pyrosetta.distributed.cluster.core.PyRosettaCluster Class Reference

Inheritance diagram for pyrosetta.distributed.cluster.core.PyRosettaCluster:

Public Member Functions
def	__attrs_post_init__
def	distribute
Public Member Functions inherited from pyrosetta.distributed.cluster.logging_support.LoggingSupport
def	__init__

Static Public Attributes
tuple	tasks
tuple	nstruct
tuple	tasks_size
tuple	input_packed_pose
tuple	seeds
tuple	decoy_ids
tuple	client
tuple	scheduler
tuple	cores
tuple	processes
tuple	memory
tuple	scratch_dir
tuple	min_workers
tuple	max_workers
tuple	dashboard_address
tuple	project_name
tuple	simulation_name
tuple	output_path
tuple	scorefile_name
tuple	scorefile_path
tuple	simulation_records_in_scorefile
tuple	decoy_dir_name
tuple	decoy_path
tuple	logs_dir_name
tuple	logs_path
tuple	logging_level
tuple	logging_file
tuple	compressed
tuple	sha1
tuple	ignore_errors
tuple	timeout
tuple	save_all
tuple	dry_run
tuple	protocols_key
tuple	system_info
tuple	pyrosetta_build
tuple	environment
tuple	environment_file
Static Public Attributes inherited from pyrosetta.distributed.cluster.io.IO
tuple	instance_state = dict(zip(self.__slots__, self.__getstate__()))
tuple	instance_kwargs = copy.deepcopy(instance_state)
list	out = [cls._format_result(results)]
Static Public Attributes inherited from pyrosetta.distributed.cluster.base.TaskBase
tuple	protocol = protocols.pop(0)
tuple	seed = self._get_seed(protocols)
tuple	kwargs = self._setup_seed(kwargs, seed)
string	jran = f" -run:constant_seed 1 -run:jran {seed}"
string	split_str = " -run:constant_seed 1 -run:jran "
tuple	flags = pyrosetta.distributed._normflags(kwargs["extra_options"])

Additional Inherited Members
Public Attributes inherited from pyrosetta.distributed.cluster.utilities.SchedulerManager
	scheduler

Member Function Documentation

def pyrosetta.distributed.cluster.core.PyRosettaCluster.__attrs_post_init__

(

self

)

References pyrosetta.distributed.cluster.initialization._maybe_init_master(), pyrosetta.distributed.cluster.logging_support.LoggingSupport._setup_logger(), pyrosetta.distributed.cluster.io.IO._write_environment_file(), and pyrosetta.distributed.cluster.core.PyRosettaCluster.environment_file.

def pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute	(		self,
			args
	)

References pyrosetta.distributed.cluster.logging_support.LoggingSupport._close_logger(), pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_adapt(), pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_teardown(), pyrosetta.distributed.cluster.io.IO._save_results(), pyrosetta.distributed.cluster.utilities.SchedulerManager._setup_client_cluster_adaptive(), pyrosetta.distributed.cluster.base.TaskBase._setup_initial_kwargs(), pyrosetta.distributed.cluster.base.TaskBase._setup_kwargs(), pyrosetta.distributed.cluster.base.TaskBase._setup_protocols_protocol_seed(), pyrosetta.distributed.cluster.core.PyRosettaCluster.decoy_ids, basic::options::OptionKeys::stepwise.enumerate, pyrosetta.tests.distributed.test_dask.format, pyrosetta.distributed.cluster.core.PyRosettaCluster.ignore_errors, pyrosetta.distributed.cluster.core.PyRosettaCluster.input_packed_pose, pyrosetta.distributed.cluster.core.PyRosettaCluster.logging_file, pyrosetta.distributed.cluster.core.PyRosettaCluster.logging_level, pyrosetta.distributed.cluster.core.PyRosettaCluster.nstruct, pyrosetta.distributed.cluster.core.PyRosettaCluster.protocols_key, basic::options::OptionKeys::relax::range.range, pyrosetta.distributed.cluster.core.PyRosettaCluster.save_all, pyrosetta.distributed.cluster.core.PyRosettaCluster.tasks, pyrosetta.distributed.cluster.core.PyRosettaCluster.tasks_size, and pyrosetta.distributed.cluster.core.PyRosettaCluster.timeout.

