Wow, it really does not want to show the output of those print statements in stdout. Here's the output of the task from the console after cloning it. Confirmed that the setup script and all code changes are present:

Remove this from your startup script:

#!/bin/bash 

there is no need that, it actually "markes out" the entire thing

Haha, that was a total gotcha for me. Yeah, a lot just wasn't even getting run due to the #!/bin/bash part.

Anyway, wow! I finally got the precious console logs you thought to find, here they are:

2023-05-06 00:19:21
User aborted: stopping task (3)
2023-05-06 00:19:21
Successfully installed PyYAML-6.0 attrs-22.2.0 certifi-2022.12.7 charset-normalizer-3.1.0 clearml-agent-1.5.2 distlib-0.3.6 filelock-3.12.0 furl-2.1.3 idna-3.4 jsonschema-4.17.3 orderedmultidict-1.0.1 pathlib2-2.3.7.post1 platformdirs-3.5.0 psutil-5.9.5 pyjwt-2.6.0 pyparsing-3.0.9 pyrsistent-0.19.3 python-dateutil-2.8.2 requests-2.28.2 six-1.16.0 urllib3-1.26.15 virtualenv-20.23.0
WARNING: You are using pip version 20.1.1; however, version 23.1.2 is available.
You should consider upgrading via the '/usr/local/bin/python3.9 -m pip install --upgrade pip' command.
+ ls -la /.ssh
total 12
drwx------ 2 root root   61 May  6 06:18 .
drwxr-xr-x 1 root root  123 May  6 06:18 ..
-rw------- 1 root root  722 May  6 06:15 authorized_keys
-rw------- 1 root root 2603 May  6 06:18 id_rsa
-rw------- 1 root root  568 May  6 06:18 id_rsa.pub
+ ls -la /root/.ssh
total 12
drwx------ 2 root root   61 May  6 06:19 .
drwx------ 1 root root   48 May  6 06:19 ..
-rw------- 1 root root  722 May  6 06:19 authorized_keys
-rw------- 1 root root 2603 May  6 06:19 id_rsa
-rw------- 1 root root  568 May  6 06:19 id_rsa.pub
+ whoami
root
+ cat /root/.ssh/id_rsa
+ head -n 3
-----BEGIN OPENSSH PRIVATE KEY-----
b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAABlwAAAAdzc2gtcn
NhAAAAAwEAAQAAAYEA8IluYkpM1l7TK/O1JnhEzeLJKa7+aWO+Gn20R4Ql59FlxQsTq/UE

Well wow, I figured it out. You equiped me with a solid debugging tool AKA running bash commands within the docker container.

I had to pre-add GitHub and Bitbucket to known hosts by adding keyscan commands

configurations:
  extra_clearml_conf: ""
  extra_trains_conf: ""
  extra_vm_bash_script: |
    echo "fetching github key" && (aws ssm get-parameter --region us-west-2 --name /clearml/github_ssh_private_key --with-decryption --query Parameter.Value --output text > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa) || echo "failed"
    source /clearml_agent_venv/bin/activate
    echo "fetching github key" && (aws ssm get-parameter --region us-west-2 --name /clearml/github_ssh_public_key --with-decryption --query Parameter.Value --output text > ~/.ssh/id_rsa.pub && chmod 600 ~/.ssh/id_rsa.pub) || echo "failed"
    source /clearml_agent_venv/bin/activate

    # I added these new lines:
    ssh-keyscan github.com >> ~/.ssh/known_hosts
    ssh-keyscan bitbucket.org >> ~/.ssh/known_hosts