[ARVADOS] created: 1.1.3-251-ga768fc7
Git user
git at public.curoverse.com
Wed Mar 28 15:07:12 EDT 2018
at a768fc771d1135094a33422fc4be4bdf760a03c2 (commit)
commit a768fc771d1135094a33422fc4be4bdf760a03c2
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Wed Mar 28 15:06:58 2018 -0400
13282: First pass at reorganizing
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/doc/_config.yml b/doc/_config.yml
index 011be51..ebb4cd6 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -17,17 +17,6 @@ arvados_workbench_host: http://localhost
exclude: ["Rakefile", "tmp", "vendor"]
navbar:
- #start:
- #- Getting Started:
- #- start/index.html.textile.liquid
- #- Quickstart:
- #- start/getting_started/publicproject.html.textile.liquid
- #- start/getting_started/firstpipeline.html.textile.liquid
- #- Common Use Cases:
- #- start/getting_started/sharedata.html.textile.liquid
- #- Next Steps:
- #- start/getting_started/nextsteps.html.textile.liquid
-
userguide:
- Welcome:
- user/index.html.textile.liquid
@@ -67,17 +56,11 @@ navbar:
- user/tutorials/tutorial-firstscript.html.textile.liquid
- user/tutorials/tutorial-submit-job.html.textile.liquid
- user/topics/tutorial-parallel.html.textile.liquid
- - Develop a web service:
- - user/topics/arv-web.html.textile.liquid
- Reference:
- user/reference/cookbook.html.textile.liquid
- user/topics/run-command.html.textile.liquid
- user/reference/job-pipeline-ref.html.textile.liquid
- user/examples/crunch-examples.html.textile.liquid
- - Admin tools:
- - user/topics/arvados-sync-groups.html.textile.liquid
- - admin/change-account-owner.html.textile.liquid
- - admin/merge-remote-account.html.textile.liquid
- Query the metadata database:
- user/topics/tutorial-trait-search.html.textile.liquid
- Arvados License:
@@ -155,6 +138,15 @@ navbar:
- api/methods/humans.html.textile.liquid
- api/methods/specimens.html.textile.liquid
- api/methods/traits.html.textile.liquid
+ admin:
+ - Overview:
+ - admin/index.html.textile.liquid
+ - Topics:
+ - admin/upgrading.html.textile.liquid
+ - admin/merge-remote-account.html.textile.liquid
+ - user/topics/arvados-sync-groups.html.textile.liquid
+ - install/migrate-docker19.html.textile.liquid
+ - install/cheat_sheet.html.textile.liquid
installguide:
- Overview:
- install/index.html.textile.liquid
@@ -186,8 +178,3 @@ navbar:
- Jobs API support (deprecated):
- install/install-crunch-dispatch.html.textile.liquid
- install/install-compute-node.html.textile.liquid
- - Helpful hints:
- - install/copy_pipeline_from_curoverse.html.textile.liquid
- - install/cheat_sheet.html.textile.liquid
- - Migrating from Docker 1.9:
- - install/migrate-docker19.html.textile.liquid
diff --git a/doc/_includes/_navbar_top.liquid b/doc/_includes/_navbar_top.liquid
index b09f9ac..017845a 100644
--- a/doc/_includes/_navbar_top.liquid
+++ b/doc/_includes/_navbar_top.liquid
@@ -21,6 +21,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
<li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/index.html">User Guide</a></li>
<li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/index.html">SDKs</a></li>
<li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/index.html">API</a></li>
+ <li {% if page.navsection == 'admin' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/index.html">Admin</a></li>
<li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/index.html">Install</a></li>
<li><a href="https://arvados.org" style="padding-left: 2em">arvados.org »</a></li>
</ul>
diff --git a/doc/admin/change-account-owner.html.textile.liquid b/doc/admin/change-account-owner.html.textile.liquid
deleted file mode 100644
index d48572b..0000000
--- a/doc/admin/change-account-owner.html.textile.liquid
+++ /dev/null
@@ -1,41 +0,0 @@
----
-layout: default
-navsection: userguide
-title: "Changing account ownership"
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-It is sometimes necessary to reassign an existing Arvados user account to a new Google account.
-
-Examples:
-* A user’s email address has changed from <code>person at old.example.com</code> to <code>person at new.example.com</code>.