Member Data Documentation

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.client

static

Initial value:

= attr.ib(
        type=distributed.client.Client,
        default=None,
        validator=attr.validators.optional(
            attr.validators.instance_of(distributed.client.Client)
        ),
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_adapt(), pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_teardown(), pyrosetta.distributed.cluster.utilities.SchedulerManager._setup_client_cluster_adaptive(), pyrosetta.tests.distributed.test_dask.TestDaskDistribution.test_basic(), and pyrosetta.tests.distributed.test_dask.TestDaskDistribution.test_rosetta_scripts().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.compressed

static

Initial value:

= attr.ib(
        type=bool,
        default=True,
        validator=attr.validators.instance_of(bool),
        converter=attr.converters.default_if_none(default=True),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._save_results().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.cores

static

Initial value:

= attr.ib(
        type=int,
        default=1,
        validator=[_validate_int, attr.validators.instance_of(int)],
        converter=attr.converters.default_if_none(default=1),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.dashboard_address

static

Initial value:

= attr.ib(
        type=str,
        default=":8787",
        validator=attr.validators.instance_of(str),
        converter=attr.converters.default_if_none(default=":8787"),
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._get_cluster().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.decoy_dir_name

static

Initial value:

= attr.ib(
        type=str,
        default="decoys",
        validator=attr.validators.instance_of(str),
        converter=attr.converters.default_if_none(default="decoys"),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.decoy_ids

static

Initial value:

= attr.ib(
        type=list,
        default=None,
        validator=attr.validators.optional(attr.validators.instance_of(list)),
        converter=attr.converters.optional(_parse_decoy_ids),
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.decoy_path

static

Initial value:

= attr.ib(
        type=str,
        default=attr.Factory(
            lambda self: os.path.abspath(
                os.path.join(self.output_path, self.decoy_dir_name)
            ),
            takes_self=True,
        ),
        init=False,
        validator=attr.validators.instance_of(str),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._save_results().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.dry_run

static

Initial value:

= attr.ib(
        type=bool,
        default=False,
        validator=attr.validators.instance_of(bool),
        converter=attr.converters.default_if_none(False),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._save_results(), and pyrosetta.distributed.cluster.io.IO._write_environment_file().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.environment

static

Initial value:

= attr.ib(
        type=str,
        default=None,
        validator=attr.validators.instance_of(str),
        converter=_parse_environment,
    )

Referenced by pyrosetta.distributed.cluster.io.IO._write_environment_file().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.environment_file

static

Initial value:

= attr.ib(
        type=str,
        default=attr.Factory(
            lambda self: os.path.join(
                self.output_path,
                "_".join(
                    [
                        self.project_name.replace(" ", "-"),
                        self.simulation_name.replace(" ", "-"),
                        "environment.yml",
                    ]
                ),
            ),
            takes_self=True,
        ),
        init=False,
        validator=attr.validators.instance_of(str),
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.__attrs_post_init__(), and pyrosetta.distributed.cluster.io.IO._save_results().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.ignore_errors

static

Initial value:

= attr.ib(
        type=bool,
        default=False,
        validator=attr.validators.instance_of(bool),
        converter=attr.converters.default_if_none(default=False),
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.input_packed_pose

static

Initial value:

= attr.ib(
        type=PackedPose,
        default=None,
        validator=attr.validators.optional(attr.validators.instance_of(PackedPose)),
        converter=_parse_input_packed_pose,
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.logging_file

static

Initial value:

= attr.ib(
        type=str,
        default=attr.Factory(
            lambda self: os.path.join(
                self.logs_path,
                "_".join(
                    [
                        self.project_name.replace(" ", "-"),
                        self.simulation_name.replace(" ", "-") + ".log",
                    ]
                ),
            ),
            takes_self=True,
        ),
        init=False,
        validator=attr.validators.instance_of(str),
    )

Referenced by pyrosetta.distributed.cluster.base.TaskBase._setup_initial_kwargs(), and pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.logging_level

static

Initial value:

= attr.ib(
        type=str,
        default="INFO",
        validator=[
            attr.validators.in_(
                ["NOTSET", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
            ),
            attr.validators.instance_of(str),
        ],
        converter=attr.converters.default_if_none(default="NOTSET"),
    )

Referenced by pyrosetta.distributed.cluster.logging_support.LoggingSupport._setup_logger(), and pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.logs_dir_name

static

Initial value:

= attr.ib(
        type=str,
        default="logs",
        validator=attr.validators.instance_of(str),
        converter=attr.converters.default_if_none(default="logs"),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.logs_path

static

Initial value:

= attr.ib(
        type=str,
        default=attr.Factory(
            lambda self: os.path.abspath(
                os.path.join(self.output_path, self.logs_dir_name)
            ),
            takes_self=True,
        ),
        init=False,
        validator=attr.validators.instance_of(str),
    )

Referenced by pyrosetta.distributed.cluster.logging_support.LoggingSupport._setup_logger().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.max_workers

static

Initial value:

= attr.ib(
        type=int,
        default=attr.Factory(
            lambda self: 1000 if (self.tasks_size < 1000) else self.tasks_size,
            takes_self=True,
        ),
        validator=[_validate_int, attr.validators.instance_of(int)],
        converter=attr.converters.default_if_none(default=1000),
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._get_cluster(), pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_adapt(), and pyrosetta.distributed.cluster.utilities.SchedulerManager._setup_client_cluster_adaptive().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.memory

static

Initial value:

= attr.ib(
        type=str,
        default="4g",
        validator=attr.validators.optional(attr.validators.instance_of(str)),
        converter=attr.converters.default_if_none(default="4g"),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.min_workers

static

Initial value:

= attr.ib(
        type=int,
        default=1,
        validator=[_validate_int, attr.validators.instance_of(int)],
        converter=attr.converters.default_if_none(default=1),
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._setup_client_cluster_adaptive().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.nstruct

static

Initial value:

= attr.ib(
        type=int,
        default=1,
        validator=[_validate_int, attr.validators.instance_of(int)],
        converter=attr.converters.default_if_none(default=1),
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute(), and pyrosetta.toolbox.py_jobdistributor.PyJobDistributor.output_decoy().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.output_path

static

Initial value:

= attr.ib(
        type=str,
        default=os.path.abspath(os.path.join(os.getcwd(), "outputs")),
        validator=[_validate_dirs, attr.validators.instance_of(str)],
        converter=attr.converters.default_if_none(
            default=os.path.abspath(os.path.join(os.getcwd(), "outputs"))
        ),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.processes

static

Initial value:

= attr.ib(
        type=int,
        default=1,
        validator=[_validate_int, attr.validators.instance_of(int)],
        converter=attr.converters.default_if_none(default=1),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.project_name

static

Initial value:

= attr.ib(
        type=str,
        default=datetime.now().strftime("%Y.%m.%d.%H.%M.%S.%f"),
        validator=attr.validators.optional(attr.validators.instance_of(str)),
        converter=attr.converters.default_if_none(default="PyRosettaCluster"),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.protocols_key

static

Initial value:

= attr.ib(
        type=str,
        default="PyRosettaCluster_protocols_container",
        init=False,
        validator=attr.validators.instance_of(str),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._process_kwargs(), pyrosetta.distributed.cluster.base.TaskBase._setup_initial_kwargs(), pyrosetta.distributed.cluster.base.TaskBase._setup_kwargs(), and pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.pyrosetta_build

static

Initial value:

