- install/arvados-on-kubernetes.html.textile.liquid
- Manual installation:
- install/install-manual-prerequisites.html.textile.liquid
+ - install/install-components.html.textile.liquid
+ - Core:
- install/install-postgresql.html.textile.liquid
- - install/install-sso.html.textile.liquid
- install/install-api-server.html.textile.liquid
- - install/install-ws.html.textile.liquid
- - install/install-arv-git-httpd.html.textile.liquid
- - install/install-workbench-app.html.textile.liquid
- - install/install-composer.html.textile.liquid
- - install/install-shell-server.html.textile.liquid
- - install/create-standard-objects.html.textile.liquid
+ - Keep:
- install/install-keepstore.html.textile.liquid
- install/configure-fs-storage.html.textile.liquid
- install/configure-s3-object-storage.html.textile.liquid
- install/install-keepproxy.html.textile.liquid
- install/install-keep-web.html.textile.liquid
- install/install-keep-balance.html.textile.liquid
+ - User interface:
+ - install/install-sso.html.textile.liquid
+ - install/install-workbench-app.html.textile.liquid
+ - install/install-composer.html.textile.liquid
+ - Additional services:
+ - install/install-ws.html.textile.liquid
+ - install/install-shell-server.html.textile.liquid
+ - install/install-arv-git-httpd.html.textile.liquid
- Containers API support on SLURM:
- install/crunch2-slurm/install-prerequisites.html.textile.liquid
- install/crunch2-slurm/install-slurm.html.textile.liquid
</notextile>
Finally, reboot the system to make these changes effective.
+
+h2. Create a project for Docker images
+
+Here we create a default project for the standard Arvados Docker images, and give all users read access to it. The project is owned by the system user.
+
+<notextile>
+<pre><code>~$ <span class="userinput">project_uuid=`arv --format=uuid group create --group "{\"owner_uuid\":\"$prefix-tpzed-000000000000000\", \"name\":\"Arvados Standard Docker Images\"}"`</span>
+~$ <span class="userinput">echo "Arvados project uuid is '$project_uuid'"</span>
+~$ <span class="userinput">read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"</span>
+<span class="userinput">{
+ "tail_uuid":"$all_users_group_uuid",
+ "head_uuid":"$project_uuid",
+ "link_class":"permission",
+ "name":"can_read"
+}
+EOF</span>
+</code></pre></notextile>
+
+h2. Download and tag the latest arvados/jobs docker image
+
+In order to start workflows from workbench, there needs to be Docker image tagged @arvados/jobs:latest@. The following command downloads the latest arvados/jobs image from Docker Hub, loads it into Keep, and tags it as 'latest'. In this example @$project_uuid@ should be the the UUID of the "Arvados Standard Docker Images" project.
+
+<notextile>
+<pre><code>~$ <span class="userinput">arv-keepdocker --project-uuid $project_uuid --pull arvados/jobs latest</span>
+</code></pre></notextile>
+
+If the image needs to be downloaded from Docker Hub, the command can take a few minutes to complete, depending on available network bandwidth.
+++ /dev/null
----
-layout: default
-navsection: installguide
-title: Create standard objects
-
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-In these steps we use the Arvados CLI tools on the <strong>shell server</strong> to create a few Arvados objects. The CLI tools require an ARVADOS_API_TOKEN environment variable with a valid admin token. If you haven't already done so, set that up as shown in the "API token guide":../user/reference/api-tokens.html.
-
-h3. Arvados repository
-
-Here we create a repository object which will be used to set up a hosted clone of the arvados repository on this cluster.
-
-<notextile>
-<pre><code>~$ <span class="userinput">prefix=`arv --format=uuid user current | cut -d- -f1`</span>
-~$ <span class="userinput">echo "Site prefix is '$prefix'"</span>
-~$ <span class="userinput">all_users_group_uuid="$prefix-j7d0g-fffffffffffffff"</span>
-~$ <span class="userinput">repo_uuid=`arv --format=uuid repository create --repository "{\"owner_uuid\":\"$prefix-tpzed-000000000000000\", \"name\":\"arvados\"}"`</span>
-~$ <span class="userinput">echo "Arvados repository uuid is '$repo_uuid'"</span>
-</code></pre></notextile>
-
-Create a link object to make the repository object readable by the "All users" group, and therefore by every active user. This makes it possible for users to run the bundled Crunch scripts by specifying @"script_version":"master","repository":"arvados"@ rather than pulling the Arvados source tree into their own repositories.
