Training Infrastructure as a Service (TIaaS)

Overview
Creative Commons License: CC-BY Questions:
  • How to deploy EU’s TIaaS

Objectives:
  • Setup TIaaS

  • Request and manage trainings

  • Join a training

Requirements:
Time estimation: 30 minutes
Supporting Materials:
Published: Feb 12, 2020
Last modification: Jan 31, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00022
rating Rating: 5.0 (0 recent ratings, 1 all time)
version Revision: 102

Galaxy is widely used for teaching. In order to facilitate instructors, the Galaxy Project has developed Training Infrastructure as a Service (TIaaS). Workshop instructors can apply for TIaaS, and on the day of their workshop, their participants will be placed in a special group and use dedicated resources, thus reducing queue times on the day of the training.

TIaaS concept. Open image in new tab

Figure 1: With TIaaS, all of your users visit the same server. In the background, the scheduler recognises which users are training users, and directs their jobs to special resources. In the EU deployment of TIaaS jobs preferentially use private resources, but can spill over to the main queue if there is not enough space available.

This tutorial will go cover how to set up such a service on your own Galaxy server.

Agenda
  1. Setting up TIaaS
  2. Job Configuration
Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

  1. Step 1
    ansible-galaxy
  2. Step 2
    backup-cleanup
  3. Step 3
    customization
  4. Step 4
    tus
  5. Step 5
    cvmfs
  6. Step 6
    apptainer
  7. Step 7
    tool-management
  8. Step 8
    reference-genomes
  9. Step 9
    data-library
  10. Step 10
    dev/bioblend-api
  11. Step 11
    connect-to-compute-cluster
  12. Step 12
    job-destinations
  13. Step 13
    pulsar
  14. Step 14
    celery
  15. Step 15
    gxadmin
  16. Step 16
    reports
  17. Step 17
    monitoring
  18. Step 18
    tiaas
  19. Step 19
    sentry
  20. Step 20
    ftp
  21. Step 21
    beacon

Setting up TIaaS

Hands-on: Setup TIaaS
  1. In your requirements.yml add the TIaaS ansible role:

    --- a/requirements.yml
    +++ b/requirements.yml
    @@ -51,3 +51,6 @@
       version: 6f6fdf7f5ead491560783d52528b79e9e088bd5b
     - src: cloudalchemy.grafana
       version: 0.14.2
    +# Training Infrastructure as a Service
    +- src: galaxyproject.tiaas2
    +  version: 2.1.5
       
    

    And run the install step:

    Input: Bash
    ansible-galaxy install -p roles -r requirements.yml
    

    If you haven’t worked with diffs before, this can be something quite new or different.

    If we have two files, let’s say a grocery list, in two files. We’ll call them ‘a’ and ‘b’.

    Input: Old
    $ cat old
    🍎
    🍐
    🍊
    🍋
    🍒
    🥑
    Output: New
    $ cat new
    🍎
    🍐
    🍊
    🍋
    🍍
    🥑

    We can see that they have some different entries. We’ve removed 🍒 because they’re awful, and replaced them with an 🍍

    Diff lets us compare these files

    $ diff old new
    5c5
    < 🍒
    ---
    > 🍍

    Here we see that 🍒 is only in a, and 🍍 is only in b. But otherwise the files are identical.

    There are a couple different formats to diffs, one is the ‘unified diff’

    $ diff -U2 old new
    --- old 2022-02-16 14:06:19.697132568 +0100
    +++ new 2022-02-16 14:06:36.340962616 +0100
    @@ -3,4 +3,4 @@
    🍊
    🍋
    -🍒
    +🍍
    🥑

    This is basically what you see in the training materials which gives you a lot of context about the changes:

    • --- old is the ‘old’ file in our view
    • +++ new is the ‘new’ file
    • @@ these lines tell us where the change occurs and how many lines are added or removed.
    • Lines starting with a - are removed from our ‘new’ file
    • Lines with a + have been added.