-* A user who used to authenticate via LDAP is switching to Google login.
-
-This can be done by an administrator using Arvados APIs.
-
-First, determine the user’s existing UUID, e.g., @aaaaa-tpzed-abcdefghijklmno at .
-
-Ensure the new email address is not already associated with a different Arvados account. If it is, disassociate it by clearing that account’s @identity_url@ and @email@ fields.
-
-Clear the @identity_url@ field of the existing user record.
-
-Create a Link object with the following attributes (where @tail_uuid@ is the new email address, and @head_uuid@ is the existing user UUID):
-
-<notextile>
-<pre><code>{
- "link_class":"permission",
- "name":"can_login",
- "tail_uuid":"<span class="userinput">person at new.example.com</span>",
- "head_uuid":"<span class="userinput">aaaaa-tpzed-abcdefghijklmno</span>",
- "properties":{
- "identity_url_prefix":"https://www.google.com/"
- }
-}
-</code></pre>
-</notextile>
-
-Have the user log in using their <code>person at new.example.com</code> Google account. You can verify this by checking that the @identity_url@ field has been populated.
diff --git a/doc/admin/index.html.textile.liquid b/doc/admin/index.html.textile.liquid
new file mode 100644
index 0000000..1123312
--- /dev/null
+++ b/doc/admin/index.html.textile.liquid
@@ -0,0 +1,13 @@
+---
+layout: default
+navsection: admin
+title: "Arvados admin overview"
+...
+
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Sysadmin guide.
diff --git a/doc/admin/merge-remote-account.html.textile.liquid b/doc/admin/merge-remote-account.html.textile.liquid
index 1ce35e9..b69730c 100644
--- a/doc/admin/merge-remote-account.html.textile.liquid
+++ b/doc/admin/merge-remote-account.html.textile.liquid
@@ -1,7 +1,7 @@
---
layout: default
-navsection: userguide
-title: "Merging a remote account"
+navsection: admin
+title: "Migrating a user to a federated account"
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
new file mode 100644
index 0000000..c1082a1
--- /dev/null
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -0,0 +1,129 @@
+---
+layout: default
+navsection: admin
+title: "Upgrading Arvados"
+...
+
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+What you need to know and do in order to upgrade your Arvados installation.
+
+h2. General process
+
+# Wait for the cluster to be idle and stop Arvados services.
+# Install new packages using @apt-get upgrade@ or @yum upgrade at .
+# Package installation scripts will perform any necessary data migrations.
+# Consult upgrade notes below to see if any manual configuration updates are necessary.
+# Restart Arvados services.
+
+h2. Upgrade notes
+
+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.
+
+{% comment %}
+Note to developers: Add new items at the top. Include the date, issue number, commit, and considerations/instructions for those about to upgrade.
+
+TODO: extract this information based on git commit messages and generate changelogs / release notes automatically.
+{% endcomment %}
+
+2017-12-08: #11908 commit:8f987a9271 now requires minimum of Postgres 9.4 (previously 9.3)
+* Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
+* Ubuntu 16.04 (pg 9.5) does not require an upgrade
+* Ubuntu 14.04 (pg 9.3) requires upgrade to Postgres 9.4: https://www.postgresql.org/download/linux/ubuntu/
+* 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
+*# Create a database backup using @pg_dump@
+*# 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/
+*# Restore from the backup using @psql@
+
+2017-09-25: #12032 commit:68bdf4cbb now requires minimum of Postgres 9.3 (previously 9.1)
+* Debian 8 (pg 9.4) and Debian 9 (pg 9.6) do not require an upgrade
+* Ubuntu 16.04 (pg 9.5) does not require an upgrade
+* Ubuntu 14.04 (pg 9.3) is compatible, however upgrading to Postgres 9.4 is recommended: https://www.postgresql.org/download/linux/ubuntu/
+* 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
+*# Create a database backup using @pg_dump@
+*# 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/
+*# Restore from the backup using @psql@
+
+2017-06-30: #11807 commit:55aafbb converts old "jobs" database records from YAML to JSON, making the upgrade process slower than usual.
+* 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 commit:660a614 and used the jobs/pipelines APIs). Otherwise, the upgrade will be no slower than usual.