-
-<notextile>
-<pre><code>~$ <span class="userinput">read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"</span>
-<span class="userinput">{
- "tail_uuid":"$all_users_group_uuid",
- "head_uuid":"$repo_uuid",
- "link_class":"permission",
- "name":"can_read"
-}
-EOF</span>
-</code></pre></notextile>
-
-In a couple of minutes, your arvados-git-sync cron job will create an empty repository on your git server. Seed it with the real arvados repository. If your git credential helpers were configured correctly when you "set up your shell server":install-shell-server.html, the "git push" command will use your API token instead of prompting you for a username and password.
-
-<notextile>
-<pre><code>~$ <span class="userinput">cd /tmp</span>
-/tmp$ <span class="userinput">git clone --bare https://github.com/curoverse/arvados.git</span>
-/tmp <span class="userinput">git --git-dir arvados.git push https://git.<b>uuid_prefix.your.domain</b>/arvados.git '*:*'</span>
-</code></pre>
-</notextile>
-
-If you did not set up a HTTPS service, you can push to <code>git@git.uuid_prefix.your.domain:arvados.git</code> using your SSH key, or by logging in to your git server and using sudo.
-
-<notextile>
-<pre><code>gitserver:~$ <span class="userinput">sudo -u git -i bash</span>
-git@gitserver:~$ <span class="userinput">git clone --bare https://github.com/curoverse/arvados.git /tmp/arvados.git</span>
-git@gitserver:~$ <span class="userinput">cd /tmp/arvados.git</span>
-git@gitserver:/tmp/arvados.git$ <span class="userinput">gitolite push /var/lib/arvados/git/repositories/<b>your_arvados_repo_uuid</b>.git '*:*'</span>
-</code></pre>
-</notextile>
-
-h3. Default project for docker images
-
-Here we create a default project for the standard Arvados Docker images, and give all users read access to it. The project is owned by the system user.
-
-<notextile>
-<pre><code>~$ <span class="userinput">project_uuid=`arv --format=uuid group create --group "{\"owner_uuid\":\"$prefix-tpzed-000000000000000\", \"name\":\"Arvados Standard Docker Images\"}"`</span>
-~$ <span class="userinput">echo "Arvados project uuid is '$project_uuid'"</span>
-~$ <span class="userinput">read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"</span>
-<span class="userinput">{
- "tail_uuid":"$all_users_group_uuid",
- "head_uuid":"$project_uuid",
- "link_class":"permission",
- "name":"can_read"
-}
-EOF</span>
-</code></pre></notextile>
-
-h3. Download and tag the latest arvados/jobs docker image
-
-The @arvados-cwl-runner@ needs access to an arvados/jobs image that is tagged as 'latest'. The following command downloads the latest arvados/jobs image from Docker Hub, loads it into Keep, and tags it as 'latest'.
-
-<notextile>
-<pre><code>~$ <span class="userinput">arv-keepdocker --pull arvados/jobs latest</span>
-</code></pre></notextile>
-
-If the image needs to be downloaded from Docker Hub, the command can take a few minutes to complete, depending on available network bandwidth.
It is not strictly necessary to deploy _both_ SSH and HTTPS access, but we recommend deploying both:
* SSH is a more appropriate way to authenticate from a user's workstation because it does not require managing tokens on the client side;
* HTTPS is a more appropriate way to authenticate from a shell VM because it does not depend on SSH agent forwarding (SSH clients' agent forwarding features tend to behave as if the remote machine is fully trusted).
+* HTTPS is also used by Arvados Composer to access git repositories from the browser.
The HTTPS instructions given below will not work if you skip the SSH setup steps.
<pre><code>gitserver:~$ <span class="userinput">sudo nginx -s reload</span>
</code></pre>
</notextile>
+
+h2. Clone Arvados repository
+
+Here we create a repository object which will be used to set up a hosted clone of the arvados repository on this cluster.