    So when you go to apply these diffs to your files in the training:

    1. Ignore the header
    2. Remove lines starting with - from your file
    3. Add lines starting with + to your file

    The other lines (🍊/🍋 and 🥑) above just provide “context”, they help you know where a change belongs in a file, but should not be edited when you’re making the above change. Given the above diff, you would find a line with a 🍒, and replace it with a 🍍

    Added & Removed Lines

    Removals are very easy to spot, we just have removed lines

    --- old	2022-02-16 14:06:19.697132568 +0100
    +++ new 2022-02-16 14:10:14.370722802 +0100
    @@ -4,3 +4,2 @@
    🍋
    🍒
    -🥑

    And additions likewise are very easy, just add a new line, between the other lines in your file.

    --- old	2022-02-16 14:06:19.697132568 +0100
    +++ new 2022-02-16 14:11:11.422135393 +0100
    @@ -1,3 +1,4 @@
    🍎
    +🍍
    🍐
    🍊

    Completely new files

    Completely new files look a bit different, there the “old” file is /dev/null, the empty file in a Linux machine.

    $ diff -U2 /dev/null old
    --- /dev/null 2022-02-15 11:47:16.100000270 +0100
    +++ old 2022-02-16 14:06:19.697132568 +0100
    @@ -0,0 +1,6 @@
    +🍎
    +🍐
    +🍊
    +🍋
    +🍒
    +🥑

    And removed files are similar, except with the new file being /dev/null

    --- old	2022-02-16 14:06:19.697132568 +0100
    +++ /dev/null 2022-02-15 11:47:16.100000270 +0100
    @@ -1,6 +0,0 @@
    -🍎
    -🍐
    -🍊
    -🍋
    -🍒
    -🥑

  2. In your galaxyservers group variables file, add the following:

    --- a/group_vars/galaxyservers.yml
    +++ b/group_vars/galaxyservers.yml
    @@ -349,3 +349,8 @@ telegraf_plugins_extra:
           - timeout = "10s"
           - data_format = "influx"
           - interval = "15s"
    +
    +# TIaaS setup
    +tiaas_dir: /srv/tiaas
    +tiaas_admin_user: admin
    +tiaas_admin_pass: changeme
       
    
  3. In the galaxyservers group variables file, we also need to set the database permissions correctly for TIaaS. It needs to be able to access some Galaxy tables, and we will carefully define only the ones we really need:

    --- a/group_vars/dbservers.yml
    +++ b/group_vars/dbservers.yml
    @@ -3,6 +3,7 @@
     postgresql_objects_users:
       - name: "{{ galaxy_user_name }}"
       - name: telegraf
    +  - name: tiaas
     postgresql_objects_databases:
       - name: "{{ galaxy_db_name }}"
         owner: "{{ galaxy_user_name }}"
    @@ -11,7 +12,26 @@ postgresql_objects_privileges:
         roles: telegraf
         privs: SELECT
         objs: ALL_IN_SCHEMA
    -
    +  - database: galaxy
    +    roles: tiaas
    +    objs: galaxy_user,galaxy_session,job,history,workflow,workflow_invocation
    +    type: table
    +    privs: SELECT
    +  - database: galaxy
    +    roles: tiaas
    +    objs: user_group_association,galaxy_group,role,group_role_association
    +    type: table
    +    privs: SELECT,INSERT
    +  - database: galaxy
    +    roles: tiaas
    +    objs: group_role_association
    +    type: table
    +    privs: DELETE
    +  - database: galaxy
    +    roles: tiaas
    +    objs: role_id_seq,galaxy_group_id_seq,group_role_association_id_seq,user_group_association_id_seq
    +    type: sequence
    +    privs: USAGE,SELECT
        
     # PostgreSQL Backups
     postgresql_backup_dir: /data/backups
       
    

    The DELETE privilege is limited in scope to one table: group_role_association. This allows TIaaS to disassociate training groups from roles in the Galaxy database after the training event date has passed, so that users who participated in a training return to using normal (non-training) resources after the training ends.

