pysqa.base.remote.RemoteQueueAdapter

class pysqa.base.remote.RemoteQueueAdapter(config: dict[str, str], directory: str = '~/.queues', execute_command: ~typing.Callable = <function execute_command>)

Bases: QueueAdapterWithConfig

A class representing a remote queue adapter.

Parameters:

• config (dict) – The configuration dictionary.

• directory (str, optional) – The directory path. Defaults to “~/.queues”.

• execute_command (Callable, optional) – The execute command function. Defaults to execute_command.

_ssh_host

The SSH host.

Type:

str

_ssh_username

The SSH username.

Type:

str

_ssh_known_hosts

The path to the known hosts file.

Type:

str

_ssh_key

The path to the SSH key file.

Type:

str

_ssh_ask_for_password

Flag indicating whether to ask for SSH password.

Type:

bool

_ssh_password

The SSH password.

Type:

str

_ssh_key_passphrase

The SSH key passphrase.

Type:

str

_ssh_two_factor_authentication

Flag indicating whether to use two-factor authentication.

Type:

bool

_ssh_authenticator_service

The SSH authenticator service.

Type:

str

_ssh_proxy_host

The SSH proxy host.

Type:

str

_ssh_remote_config_dir

The remote configuration directory.

Type:

str

_ssh_remote_path

The remote path.

Type:

str

_ssh_local_path

The local path.

Type:

str

_ssh_delete_file_on_remote

Flag indicating whether to delete files on the remote host.

Type:

bool

_ssh_port

The SSH port.

Type:

int

_ssh_continous_connection

Flag indicating whether to use continuous SSH connection.

Type:

bool

_ssh_connection

The SSH connection object.

Type:

None or paramiko.SSHClient

_ssh_proxy_connection

The SSH proxy connection object.

Type:

None or paramiko.SSHClient

_remote_flag

Flag indicating whether the adapter is for remote queue.

Type:

bool

convert_path_to_remote(path

str) -> str: Converts a local path to a remote path.

submit_job(queue

Optional[str] = None, job_name: Optional[str] = None, working_directory: Optional[str] = None,

cores: Optional[int] = None, memory_max: Optional[int] = None, run_time_max: Optional[int] = None, dependency_list: Optional[list[str]] = None, command: Optional[str] = None, **kwargs) -> int:

Submits a job to the remote queue.

enable_reservation(process_id

int) -> str: Enables a reservation for a job.

delete_job(process_id

int) -> str: Deletes a job from the remote queue.

get_queue_status(user

Optional[str] = None) -> pandas.DataFrame: Retrieves the queue status.

get_job_from_remote(working_directory

str): Retrieves the results of a calculation executed on a remote host.

transfer_file(file

str, transfer_back: bool = False, delete_file_on_remote: bool = False): Transfers a file to/from the remote host.

__del__()

Closes the SSH connections.

_check_ssh_connection()

Checks if an SSH connection is open.

_transfer_files(file_dict

dict, sftp=None, transfer_back: bool = False): Transfers files to/from the remote host.

_open_ssh_connection() → paramiko.SSHClient

Opens an SSH connection.

__init__(config: dict[str, str], directory: str = '~/.queues', execute_command: ~typing.Callable = <function execute_command>)

Methods

__init__(config[, directory, execute_command])
check_queue_parameters(queue[, cores, ...])	Check the parameters of a queue.
convert_path_to_remote(path)	Converts a local path to a remote path.
delete_job(process_id)	Deletes a job from the remote queue.
enable_reservation(process_id)	Enables a reservation for a job.
get_job_from_remote(working_directory)	Retrieves the results of a calculation executed on a remote host.
get_queue_status([user])	Retrieves the queue status.
get_status_of_job(process_id)	Get the status of a job.
get_status_of_jobs(process_id_lst)	Get the status of multiple jobs.
get_status_of_my_jobs()	Get the status of the user's jobs.
submit_job([queue, job_name, ...])	Submits a job to the remote queue.
transfer_file(file[, transfer_back, ...])	Transfers a file to/from the remote host.