= attr.ib(
        type=str,
        default=None,
        validator=attr.validators.instance_of(str),
        converter=_parse_pyrosetta_build,
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.save_all

static

Initial value:

= attr.ib(
        type=bool,
        default=False,
        validator=attr.validators.instance_of(bool),
        converter=attr.converters.default_if_none(default=False),
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.scheduler

static

Initial value:

= attr.ib(
        type=str,
        default=None,
        validator=attr.validators.optional(
            [attr.validators.in_(["sge", "slurm"]), attr.validators.instance_of(str),],
        ),
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._get_cluster(), pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_adapt(), and pyrosetta.distributed.cluster.utilities.SchedulerManager._setup_client_cluster_adaptive().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.scorefile_name

static

Initial value:

= attr.ib(
        type=str,
        default="scores.json",
        validator=attr.validators.instance_of(str),
        converter=attr.converters.default_if_none(default="scores.json"),
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.scorefile_path

static

Initial value:

= attr.ib(
        type=str,
        default=attr.Factory(
            lambda self: os.path.abspath(
                os.path.join(self.output_path, self.scorefile_name)
            ),
            takes_self=True,
        ),
        init=False,
        validator=attr.validators.instance_of(str),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._save_results().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.scratch_dir

static

Initial value:

= attr.ib(
        type=str,
        default=None,
        validator=[_validate_dir, attr.validators.instance_of(str)],
        converter=_parse_scratch_dir,
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._get_cluster().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.seeds

static

Initial value:

= attr.ib(
        type=list,
        default=None,
        validator=attr.validators.optional(attr.validators.instance_of(list)),
        converter=attr.converters.optional(_parse_seeds),
    )

Referenced by pyrosetta.distributed.cluster.base.TaskBase._get_seed().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.sha1

static

Initial value:

= attr.ib(
        type=str,
        default="",
        validator=attr.validators.instance_of(str),
        converter=_parse_sha1,
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.simulation_name

static

Initial value:

= attr.ib(
        type=str,
        default=attr.Factory(lambda self: self.project_name, takes_self=True),
        validator=attr.validators.instance_of(str),
        converter=attr.converters.default_if_none(default="PyRosettaCluster"),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._save_results().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.simulation_records_in_scorefile

static

Initial value:

= attr.ib(
        type=bool,
        default=False,
        validator=attr.validators.instance_of(bool),
        converter=attr.converters.default_if_none(default=False),
    )

Referenced by pyrosetta.distributed.cluster.io.IO._save_results(), and pyrosetta.distributed.cluster.io.IO._write_environment_file().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.system_info

static

Initial value:

= attr.ib(
        type=dict,
        default=None,
        validator=attr.validators.instance_of(dict),
        converter=_parse_system_info,
    )

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.tasks

static

Initial value:

= attr.ib(
        type=list,
        default=[{}],
        validator=attr.validators.deep_iterable(
            member_validator=attr.validators.instance_of(dict),
            iterable_validator=attr.validators.instance_of(list),
        ),
        converter=_parse_tasks,
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.tasks_size

static

Initial value:

= attr.ib(
        type=int,
        default=attr.Factory(
            lambda self: toolz.itertoolz.count(self.tasks) * self.nstruct,
            takes_self=True,
        ),
        init=False,
        validator=attr.validators.instance_of(int),
    )

Referenced by pyrosetta.distributed.cluster.utilities.SchedulerManager._maybe_adapt(), and pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

tuple pyrosetta.distributed.cluster.core.PyRosettaCluster.timeout

static

Initial value:

= attr.ib(
        type=float,
        default=0.5,
        validator=[_validate_float, attr.validators.instance_of((float, int))],
        converter=attr.converters.default_if_none(default=0.5),
    )

Referenced by pyrosetta.distributed.cluster.core.PyRosettaCluster.distribute().

---

The documentation for this class was generated from the following file:

• src/python/PyRosetta/src/pyrosetta/distributed/cluster/core.py