Commit 9c376ec8 authored by Stefano Alberto Russo's avatar Stefano Alberto Russo
Browse files

Fixed bugs in running tasks on standalone computing resources.

parent ec4eec10

services/webapp/code/rosetta/core_app/computing_managers.py

+12 −20
Original line number Diff line number Diff line
@@ -194,15 +194,16 @@ class SSHSingleNodeComputingManager(SingleNodeComputingManager, SSHComputingMana 
        from.utils import get_webapp_conn_string

        webapp_conn_string = get_webapp_conn_string()

            

        # Run the container on the host (non blocking)

        if task.container.type == 'singularity':

        # Handle container runtime 

        if task.computing.default_container_runtime == 'singularity':



            #if not task.container.supports_custom_interface_port:

            #     raise Exception('This task does not support dynamic port allocation and is therefore not supported using singularity on Slurm')



            # Set pass if any

            if task.auth_pass:

                authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.auth_pass)

            else:

            authstring = ''

            if not task.requires_proxy_auth and task.password:

                authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.password)

                

            # Set binds, only from sys config if the resource is not owned by the user

            if self.computing.user != task.user:
@@ -227,18 +228,9 @@ class SSHSingleNodeComputingManager(SingleNodeComputingManager, SSHComputingMana 
            run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)

            run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home --containall --cleanenv '.format(binds, task.uuid, task.uuid)

            

            # Set registry

            if task.container.registry == 'docker_local':

                # Get local Docker registry conn string

                from.utils import get_local_docker_registry_conn_string

                local_docker_registry_conn_string = get_local_docker_registry_conn_string()

                registry = 'docker://{}/'.format(local_docker_registry_conn_string)

            elif task.container.registry == 'docker_hub':

                registry = 'docker://'

            else:

                raise NotImplementedError('Registry {} not supported'.format(task.container.registry))

            # Container part

            run_command+='docker://{}/{}:{} &>> /tmp/{}_data/task.log & echo \$!"\''.format(task.container.registry, task.container.image, task.container.tag, task.uuid)

            

            run_command+='{}{} &>> /tmp/{}_data/task.log & echo \$!"\''.format(registry, task.container.image, task.uuid)



        else:

            raise NotImplementedError('Container {} not supported'.format(task.container.type))
@@ -274,7 +266,7 @@ class SSHSingleNodeComputingManager(SingleNodeComputingManager, SSHComputingMana 
        user = self.computing.conf.get('user')



        # Stop the task remotely

        stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.pid)

        stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.id)

        out = os_shell(stop_command, capture=True)

        if out.exit_code != 0:

            if not 'No such process' in out.stderr: