Single host Arvados

1. Single host install using the provision.sh script
2. Choose the desired configuration
   1. Single host / single hostname
   2. Single host / multiple hostnames
   3. Further customization of the installation
3. Run the provision.sh script
4. Final configuration steps
   1. Install the CA root certificate
   2. DNS configuration
5. Initial user and login
6. Test the installed cluster running a simple workflow

Single host install using the provision.sh script

NOTE: The single host installation is not recommended for production use.

This is a package-based installation method. Start with the provision.sh script which is available by cloning the main branch from https://git.arvados.org/arvados.git . The provision.sh script and its supporting files can be found in the arvados/tools/salt-install directory in the Arvados git repository.

This procedure will install all the main Arvados components to get you up and running in a single host. The whole installation procedure takes somewhere between 15 to 60 minutes, depending on the host resources and its network bandwidth. As a reference, on a virtual machine with 1 core and 1 GB RAM, it takes ~25 minutes to do the initial install.

The provision.sh script will help you deploy Arvados by preparing your environment to be able to run the installer, then running it. The actual installer is located at arvados-formula and will be cloned during the running of the provision.sh script. The installer is built using Saltstack and provision.sh performs the install using master-less mode.

After setting up a few variables in a config file (next step), you’ll be ready to run it and get Arvados deployed.

Choose the desired configuration

For documentation’s sake, we will use the cluster name arva2 and the domain arv.local. If you don’t change them as required in the next steps, installation won’t proceed.

Arvados’ single host installation can be done in two fashions:

• Using a single hostname, assigning a different port (other than 443) for each user-facing service: This choice is easier to setup, but the user will need to know the port/s for the different services she wants to connect to.
• Using multiple hostnames on the same IP: this setup involves a few extra steps but each service will have a meaningful hostname so it will make easier to access them later.

Once you decide which of these choices you prefer, copy one the two example configuration files and directory, and edit them to suit your needs.

Single host / single hostname

cp local.params.example.single_host_single_hostname local.params
cp -r config_examples/single_host/single_hostname local_config_dir

Edit the variables in the local.params file. Pay attention to the PORT, *TOKEN and KEY variables.

Single host / multiple hostnames (Alternative configuration)

cp local.params.example.single_host_multiple_hostnames local.params
cp -r config_examples/single_host/multiple_hostnames local_config_dir

Edit the variables in the local.params file.

Further customization of the installation (modifying the salt pillars and states)

If you want or need further customization, you can edit the Saltstack pillars and states files. Pay particular attention to the pillars/arvados.sls one. Any extra state file you add under local_config_dir/states will be added to the salt run and applied to the host.

Run the provision.sh script

When you finished customizing the configuration, you are ready to copy the files to the host (if needed) and run the provision.sh script:

scp -r provision.sh local* tests user@host:
ssh user@host sudo ./provision.sh

or, if you saved the local.params in another directory or with some other name

scp -r provision.sh local* tests user@host:
ssh user@host sudo ./provision.sh -c /path/to/your/local.params.file

and wait for it to finish.

If everything goes OK, you’ll get some final lines stating something like:

arvados: Succeeded: 109 (changed=9)
arvados: Failed:      0

Final configuration steps

Once the deployment went OK, you’ll need to perform a few extra steps in your local browser/host to access the cluster.

Install the CA root certificate (required in both alternatives)

Arvados uses SSL to encrypt communications. Its UI uses AJAX which will silently fail if the certificate is not valid or signed by an unknown Certification Authority.

For this reason, the arvados-formula has a helper state to create a root certificate to authorize Arvados services. The provision.sh script will leave a copy of the generated CA’s certificate (arvados-snakeoil-ca.pem) in the script’s directory so you can add it to your workstation.

Installing the root certificate into your web browser will prevent security errors when accessing Arvados services with your web browser.

1. Go to the certificate manager in your browser.
   • In Chrome, this can be found under “Settings → Advanced → Manage Certificates” or by entering chrome://settings/certificates in the URL bar.
   • In Firefox, this can be found under “Preferences → Privacy & Security” or entering about:preferences#privacy in the URL bar and then choosing “View Certificates…”.
2. Select the “Authorities” tab, then press the “Import” button. Choose arvados-snakeoil-ca.pem

The certificate will be added under the “Arvados Formula”.

To access your Arvados instance using command line clients (such as arv-get and arv-put) without security errors, install the certificate into the OS certificate storage.

• On Debian/Ubuntu:

cp arvados-root-cert.pem /usr/local/share/ca-certificates/
/usr/sbin/update-ca-certificates

• On CentOS:

cp arvados-root-cert.pem /etc/pki/ca-trust/source/anchors/
/usr/bin/update-ca-trust

DNS configuration (single host / multiple hostnames)

When using multiple hostnames, after the setup is done, you need to set up your DNS to be able to access the cluster.

