Single host Arvados

  1. Install Saltstack
  2. Single host install using the provision.sh script
  3. Final steps
    1. DNS configuration
    2. Install root certificate
  4. Initial user and login
  5. Test the installed cluster running a simple workflow

Install Saltstack

If you already have a Saltstack environment you can skip this section.

The simplest way to get Salt up and running on a node is to use the bootstrap script they provide:

curl -L https://bootstrap.saltstack.com -o /tmp/bootstrap_salt.sh
sudo sh /tmp/bootstrap_salt.sh -XUdfP -x python3

For more information check Saltstack’s documentation

Single host install using the provision.sh script

This is a package-based installation method. The Salt scripts are available from the tools/salt-install directory in the Arvados git repository.

Use the provision.sh script to deploy Arvados, which is implemented with the arvados-formula in a Saltstack master-less setup:

  • edit the variables at the very beginning of the file,
  • run the script as root
  • wait for it to finish

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

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

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

Final configuration steps

DNS configuration

After the setup is done, you need to set up your DNS to be able to access the cluster.

The simplest way to do this 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

Install root certificate

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

Initial user and login

At this point you should be able to log into the Arvados cluster.

If you changed nothing in the provision.sh script, 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 provision.sh script, 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. If you want to run it, just change to that directory and run:

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

It will create a test 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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Code samples in this documentation are licensed under the Apache License, Version 2.0.