Actually, dumb question: how do I set the setup script for a task?

Here's a screenshot if a session where I first try to clone as ssm-user , but it fails, then I change to root and it succeeds

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

configurations:
  extra_clearml_conf: ""
  extra_trains_conf: ""
  extra_vm_bash_script: |
    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
    source /clearml_agent_venv/bin/activate

hyper_params:
  iam_arn: arn:aws:iam::<my account id>:instance-profile/clearml-2-AutoscaledInstanceProfileAutoScaledEC2InstanceProfile56A5348F-90fmf6H5OUBx

I

do

have the SSH key placed at

/root/.ssh/id_rsa

on the machine,

@<1541954607595393024:profile|BattyCrocodile47> is the SSH key part of the containers? or are you saying it is on the EC2 instance ?

DM me the entire log, I would assume this is something with the configuration

I do agree with your earlier observation that the target of that mount seems wrong. I would think that the volume mount should be -v /root/.ssh:/root/.ssh but instead it's -v /root.ssh:/.ssh

So here's a snippet from my aws_autoscaler.yaml file

oh that makes sense.
I would add to your Task's docker startup script the following:

ls -la /.ssh
ls -la ~/.ssh
cat ~/.ssh/id_rsa

Let's see what you get

That's with the key at /root/.ssh/id_rsa

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

cc: @<1565509803839590400:profile|MoodyBear54>

'-v', '/tmp/clearml_agent.ssh.cbvchse1:/.ssh',

It's my bad, after that inside the container it does cp -Rf /.ssh ~/.ssh
The reason is that you cannot know the user home folder before spinning the container
Anyhow the point is, are you sure that you have ~/.ssh on the Host machine configured?
And if you do, are you saying this is part of your AMI? if not how did you put it there?

Or the log of the init script?

I don't see it as an argument in Task.init or Task.execute_remotely

Actually, dumb question: how do I set the setup script for a task?

When you clone/edit the Task in the UI, under Execution / Container you should have it
After you edit it, just push it into the execution with the autoscaler and wait 🙂

Trying as a python subprocess...

That's with the key at

/root/.ssh/id_rsa

You mean inside the container that the autoscaler spinned ?
Notice that the agent by defult would mount the Host .ssh over the existing .ssh inside the container, if you do not want this behavior you need to set: agent.disable_ssh_mount: true in clearml.conf

Actually that's wrong: really this is the current volume mount

'-v', '/tmp/clearml_agent.ssh.cbvchse1:/.ssh',

Could changing these values to /root/.ssh work? Do you know what use within the docker image ClearML is using?

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:

On it

The key seems to be placed in the expected location

I'm not seeing a extra_docker_shell_script in my clearml.conf generated by clearml-agent init like in this guide

Remove this from your startup script:

#!/bin/bash 

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

Let's see. The task log? I think this is it.

Here we go. Trying with this

I have the same behavior whether or not I put task.execute_remotely(...) before or after the call to run_shell_script()

It's an Amazon Linux AMI with the AWS CLI pre-installed on it. It uses the AWS CLI to fetch the key from AWS SSM Parameter Store. It's granted read access to that SSM Parameter via the instance role.

I can't think of any changes we might have made on our side to cause that 🤔

So, we've been able to run sudo su and then git clone with our private repos a few times now