Python fireworks.LaunchPad类代码示例

    def __init__(self, *args, **kwargs):
        super(OptTask, self).__init__(*args, **kwargs)

        # Configuration attrs
        lp = self.get("launchpad", LaunchPad.auto_load())
        if isinstance(lp, LaunchPad):
            lp = lp.to_dict()
        self.lpad = LaunchPad.from_dict(lp)
        self.opt_label = self.get("opt_label", "opt_default")
        self.c = getattr(self.lpad.db, self.opt_label)
        self.config = self.c.find_one({"doctype": "config"})
        if self.config is None:
            raise NotConfiguredError("Please use MissionControl().configure to "
                                     "configure the optimization database "
                                     "({} - {}) before running OptTask."
                                     "".format(self.lpad.db, self.opt_label))
        self.wf_creator = deserialize(self.config["wf_creator"])
        self.x_dims = self.config["dimensions"]
        self._xdim_types = self.config["dim_types"]
        self.is_discrete_all = self.config["is_discrete_all"]
        self.is_discrete_any = self.config["is_discrete_any"]
        self.wf_creator_args = self.config["wf_creator_args"] or []
        self.wf_creator_kwargs = self.config["wf_creator_kwargs"] or {}
        self.predictor = self.config["predictor"]
        self.predictor_args = self.config["predictor_args"] or []
        self.predictor_kwargs = self.config["predictor_kwargs"] or {}
        self.maximize = self.config["maximize"]
        self.n_search_pts = self.config["n_search_pts"]
        self.n_train_pts = self.config["n_train_pts"]
        self.n_bootstraps = self.config["n_bootstraps"]
        self.acq = self.config["acq"]
        self.space_file = self.config["space_file"]
        self.onehot_categorical = self.config["onehot_categorical"]
        self.duplicate_check = self.config["duplicate_check"]
        self.get_z = self.config["get_z"]
        if self.get_z:
            self.get_z = deserialize(self.config['get_z'])
        else:
            self.get_z = lambda *ars, **kws: []
        self.get_z_args = self.config["get_z_args"] or []
        self.get_z_kwargs = self.config["get_z_kwargs"] or {}
        self.z_file = self.config["z_file"]
        self.enforce_sequential = self.config["enforce_sequential"]
        self.tolerances = self.config["tolerances"]
        self.batch_size = self.config["batch_size"]
        self.timeout = self.config["timeout"]

        # Declared attrs
        self.n_objs = None
        plist = [RandomForestRegressor, GaussianProcessRegressor,
                 ExtraTreesRegressor, GradientBoostingRegressor]
        self.builtin_predictors = {p.__name__: p for p in plist}
        self._n_cats = 0
        self._encoding_info = []

        # Query formats
        self._completed = {'x': {'$exists': 1}, 'y': {'$exists': 1,
                                                      '$ne': 'reserved'},
                           'z': {'$exists': 1}}
        self._manager = {'lock': {'$exists': 1}, 'queue': {'$exists': 1}}

def lp(request):
    lp = LaunchPad(name=TESTDB_NAME, strm_lvl='ERROR')
    lp.reset(password=None, require_password=False)

    def fin():
        lp.connection.drop_database(TESTDB_NAME)

    request.addfinalizer(fin)
    return lp

 def __init__(self, *args, **kwargs):
     '''
     :param args:       (VaspFirework objects) objects to create Workflow from.  No limit
                        on the amount of VaspInputInterface objects to be given.  Entered as just
                        comma separated objects passed to class.
     :param deps_dict:  (dict) specifies the dependency of the VaspInputInterface objects given.  
                        If no dependency is given, Firworks are assumed to be 
                        sequentially dependent.
     :param name        (str) Name given to Workflow
     '''
     self.fws = []
     self.name = kwargs.get('name', 'Sequential WF')
     self.deps_dict = kwargs.get('deps_dict', {})
     self.dependency = {}
     if self.deps_dict:
         for i in self.deps_dict.keys():
             fw_deps = []
             for j in self.deps_dict[i]:
                 fw_deps.append(j.Firework)                    
             self.dependency[i.Firework]=fw_deps
     self.deps = True if self.dependency else False
     for id, fw_task in enumerate(args):
         self.fws.append(fw_task.Firework)
         if not self.deps and id != 0:
             self.dependency[self.fws[id-1]]=[fw_task.Firework]
     self.wf = Workflow(self.fws, self.dependency, name=self.name)
     # Try to establish connection with Launchpad
     try:
         self.LaunchPad=LaunchPad.from_file(os.path.join(os.environ["HOME"], ".fireworks", "my_launchpad.yaml"))
     except:
         self.LaunchPad = None