    The galaxyproject.tiaas2 role will create a cron job to perform this process every night at midnight. You can control when this runs (or disable it) using the tiaas_disassociate_training_roles variable.

    This is one of the few statements we’ve provided that presents difficulties when running the playbook completely from scratch on a blank machine. Setting postgresql roles is one of the first steps in our playbook, but the rules we’ve provided above depend on the Galaxy tables existing in that database. If those tables aren’t there, it will fail. If you do someday run this from scratch, you’ll find that you need to comment out those roles.

  4. We need to add the galaxyproject.tiaas2 role before the nginx role, as TIaaS defines variables that Nginx needs.

    --- a/galaxy.yml
    +++ b/galaxy.yml
    @@ -47,6 +47,7 @@
         - galaxyproject.nginx
         - geerlingguy.docker
         - usegalaxy_eu.rabbitmqserver
    +    - galaxyproject.tiaas2
         - galaxyproject.gxadmin
         - galaxyproject.cvmfs
         - dj-wasabi.telegraf
       
    
  5. Lastly we should add the routes for TIaaS to the NGINX template for Galaxy. TIaaS provides a set of default nginx routes that can be used.

    --- a/templates/nginx/galaxy.j2
    +++ b/templates/nginx/galaxy.j2
    @@ -113,4 +113,6 @@ server {
     		proxy_set_header Host $http_host;
     	}
        
    +	{{ tiaas_nginx_routes }}
    +
     }
       
    
  6. Run the playbook

    Input: Bash
    ansible-playbook galaxy.yml
    

TIaaS should be available now! The following routes on your server are now configured (we will run through these in the next section)

URL Use Audience
/tiaas/new/ Request a new TIaaS training Instructors
/tiaas/admin/ Approve and Manage requests Admin
/tiaas/stats/ Overall TIaaS statistics (EU Stats) Admins, Funding Agencies
/tiaas/calendar/ Calendar of trainings (EU Calendar) Admins, Funding Agencies
/join-training/ID Join an TIaaS training Participants
/join-training/ID/status Dashboard with job states of trainees. Instructors

Let’s see it in action!

Hands-on: Using TIaaS
  1. Create a new TIaaS request
    • Go to /tiaas/new
    • Here you will find the request form users will fill in to request TIaaS: TIaaS request form.
    • For “Training Identifier”, fill in gat
      • This is the <training-id> used in the URLs listed above used for:
        1. Workshop participants to join the tiaas group
        2. Workshop instructors to monitor the progress of their participants.
    • Fill in the rest of the form as you like
    • Submit the form and you should see a confirmation dialog: TIaaS requested successfully.
  2. Approve TIaaS request
    • Next, the request will have to be approved by an admin
    • Go to /tiaas/admin
    • Log in using the values you configured tiaas_admin_user and tiaas_admin_pass in your group variables file
      • Default values were admin:changeme
    • You should now see the admin panel: TIaaS admin console.
    • Click on Trainings, you should see the TIaaS request listed here: TIaaS request list.
    • Approve the request
      • Click on the training
      • Scroll down to the bottom
      • Change “Processed” to Approved and Save Approve TIaaS.
    • At this point, you would likely email the person who made the request to inform them of approval
  3. Join TIaaS Training
    • Make sure you are logged in to Galaxy
    • On the day of the workshop, participants will visit a following URL to join the TIaaS group
  4. Monitor TIaaS status
    • This is very useful for instructors to monitor the job state of their participants
    • Go to /join-training/gat
    • In the Dasboard you should see that one user (you) has joined the training \
    • Run some jobs to see the dashboard in action TIaaS dashboard.
    • Scroll down to get some more information on a per-user level (anonymized)
      • Every user designated by their own identifier and colour, but no personal information TIaaS dashboard.
Comment: Note: GDPR assistance

Since this setup tracks additional personal information (submitter name & email, users in the queue view), TIaaS includes some always-on features to assist with your GDPR compliance.