Attributes

config	Get the QueueAdapter configuration.
queue_list	Get the list of available queues.
queue_view	Get the Pandas DataFrame representation of the available queues.
queues	Get the available queues.
remote_flag	Get the value of remote_flag.
ssh_delete_file_on_remote	Get the value of ssh_delete_file_on_remote.

check_queue_parameters(queue: str | None, cores: int = 1, run_time_max: int | None = None, memory_max: int | str | None = None, active_queue: dict | None = None) → tuple[float | int | None, float | int | None, float | int | str | None]

Check the parameters of a queue.

Parameters:

• queue (str) – The queue to check.

• cores (int, optional) – The number of cores. Defaults to 1.

• run_time_max (int, optional) – The maximum run time. Defaults to None.

• memory_max (int, optional) – The maximum memory. Defaults to None.

• active_queue (dict, optional) – The active queue. Defaults to None.

Returns:

A list of queue parameters [cores, run_time_max, memory_max].

Return type:

list

property config: dict

Get the QueueAdapter configuration.

Returns:

The QueueAdapter configuration.

Return type:

dict

convert_path_to_remote(path: str) → str

Converts a local path to a remote path.

Parameters:

path (str) – The local path.

Returns:

The remote path.

Return type:

str

delete_job(process_id: int) → str

Deletes a job from the remote queue.

Parameters:

process_id (int) – The process ID.

Returns:

The output of the delete command.

Return type:

str

enable_reservation(process_id: int) → str

Enables a reservation for a job.

Parameters:

process_id (int) – The process ID.

Returns:

The output of the reservation command.

Return type:

str

get_job_from_remote(working_directory: str)

Retrieves the results of a calculation executed on a remote host.

Parameters:

working_directory (str) – The local working directory.

get_queue_status(user: str | None = None) → DataFrame

Retrieves the queue status.

Parameters:

user (str, optional) – The username.

Returns:

The queue status.

Return type:

pandas.DataFrame

get_status_of_job(process_id: int) → str | None

Get the status of a job.

Parameters:

process_id (int) – The process ID.

Returns:

The status of the job.results_lst.append(df_selected.values[0])

Return type:

str

get_status_of_jobs(process_id_lst: list[int]) → list[str]

Get the status of multiple jobs.

Parameters:

process_id_lst (list[int]) – List of process IDs.

Returns:

List of job statuses.

Return type:

list[str]

get_status_of_my_jobs() → DataFrame

Get the status of the user’s jobs.

Returns:

The status of the user’s jobs.

Return type:

pandas.DataFrame

property queue_list: list

Get the list of available queues.

Returns:

The list of available queues.

Return type:

list

property queue_view: DataFrame

Get the Pandas DataFrame representation of the available queues.

Returns:

The Pandas DataFrame representation of the available queues.

Return type:

pandas.DataFrame

property queues

Get the available queues.

Returns:

The available queues.

Return type:

Queues

property remote_flag: bool

Get the value of remote_flag.

Returns:

The value of remote_flag.

Return type:

bool

property ssh_delete_file_on_remote: bool

Get the value of ssh_delete_file_on_remote.

Returns:

The value of ssh_delete_file_on_remote.

Return type:

bool

submit_job(queue: str | None = None, job_name: str = 'pysqa', working_directory: str | None = None, cores: int = 1, memory_max: int | str | None = None, run_time_max: int | None = None, dependency_list: list[int] | None = None, command: str = '', submission_template: str | Template | None = None, **kwargs) → int

Submits a job to the remote queue.

Parameters:

• queue (str, optional) – The queue name.

• job_name (str, optional) – The job name.

• working_directory (str, optional) – The working directory.

• cores (int) – The number of cores.

• memory_max (int, optional) – The maximum memory.

• run_time_max (int, optional) – The maximum run time.

• dependency_list (list[int], optional) – The list of job dependencies.

• command (str) – The command to execute.

Returns:

The process ID of the submitted job.

Return type:

int

transfer_file(file: str, transfer_back: bool = False, delete_file_on_remote: bool = False)

Transfers a file to/from the remote host.

Parameters:

• file (str) – The file path.

• transfer_back (bool, optional) – Flag indicating whether to transfer the file back to the local host.

• delete_file_on_remote (bool, optional) – Flag indicating whether to delete the file on the remote host.