+
+<notextile>
+<pre><code>~$ <span class="userinput">prefix=`arv --format=uuid user current | cut -d- -f1`</span>
+~$ <span class="userinput">echo "Site prefix is '$prefix'"</span>
+~$ <span class="userinput">all_users_group_uuid="$prefix-j7d0g-fffffffffffffff"</span>
+~$ <span class="userinput">repo_uuid=`arv --format=uuid repository create --repository "{\"owner_uuid\":\"$prefix-tpzed-000000000000000\", \"name\":\"arvados\"}"`</span>
+~$ <span class="userinput">echo "Arvados repository uuid is '$repo_uuid'"</span>
+</code></pre></notextile>
+
+Create a link object to make the repository object readable by the "All users" group, and therefore by every active user. This makes it possible for users to run the bundled Crunch scripts by specifying @"script_version":"master","repository":"arvados"@ rather than pulling the Arvados source tree into their own repositories.
+
+<notextile>
+<pre><code>~$ <span class="userinput">read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"</span>
+<span class="userinput">{
+ "tail_uuid":"$all_users_group_uuid",
+ "head_uuid":"$repo_uuid",
+ "link_class":"permission",
+ "name":"can_read"
+}
+EOF</span>
+</code></pre></notextile>
+
+In a couple of minutes, your arvados-git-sync cron job will create an empty repository on your git server. Seed it with the real arvados repository. If your git credential helpers were configured correctly when you "set up your shell server":install-shell-server.html, the "git push" command will use your API token instead of prompting you for a username and password.
+
+<notextile>
+<pre><code>~$ <span class="userinput">cd /tmp</span>
+/tmp$ <span class="userinput">git clone --bare https://github.com/curoverse/arvados.git</span>
+/tmp <span class="userinput">git --git-dir arvados.git push https://git.<b>uuid_prefix.your.domain</b>/arvados.git '*:*'</span>
+</code></pre>
+</notextile>
+
+If you did not set up a HTTPS service, you can push to <code>git@git.uuid_prefix.your.domain:arvados.git</code> using your SSH key, or by logging in to your git server and using sudo.
+
+<notextile>
+<pre><code>gitserver:~$ <span class="userinput">sudo -u git -i bash</span>
+git@gitserver:~$ <span class="userinput">git clone --bare https://github.com/curoverse/arvados.git /tmp/arvados.git</span>
+git@gitserver:~$ <span class="userinput">cd /tmp/arvados.git</span>
+git@gitserver:/tmp/arvados.git$ <span class="userinput">gitolite push /var/lib/arvados/git/repositories/<b>your_arvados_repo_uuid</b>.git '*:*'</span>
+</code></pre>
+</notextile>
--- /dev/null
+---
+layout: default
+navsection: installguide
+title: Choosing which components to install
+...
+
+Arvados consists of many components, some of which may be omitted (at the cost of reduced functionality.)
+
+h2. Core
+
+table(table table-bordered table-condensed).
+|_. Component|_. Purpose|_. Dependency|
+|"Postgres database":install-postgresql.html |Stores data for the API server.|Required.|
+|"API server":install-api-server.html |Core Arvados logic for managing users, groups, collections, containers, and enforcing permissions.|Required.|
+
+h2. Keep (storage)
+
+table(table table-bordered table-condensed).
+|_. Component|_. Purpose|_. Dependency|
+|"Keepstore":install-keepstore.html |Stores content-addressed blocks in a variety of backends (local filesystem, cloud object storage).|Required.|
+|"Keepproxy":install-keepproxy.html |Gateway service to access keep servers from external networks.|Required to be able to use arv-put, arv-get, or arv-mount outside the private Arvados network.|
+|"Keep-web":install-keep-web.html |Gateway service providing read/write HTTP and WebDAV support on top of Keep.|Required to be able to download files from Keep over plain HTTP in Workbench.|
+|"Keep-balance":install-keep-balance.html |Storage cluster maintenance daemon responsible for moving blocks to their optimal server location, adjusting block replication levels, and trashing unreferenced blocks.|Required to free deleted data from underlying storage, and to ensure proper replication and block distribution (including support for storage classes).|
+
+h2. User interface
+
+table(table table-bordered table-condensed).