+* The conversion runs as a database migration, i.e., during the deb/rpm package upgrade process, while your API server is unavailable.
+* Expect it to take about 1 minute per 20K jobs that have ever been created/run.
+
+2017-06-05: #9005 commit:cb230b0 reduces service discovery overhead in keep-web requests.
+* 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.
+
+2017-04-12: #11349 commit:2c094e2 adds a "management" http server to nodemanager.
+* To enable it, add to your configuration file: <pre>[Manage]
+ address = 127.0.0.1
+ port = 8989</pre> (see example configuration files in source:services/nodemanager/doc or https://doc.arvados.org/install/install-nodemanager.html for more info)
+* The server responds to @http://{address}:{port}/status.json@ with a summary of how many nodes are in each state (booting, busy, shutdown, etc.)
+
+2017-03-23: #10766 commit:e8cc0d7 replaces puma with arvados-ws as the recommended websocket server.
+* See http://doc.arvados.org/install/install-ws.html for install/upgrade instructions.
+* Remove the old puma server after the upgrade is complete. Example, with runit: <pre>
+$ sudo sv down /etc/sv/puma
+$ sudo rm -r /etc/sv/puma
+</pre> Example, with systemd: <pre>
+$ systemctl disable puma
+$ systemctl stop puma
+</pre>
+
+2017-03-06: #11168 commit:660a614 uses JSON instead of YAML to encode hashes and arrays in the database.
+* Aside from a slight performance improvement, this should have no externally visible effect.
+* Downgrading past this version is not supported, and is likely to cause errors. If this happens, the solution is to upgrade past this version.
+* After upgrading, make sure to restart puma and crunch-dispatch-* processes.
+
+2017-02-03: #10969 commit:74a9dec introduces a Docker image format compatibility check: the @arv keep docker@ command prevents users from inadvertently saving docker images that compute nodes won't be able to run.
+* 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>
+* 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 for more detail.
+* *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.*
+
+2016-09-27: several Debian and RPM packages -- keep-balance (commit:d9eec0b), keep-web (commit:3399e63), keepproxy (commit:6de67b6), and arvados-git-httpd (commit:9e27ddf) -- now enable their respective components using systemd. These components prefer YAML configuration files over command line flags (commit:3bbe1cd).
+* On Debian-based systems using systemd, services are enabled automatically when packages are installed.
+* 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>.
+* 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>
+* To migrate from runit to systemd after installing the new packages, we recommend the following procedure:
+*# Bring down the runit service: "sv down /etc/sv/keep-web"
+*# Create a JSON configuration file (e.g., /etc/arvados/keep-web/keep-web.yml -- see "keep-web -help")
+*# Ensure the service is running correctly under systemd: "systemctl status keep-web" / "journalctl -u keep-web"
+*# Remove the runit service so it doesn't start at next boot
+* Affected services:
+** keep-balance - /etc/arvados/keep-balance/keep-balance.yml
+** keep-web - /etc/arvados/keep-web/keep-web.yml
+** keepproxy - /etc/arvados/keepproxy/keepproxy.yml
+** arvados-git-httpd - /etc/arvados/arv-git-httpd/arv-git-httpd.yml
+
+2016-05-31: commit:ae72b172c8 and commit:3aae316c25 install Python modules and scripts to different locations on the filesystem.
+* 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 at . This improves compatibility with other Python packages provided by the distribution. See #9242 for more background.
+* 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.
+
+2016-04-25: commit:eebcb5e requires the crunchrunner package to be installed on compute nodes and shell nodes in order to run CWL workflows.
+* On each Debian-based compute node and shell node, run: @sudo apt-get install crunchrunner@
+* On each Red Hat-based compute node and shell node, run: @sudo yum install crunchrunner@
+
+2016-04-21: commit:3c88abd changes the Keep permission signature algorithm.
+* 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.
+* Jobs and client operations that are in progress during the upgrade (including arv-put's "resume cache") will fail.
+
+2015-01-05: commit:e1276d6e disables Workbench's "Getting Started" popup by default.
+* If you want new users to continue seeing this popup, set @enable_getting_started_popup: true@ in Workbench's @application.yml@ configuration.
+
+2015-12-03: commit:5590c9ac makes a Keep-backed writable scratch directory available in crunch jobs (see #7751)
+* 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 commit:346a558
+* 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.
