moved to their own project
344 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.
346 h2(#v2_0_0). v2.0.0 (2020-02-07)
348 "previous: Upgrading to 1.4.1":#v1_4_1
350 Arvados 2.0 is a major upgrade, with many changes. Please read these upgrade notes carefully before you begin.
352 h3. Migrating to centralized config.yml
354 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@.
356 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:
363 ExternalURL: "https://zzzzz.example.com"
366 h3. Keep-balance configuration migration
368 (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.
370 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.
372 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.
374 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.
376 h3. Arv-git-httpd configuration migration
378 (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.
380 h3. Keepstore and keep-web configuration migration
382 keepstore and keep-web no longer support configuration via (previously deprecated) command line configuration flags and environment variables.
384 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.
386 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.
388 h3. Keepproxy configuration migration
390 (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.
392 h3. Delete "keep_services" records
394 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.
396 <notextile><pre><code>$ export ARVADOS_API_HOST=...
397 $ export ARVADOS_API_TOKEN=...
398 $ arv --format=uuid keep_service list | xargs -n1 arv keep_service delete --uuid
399 </code></pre></notextile>
401 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.
403 h3. Enabling Postgres trigram indexes
405 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.
407 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:
409 <strong>Centos 7</strong>
411 <pre><code>~$ <span class="userinput">sudo yum install -y postgresql95-contrib</span>
412 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
416 <strong>RHEL 7</strong>
418 <pre><code>~$ <span class="userinput">sudo yum install -y rh-postgresql95-postgresql-contrib</span>
419 ~$ <span class="userinput">su - postgres -c "psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'"</span>
423 <strong>Debian or Ubuntu</strong>
425 <pre><code>~$ <span class="userinput">sudo apt-get install -y postgresql-contrib-9.5</span>
426 ~$ <span class="userinput">sudo -u postgres psql -d 'arvados_production' -c 'CREATE EXTENSION IF NOT EXISTS pg_trgm'</span>
430 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@.
434 Workbench 2 is now ready for regular use. Follow the instructions to "install workbench 2":../install/install-workbench2-app.html
436 h3. New property vocabulary format for Workbench2
438 (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.
440 h3. Cloud installations only: node manager replaced by arvados-dispatch-cloud
442 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
444 *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@.
447 <pre><code>~$ <span class="userinput">sudo systemctl --now disable crunch-dispatch-slurm</span>
448 ~$ <span class="userinput">sudo apt-get remove crunch-dispatch-slurm</span>
452 h3. Jobs API is read-only
454 (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.
456 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@.
458 h3. "/" prohibited in collection and project names
460 (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.
462 h3. No longer stripping ':' from strings in serialized database columns
464 (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.
466 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@.
468 h3. Scoped tokens should use PATCH for updates
470 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.
474 h2(#v1_4_1). v1.4.1 (2019-09-20)
476 "previous: Upgrading to 1.4.0":#v1_4_0
478 h3. Centos7 Python 3 dependency upgraded to rh-python36
480 The Python 3 dependency for Centos7 Arvados packages was upgraded from rh-python35 to rh-python36.
482 h2(#v1_4_0). v1.4.0 (2019-06-05)
484 "previous: Upgrading to 1.3.3":#v1_3_3
486 h3. Populating the new file_count and file_size_total columns on the collections table
488 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.
490 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.
492 h3. Stricter collection manifest validation on the API server
494 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.
496 You could set up a new rvm gemset and install the specific arvados gem for testing, like so:
499 <pre><code>~$ <span class="userinput">rvm gemset create rubysdk-test</span>
500 ~$ <span class="userinput">rvm gemset use rubysdk-test</span>
501 ~$ <span class="userinput">gem install arvados -v 1.3.1.20190301212059</span>
505 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:
507 {% codeblock as ruby %}
509 require 'arvados/keep'
518 req = api.collection.index(
519 :select => [:uuid, :created_at, :manifest_text],
520 :include_trash => true, :include_old_versions => true,
521 :limit => batch_size, :offset => offset)
523 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
527 req[:items].each do |col|
529 Keep::Manifest.validate! col[:manifest_text]
530 rescue Exception => e
531 puts "Collection #{col[:uuid]} manifest not valid"
532 invalid << {uuid: col[:uuid], error: e, created_at: col[:created_at]}
535 puts "Checked #{offset} / #{req[:items_available]} - Invalid: #{invalid.size}"
536 offset += req[:limit]
537 break if offset > req[:items_available]
541 puts "No invalid collection manifests found"
543 invalid.each {|c| puts "#{c[:uuid]} (Created at #{c[:created_at]}): #{c[:error]}" }
547 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.