  • Users in public status dashboard are only visible by an anonymized identifier and colour
  • Email addressses in the TIaaS admin panel will be automatically expunged 60 days after a training event

Of course you need to review any GDPR compliance concerns with your group’s legal representative(s), this only attempts to ensure some protections exist for the users of the system.

Job Configuration

While observability for teachers or trainers is already a huge benefit, one of the primary benefits of TIaaS is that your jobs get sent to dedicated compute resources, which won’t be used by anyone else, during the period of the training. We will send all of the training jobs to pulsar if you have completed that tutorial, or one of the slurm destinations from the job configuration training.

In order to achieve this, we first need some way to sort the jobs of the training users into these private queues, while letting the other jobs continue on. So let’s create a traffic controller to figure out where jobs belong.

Hands-on: Writing a dynamic job destination
  1. This destination will check that the user_email is in a training group (role starting with training-).

    --- a/files/galaxy/config/tpv_rules_local.yml
    +++ b/files/galaxy/config/tpv_rules_local.yml
    @@ -35,6 +35,15 @@ tools:
           require:
             - pulsar
        
    +roles:
    +  training.*:
    +    max_cores: 2
    +    max_mem: max_cores * 3.8  # TODO check multiplier
    +    scheduling:
    +      require:
    +        - slurm
    +        - training
    +
     destinations:
       local_env:
         runner: local_runner
    @@ -62,6 +71,19 @@ destinations:
         max_mem: 8
         params:
           native_specification: --nodes=1 --ntasks=1 --cpus-per-task={cores} --time={params['walltime']}:00:00
    +  slurm-training:
    +    inherits: singularity
    +    runner: slurm
    +    max_accepted_cores: 12
    +    max_accepted_mem: 120
    +    max_cores: 2 # Limit the cores
    +    max_mem: 8 # Limit the memory
    +    params:
    +      native_specification: --nodes=1 --ntasks=1 --mem={round(mem*1024)} --cpus-per-task={cores} --time=00:30:00
    +    scheduling:
    +      require:
    +        - slurm
    +        - training
        
       pulsar:
         runner: pulsar_runner
       
    
  2. Run the playbook

    Input: Bash
    ansible-playbook galaxy.yml
    
  3. Ensure your user is joined to a training

  4. Run a job and observe the logs to see where it goes (journalctl -u galaxy -f)

Congratulations! you have now set up TIaaS on your Galaxy server.

Hands-on: Time to git commit

It’s time to commit your work! Check the status with

git status

Add your changed files with

git add ... # any files you see that are changed

And then commit it!

git commit -m 'Finished Training Infrastructure as a Service (TIaaS)'

Comment: Got lost along the way?

If you missed any steps, you can compare against the reference files, or see what changed since the previous tutorial.

If you’re using git to track your progress, remember to add your changes and commit with a good commit message!

Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

  1. Step 1
    ansible-galaxy
  2. Step 2
    backup-cleanup
  3. Step 3
    customization
  4. Step 4
    tus
  5. Step 5
    cvmfs
  6. Step 6
    apptainer
  7. Step 7
    tool-management
  8. Step 8
    reference-genomes
  9. Step 9
    data-library
  10. Step 10
    dev/bioblend-api
  11. Step 11
    connect-to-compute-cluster
  12. Step 12
    job-destinations
  13. Step 13
    pulsar
  14. Step 14
    celery
  15. Step 15
    gxadmin
  16. Step 16
    reports
  17. Step 17
    monitoring
  18. Step 18
    tiaas
  19. Step 19
    sentry
  20. Step 20
    ftp
  21. Step 21
    beacon