+
+2015-11-11: commit:1e2ace5 changes recommended config for keep-web (see #5824)
+* proxy/dns/ssl config should be updated to route "https://download.uuid_prefix.arvadosapi.com/" requests to keep-web (alongside the existing "collections" routing)
+* keep-web command line adds @-attachment-only-host download.uuid_prefix.arvadosapi.com@
+* Workbench config adds @keep_web_download_url@
+* More info on the (still beta/non-TOC-linked) "keep-web doc page":http://doc.arvados.org/install/install-keep-web.html
+
+2015-11-04: commit:1d1c6de removes stopped containers (see #7444)
+* arvados-docker-cleaner removes _all_ docker containers as soon as they exit, effectively making @docker run@ default to @--rm at . 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.
+
+2015-11-04: commit:21006cf adds a keep-web service (see #5824)
+* Nothing relies on it 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).
diff --git a/doc/index.html.liquid b/doc/index.html.liquid
index 22e74ac..025bec6 100644
--- a/doc/index.html.liquid
+++ b/doc/index.html.liquid
@@ -44,7 +44,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
</div>
<div class="col-sm-6" style="border-left: solid; border-width: 1px">
- <p><strong>Quickstart</strong>
+ <p><strong>Quickstart</strong>
<p>
Try any pipeline from the <a href="https://cloud.curoverse.com/projects/public">list of public pipelines</a>. For instance, the <a href="http://curover.se/pathomap">Pathomap Pipeline</a> links to these <a href="https://dev.arvados.org/projects/arvados/wiki/pathomap_tutorial/">step-by-step instructions</a> for trying Arvados out right in your browser using Curoverse's <a href="http://lp.curoverse.com/beta-signup/">public Arvados instance</a>.
</p>
@@ -82,7 +82,10 @@ SPDX-License-Identifier: CC-BY-SA-3.0
<a href="{{ site.baseurl }}/api/index.html">API Reference</a> — Details about the the Arvados REST API.
</p>
<p>
- <a href="{{ site.baseurl }}/install/index.html">Install Guide</a> — How to install Arvados on a cloud platform.
+ <a href="{{ site.baseurl }}/admin/index.html">Admin Guide</a> — Details about administering an Arvados cluster.
+ </p>
+ <p>
+ <a href="{{ site.baseurl }}/install/index.html">Install Guide</a> — How to install Arvados.
</p>
</div>
</div>
diff --git a/doc/install/cheat_sheet.html.textile.liquid b/doc/install/cheat_sheet.html.textile.liquid
index bc9d164..afff1f4 100644
--- a/doc/install/cheat_sheet.html.textile.liquid
+++ b/doc/install/cheat_sheet.html.textile.liquid
@@ -1,7 +1,7 @@
---
layout: default
-navsection: installguide
-title: Cheat Sheet
+navsection: admin
+title: User management
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
diff --git a/doc/install/migrate-docker19.html.textile.liquid b/doc/install/migrate-docker19.html.textile.liquid
index 688850c..7b7e2a8 100644
--- a/doc/install/migrate-docker19.html.textile.liquid
+++ b/doc/install/migrate-docker19.html.textile.liquid
@@ -1,7 +1,7 @@
---
layout: default
-navsection: installguide
-title: Migrating Docker images
+navsection: admin
+title: Migrating from Docker 1.9
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
diff --git a/doc/user/topics/arvados-sync-groups.html.textile.liquid b/doc/user/topics/arvados-sync-groups.html.textile.liquid
index c9f74b5..9a60903 100644
--- a/doc/user/topics/arvados-sync-groups.html.textile.liquid
+++ b/doc/user/topics/arvados-sync-groups.html.textile.liquid
@@ -1,7 +1,7 @@
---
layout: default
-navsection: userguide
-title: "Using arvados-sync-groups"
+navsection: admin
+title: "Synchronizing external groups"
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
@@ -9,7 +9,7 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-The @arvados-sync-groups@ tool allows to synchronize remote groups into Arvados from an external source.
+The @arvados-sync-groups@ tool allows to synchronize groups in Arvados from an external source.
h1. Using arvados-sync-groups
-----------------------------------------------------------------------
hooks/post-receive
--
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