549 h3. Python packaging change
551 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.
553 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.).
555 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.
557 This can be done by activating the virtualenv outside of the script:
560 <pre>~$ <code class="userinput">source /usr/share/python2.7/dist/python-arvados-python-client/bin/activate</code>
561 (python-arvados-python-client) ~$ <code class="userinput">path-to-the-python-script</code>
565 Or alternatively, by updating the shebang line at the start of the script to:
569 #!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
573 h3. python-arvados-cwl-runner deb/rpm package now conflicts with python-cwltool deb/rpm package
575 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.
577 h3. Centos7 Python 3 dependency upgraded to rh-python35
579 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.
581 h3. Centos7 package for libpam-arvados depends on the python-pam package, which is available from EPEL
583 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.
585 h3. New configuration
587 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.
589 h2(#v1_3_3). v1.3.3 (2019-05-14)
591 "previous: Upgrading to 1.3.0":#v1_3_0
593 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.
595 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.
597 h2(#v1_3_0). v1.3.0 (2018-12-05)
599 "previous: Upgrading to 1.2":#v1_2_0
601 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.
603 The @arvados-controller@ component now requires the /etc/arvados/config.yml file to be present.
605 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.
607 h2(#v1_2_1). v1.2.1 (2018-11-26)
609 There are no special upgrade notes for this release.
611 h2(#v1_2_0). v1.2.0 (2018-09-05)
613 "previous: Upgrading to 1.1.2 or 1.1.3":#v1_1_2
615 h3. Regenerate Postgres table statistics
617 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:
625 tables=`echo "\dt" | psql arvados_production | grep public|awk -e '{print $3}'`
628 echo "echo 'analyze $t' | psql arvados_production"
629 time echo "analyze $t" | psql arvados_production
633 If you also need to do the vacuum, you could adapt the script to run 'vacuum analyze' instead of 'analyze'.
635 h3. New component: arvados-controller
637 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.
639 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.
641 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.
643 h2(#v1_1_4). v1.1.4 (2018-04-10)
645 "previous: Upgrading to 1.1.3":#v1_1_3
647 h3. arvados-cwl-runner regressions (2018-04-05)
649 <strong>Secondary files missing from toplevel workflow inputs</strong>
651 This only affects workflows that rely on implicit discovery of secondaryFiles.
653 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.
655 As an example, the following workflow will fail because the @toplevel_input@ does not declare the @secondaryFiles@ that are expected by @step_input@:
666 step_input: toplevel_input
670 class: CommandLineTool
680 When run, this produces an error like this:
683 cwltool ERROR: [step step1] Cannot make job: Missing required secondary file 'hello.txt.idx' from file object: {
684 "basename": "hello.txt",
686 "location": "keep:ade9d0e032044bd7f58daaecc0d06bc6+51/hello.txt",
694 To fix this error, add the appropriate @secondaryFiles@ section to @toplevel_input@
697 <pre><code>class: Workflow
700 <span class="userinput">toplevel_input:
708 step_input: toplevel_input
712 class: CommandLineTool
723 This bug has been fixed in Arvados release v1.2.0.
725 <strong>Secondary files on default file inputs</strong>
727 @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:
730 class: CommandLineTool
743 When run, this produces an error like this:
746 2018-05-03 10:58:47 cwltool ERROR: Unhandled error, try again with --debug for more information:
747 [Errno 2] File not found: u'hello.txt.idx'
750 To fix this, manually upload the primary and secondary files to keep and explicitly declare @secondaryFiles@ on the default primary file:
753 <pre><code>class: CommandLineTool
759 <span class="userinput">default:
761 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt
764 location: keep:4d8a70b1e63b2aad6984e40e338e2373+69/hello.txt.idx</span>
770 This bug has been fixed in Arvados release v1.2.0.
772 h2(#v1_1_3). v1.1.3 (2018-02-08)
774 There are no special upgrade notes for this release.
776 h2(#v1_1_2). v1.1.2 (2017-12-22)
778 "previous: Upgrading to 1.1.0 or 1.1.1":#v1_1_0
780 h3. The minimum version for Postgres is now 9.4 (2017-12-08)
782 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.
784 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
785 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
786 * Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
787 * 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
788 *# Create a database backup using @pg_dump@
789 *# 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/
790 *# Restore from the backup using @psql@
792 h2(#v1_1_1). v1.1.1 (2017-11-30)
794 There are no special upgrade notes for this release.
796 h2(#v1_1_0). v1.1.0 (2017-10-24)
798 h3. The minimum version for Postgres is now 9.3 (2017-09-25)
800 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.
802 * Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
803 * Ubuntu 16.04 (pg 9.5) does not require an upgrade
804 * Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
805 * 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
806 *# Create a database backup using @pg_dump@
807 *# 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/
808 *# Restore from the backup using @psql@
810 h2(#older). Older versions
812 h3. Upgrade slower than usual (2017-06-30)
814 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.
816 * 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.
817 * The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
818 * Expect it to take about 1 minute per 20K jobs that have ever been created/run.
820 h3. Service discovery overhead change in keep-web (2017-06-05)
822 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.
824 * 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.
826 h3. Node manager now has an http endpoint for management (2017-04-12)
828 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.
830 * To enable it, add to your configuration file: <pre>[Manage]
833 * The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
835 h3. New websockets component (2017-03-23)
837 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.
838 * See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
839 * Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
840 $ sudo sv down /etc/sv/puma
841 $ sudo rm -r /etc/sv/puma
842 </pre> Example, with systemd: <pre>
843 $ systemctl disable puma
844 $ systemctl stop puma
847 h3. Change of database encoding for hashes and arrays (2017-03-06)
849 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.
851 * Aside from a slight performance improvement, this should have no externally visible effect.
852 * Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
853 * After upgrading, make sure to restart puma and crunch-dispatch-* processes.
855 h3. Docker image format compatibility check (2017-02-03)
857 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.
858 * 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>
859 * 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.
860 * *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.*
862 h3. Debian and RPM packages now have systemd unit files (2016-09-27)
864 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).
866 * On Debian-based systems using systemd, services are enabled automatically when packages are installed.
867 * 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>.
868 * 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>
869 * To migrate from runit to systemd after installing the new packages, we recommend the following procedure:
870 *# Bring down the runit service: "sv down /etc/sv/keep-web"
871 *# Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml -- see "keep-web -help")
872 *# Ensure the service is running correctly under systemd: "systemctl status keep-web" / "journalctl -u keep-web"
873 *# Remove the runit service so it doesn't start at next boot
875 ** keep-balance - /etc/arvados/keep-balance/keep-balance.yml
876 ** keep-web - /etc/arvados/keep-web/keep-web.yml
877 ** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
878 ** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
880 h3. Installation paths for Python modules and script changed (2016-05-31)
882 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.
884 * 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.
885 * 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.
887 h3. Crunchrunner package is required on compute and shell nodes (2016-04-25)
889 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.
891 * On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
892 * On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
894 h3. Keep permission signature algorithm change (2016-04-21)
896 Commit "3c88abd":https://dev.arvados.org/projects/arvados/repository/revisions/3c88abd changes the Keep permission signature algorithm.
898 * 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.
899 * Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
901 h3. Workbench's "Getting Started" popup disabled by default (2015-01-05)
903 Commit "e1276d6e":https://dev.arvados.org/projects/arvados/repository/revisions/e1276d6e disables Workbench's "Getting Started" popup by default.
905 * If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
907 h3. Crunch jobs now have access to Keep-backed writable scratch storage (2015-12-03)
909 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)
911 * 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
912 * 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.
914 h3. Recommended configuration change for keep-web (2015-11-11)
916 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)
918 * proxy/dns/ssl config should be updated to route "https://download.ClusterID.example.com/" requests to keep-web (alongside the existing "collections" routing)
919 * keep-web command line adds @-attachment-only-host download.ClusterID.example.com@
920 * Workbench config adds @keep_web_download_url@
921 * More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
923 h3. Stopped containers are now automatically removed on compute nodes (2015-11-04)
925 Commit "1d1c6de":https://dev.arvados.org/projects/arvados/repository/revisions/1d1c6de removes stopped containers (see "#7444":https://dev.arvados.org/issues/7444)
927 * 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.
929 h3. New keep-web service (2015-11-04)
931 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).
933 * 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).