+|_. Component|_. Purpose|_. Dependency|
+|"Single Sign On server":install-sso.html |Login server.|Required for web based login to Workbench.|
+|"Workbench":install-workbench-app.html |Primary graphical user interface for working with file collections and running containers.|Optional. Depends on API server, SSO server, keep-web, websockets server.|
+|"Workflow Composer":install-composer.html |Graphical user interface for editing Common Workflow Language workflows.|Optional. Depends on git server (arv-git-httpd).|
+
+h2. Additional services
+
+table(table table-bordered table-condensed).
+|_. Component|_. Purpose|_. Dependency|
+|"Websockets server":install-ws.html |Event distribution server.|Required to view streaming container logs in Workbench.|
+|"Shell server":install-shell-server.html |Synchronize (create/delete/configure) Unix shell accounts with Arvados users.|Optional.|
+|"Git server":install-arv-git-httpd.html |Arvados-hosted git repositories, with Arvados-token based authentication.|Optional, but required by Workflow Composer.|
+
+h2. Crunch (running containers)
+
+table(table table-bordered table-condensed).
+|_. Component|_. Purpose|_. Dependency|
+|"crunch-dispatch-slurm":crunch2-slurm/install-prerequisites.html |Run analysis workflows using Docker containers distributed across a SLURM cluster.|Optional if you wish to use Arvados for data management only.|
+|"Node Manager":install-nodemanager.html |Allocate and free cloud VM instances on demand based on workload.|Optional, not needed for a static SLURM cluster (such as on-premise HPC).|
<div class="offset1">
table(table table-bordered table-condensed).
-|_Function_|_Number of nodes_|
+|_. Function|_. Number of nodes|
|Arvados API, Crunch dispatcher, Git, Websockets and Workbench|1|
|Arvados Compute node|1|
|Arvados Keepproxy and Keep-web server|1|
h2. Supported GNU/Linux distributions
table(table table-bordered table-condensed).
-|_Distribution_|_State_|_Last supported version_|
+|_. Distribution|_. State|_. Last supported version|
|CentOS 7|Supported|Latest|
|Debian 8 ("jessie")|Supported|Latest|
|Debian 9 ("stretch")|Supported|Latest|
Configure apt to retrieve packages from the Arvados package repository. This command depends on your OS vendor and version:
table(table table-bordered table-condensed).
-|OS version|Command|
+|_. OS version|_. Command|
|Debian 8 ("jessie")|<notextile><code><span class="userinput">echo "deb http://apt.arvados.org/ jessie main" | sudo tee /etc/apt/sources.list.d/arvados.list</span></code></notextile>|
|Debian 9 ("stretch")|<notextile><code><span class="userinput">echo "deb http://apt.arvados.org/ stretch main" | sudo tee /etc/apt/sources.list.d/arvados.list</span></code></notextile>|
|Ubuntu 14.04 ("trusty")[1]|<notextile><code><span class="userinput">echo "deb http://apt.arvados.org/ trusty main" | sudo tee /etc/apt/sources.list.d/arvados.list</span></code></notextile>|
<div class="offset1">
table(table table-bordered table-condensed).
-|_Function_|_Hostname_|
+|_. Function|_. Hostname|
|Arvados API|@uuid_prefix@.your.domain|
|Arvados Git server|git.@uuid_prefix@.your.domain|
|Arvados Keepproxy server|keep.@uuid_prefix@.your.domain|
Arvados Node Manager provides elastic computing for Arvados and SLURM by creating and destroying virtual machines on demand. Node Manager currently supports Amazon Web Services (AWS), Google Cloud Platform (GCP) and Microsoft Azure.
-Note: node manager is only required for elastic computing cloud environments. Fixed size clusters do not require node manager.
+Note: node manager is only required for elastic computing cloud environments. Fixed size clusters (such as on-premise HPC) do not require node manager.
h2. Install
projects / arvados.git / commitdiff