If you don’t have access to the domain’s DNS to add the required entries, the simplest way to do it is to edit your /etc/hosts file (as root):

export CLUSTER="arva2"
export DOMAIN="arv.local"
export HOST_IP="127.0.0.2"    # This is valid either if installing in your computer directly
                              # or in a Vagrant VM. If you're installing it on a remote host
                              # just change the IP to match that of the host.
echo "${HOST_IP} api keep keep0 collections download ws workbench workbench2 ${CLUSTER}.${DOMAIN} api.${CLUSTER}.${DOMAIN} keep.${CLUSTER}.${DOMAIN} keep0.${CLUSTER}.${DOMAIN} collections.${CLUSTER}.${DOMAIN} download.${CLUSTER}.${DOMAIN} ws.${CLUSTER}.${DOMAIN} workbench.${CLUSTER}.${DOMAIN} workbench2.${CLUSTER}.${DOMAIN}" >> /etc/hosts

Initial user and login

At this point you should be able to log into the Arvados cluster. The initial URL will be:

• https://workbench.arva2.arv.local

or, in general, the url format will be:

• https://workbench.<cluster>.<domain>

By default, the provision script creates an initial user for testing purposes. This user is configured as administrator of the newly created cluster.

Assuming you didn’t change these values in the local.params file, the initial credentials are:

• User: ‘admin’
• Password: ‘password’
• Email: ‘admin@arva2.arv.local’

Test the installed cluster running a simple workflow

The provision.sh script saves a simple example test workflow in the /tmp/cluster_tests directory in the node. If you want to run it, just ssh to the node, change to that directory and run:

cd /tmp/cluster_tests
sudo ./run-test.sh

It will create a test user (by default, the same one as the admin user), upload a small workflow and run it. If everything goes OK, the output should similar to this (some output was shortened for clarity):

Creating Arvados Standard Docker Images project
Arvados project uuid is 'arva2-j7d0g-0prd8cjlk6kfl7y'
{
 ...
 "uuid":"arva2-o0j2j-n4zu4cak5iifq2a",
 "owner_uuid":"arva2-tpzed-000000000000000",
 ...
}
Uploading arvados/jobs' docker image to the project
2.1.1: Pulling from arvados/jobs
8559a31e96f4: Pulling fs layer
...
Status: Downloaded newer image for arvados/jobs:2.1.1
docker.io/arvados/jobs:2.1.1
2020-11-23 21:43:39 arvados.arv_put[32678] INFO: Creating new cache file at /home/vagrant/.cache/arvados/arv-put/c59256eda1829281424c80f588c7cc4d
2020-11-23 21:43:46 arvados.arv_put[32678] INFO: Collection saved as 'Docker image arvados jobs:2.1.1 sha256:0dd50'
arva2-4zz18-1u5pvbld7cvxuy2
Creating initial user ('admin')
Setting up user ('admin')
{
 "items":[
  {
   ...
   "owner_uuid":"arva2-tpzed-000000000000000",
   ...
   "uuid":"arva2-o0j2j-1ownrdne0ok9iox"
  },
  {
   ...
   "owner_uuid":"arva2-tpzed-000000000000000",
   ...
   "uuid":"arva2-o0j2j-1zbeyhcwxc1tvb7"
  },
  {
   ...
   "email":"admin@arva2.arv.local",
   ...
   "owner_uuid":"arva2-tpzed-000000000000000",
   ...
   "username":"admin",
   "uuid":"arva2-tpzed-3wrm93zmzpshrq2",
   ...
  }
 ],
 "kind":"arvados#HashList"
}
Activating user 'admin'
{
 ...
 "email":"admin@arva2.arv.local",
 ...
 "username":"admin",
 "uuid":"arva2-tpzed-3wrm93zmzpshrq2",
 ...
}
Running test CWL workflow
INFO /usr/bin/cwl-runner 2.1.1, arvados-python-client 2.1.1, cwltool 3.0.20200807132242
INFO Resolved 'hasher-workflow.cwl' to 'file:///tmp/cluster_tests/hasher-workflow.cwl'
...
INFO Using cluster arva2 (https://arva2.arv.local:8443/)
INFO Upload local files: "test.txt"
INFO Uploaded to ea34d971b71d5536b4f6b7d6c69dc7f6+50 (arva2-4zz18-c8uvwqdry4r8jao)
INFO Using collection cache size 256 MiB
INFO [container hasher-workflow.cwl] submitted container_request arva2-xvhdp-v1bkywd58gyocwm
INFO [container hasher-workflow.cwl] arva2-xvhdp-v1bkywd58gyocwm is Final
INFO Overall process status is success
INFO Final output collection d6c69a88147dde9d52a418d50ef788df+123
{
    "hasher_out": {
        "basename": "hasher3.md5sum.txt",
        "class": "File",
        "location": "keep:d6c69a88147dde9d52a418d50ef788df+123/hasher3.md5sum.txt",
        "size": 95
    }
}
INFO Final process status is success

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