Commit 1fbf9cd8 authored by Stefano Alberto Russo's avatar Stefano Alberto Russo
Browse files

Added support for custom singularity bindings for user-owned computing resources.

parent 73c88b8f

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

+30 −6
Original line number Diff line number Diff line
@@ -185,10 +185,20 @@ class RemoteComputingManager(ComputingManager): 
            else:

                authstring = ''



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

            if task.computing.user != task.user:

                bindings = task.computing.get_conf_param('bindings', from_sys_only=True )

            else:

                bindings = task.computing.get_conf_param('bindings')

            if not bindings:

                bindings = ''

            else:

                bindings = '-B {}'.format(bindings)



            run_command  = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)

            run_command += '/bin/bash -c \'"wget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> /dev/null && export BASE_PORT=\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)

            run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)

            run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '

            run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)

            

            # Set registry

            if task.container.registry == 'docker_local':
@@ -325,7 +335,11 @@ class SlurmComputingManager(ComputingManager): 
            else:

                authstring = ''



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

            if task.computing.user != task.user:

                bindings = task.computing.get_conf_param('bindings', from_sys_only=True )

            else:

                bindings = task.computing.get_conf_param('bindings')

            if not bindings:

                bindings = ''

            else:
@@ -443,7 +457,7 @@ class RemotehopComputingManager(ComputingManager): 
        second_user = task.computing.get_conf_param('second_user')

        setup_command = task.computing.get_conf_param('setup_command')



        # De hard-code

        # TODO: De hard-code

        use_agent = False



        # Get user keys
@@ -468,6 +482,16 @@ class RemotehopComputingManager(ComputingManager): 
            else:

                authstring = ''



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

            if task.computing.user != task.user:

                bindings = task.computing.get_conf_param('bindings', from_sys_only=True )

            else:

                bindings = task.computing.get_conf_param('bindings')

            if not bindings:

                bindings = ''

            else:

                bindings = '-B {}'.format(bindings)



            run_command  = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)

            run_command += '"ssh -4 -o StrictHostKeyChecking=no {}@{} /bin/bash -c \''.format(second_user, second_host)
@@ -476,13 +500,13 @@ class RemotehopComputingManager(ComputingManager): 
                if setup_command:

                    run_command += setup_command + ' && '

                run_command += '\'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)

                run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '

                run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)

            else:

                run_command += ' : && ' # Trick to prevent some issues in exporting variables                

                if setup_command:

                    run_command += setup_command + ' && '

                run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT={} && {} '.format(task.port, authstring)

                run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '

                run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)

             

            # Set registry

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