    def test_get_lp_and_fw_id_from_task(self):
        """
        Tests the get_lp_and_fw_id_from_task. This test relies on the fact that the LaunchPad loaded from auto_load
        will be different from what is defined in TESTDB_NAME. If this is not the case the test will be skipped.
        """
        lp = LaunchPad.auto_load()

        if not lp or lp.db.name == TESTDB_NAME:
            raise unittest.SkipTest("LaunchPad lp {} is not suitable for this test. Should be available and different"
                                    "from {}".format(lp, TESTDB_NAME))

        task = LpTask()
        # this will pass the lp
        fw1 = Firework([task], spec={'_add_launchpad_and_fw_id': True}, fw_id=1)
        # this will not have the lp and should fail
        fw2 = Firework([task], spec={}, fw_id=2, parents=[fw1])
        wf = Workflow([fw1, fw2])
        self.lp.add_wf(wf)

        rapidfire(self.lp, self.fworker, m_dir=MODULE_DIR, nlaunches=1)

        fw = self.lp.get_fw_by_id(1)

        assert fw.state == "COMPLETED"

        rapidfire(self.lp, self.fworker, m_dir=MODULE_DIR, nlaunches=1)

        fw = self.lp.get_fw_by_id(2)

        assert fw.state == "FIZZLED"

def launch():
    descr  = "Smart rocket launcher."\
        "Uses the execution termination emails send by the batch system to "\
        "launch fireworks that depend on other fireworks i.e fireworks that "\
        "have 'cal_objs' in their spec."\
        "Takes in fw_ids of fireworks to be launched. "\
        "Range specification of fw_ids is also supported."\
        "All the jobs are launched to hipergator remotely using fabric."\
        "Note: Ensure that the submit scripts have the appropriate email settings and "\
        "that the mail daemon is fetching emails to the folder polled by this script."\
        "Note: All rocket launches take place in the home directory. If "\
        "_launch_dir spec is set for the firework the job files will be written to "\
        "that folder and jobs to the batch system will be done from there."
    parser = ArgumentParser(description=descr)
    parser.add_argument('-f', '--fw_ids', help='one or more of fw_ids to run', 
                        default=None, type=int, nargs='+')
    parser.add_argument('-r', '--r_fw_ids', 
                        help='start and end fw_ids of the range of fw_ids to run', 
                        default=None, type=int, nargs=2)
    args = parser.parse_args()
    fw_ids = args.fw_ids
    if args.r_fw_ids is not None:
        fw_ids += range(args.r_fw_ids[0], args.r_fw_ids[1])
    job_ids = None
    lp = LaunchPad.from_file(LAUNCHPAD_LOC)
    print('Firework ids: ',fw_ids)
    if fw_ids is None:
        print('No fw ids given')
        return
    for fid in fw_ids:
        m_fw = lp._get_a_fw_to_run(fw_id=fid, checkout=False)
        if m_fw is None:
            print('No firework with that id')
            return
        fw_spec = dict(m_fw.spec)
        done = []
        if fw_spec.get('cal_objs',None) is not None:
            for calparams in fw_spec['cal_objs']:
                if calparams.get('job_ids', None) is not None:
                    job_ids = calparams.get('job_ids', None)
                    print(fid,' depends on jobs with ids : ',job_ids)
                    if job_ids is not None:
                        for jid in job_ids:
                            done.append(check_done(jid))
                    else:
                        print('job_ids not set')
        else:
            print('This firework doesnt depend on any other fireworks.')
            done.append(True)
        if done and all(done):
            print('Launching ', fid, ' ...')
            with settings(host_string='[email protected]'):
                run("ssh dev1 rlaunch singleshot -f "+str(fid))
        else:
            print("Haven't recieved execution termination confirmation for the jobs in the firework from hipergator resource manager")
        time.sleep(3)
    return

 def setUp(self):
     if os.path.exists(self.scratch_dir):
         shutil.rmtree(self.scratch_dir)
     os.makedirs(self.scratch_dir)
     os.chdir(self.scratch_dir)
     try:
         self.lp = LaunchPad.from_file(os.path.join(db_dir, "my_launchpad.yaml"))
         self.lp.reset("", require_password=False)
     except:
         raise unittest.SkipTest(
             'Cannot connect to MongoDB! Is the database server running? '
             'Are the credentials correct?')

def main():
    # set up the LaunchPad and reset it
    launchpad = LaunchPad()
    launchpad.reset('', require_password=False)

    # Build the flow
    nflows = 2
    for i in range(nflows):
        flow = build_flow("flow_" + str(i))
        flow.build_and_pickle_dump()

        # create the Firework consisting of a single task
        firework = Firework(FireTaskWithFlow(flow=flow))

        # store workflow 
        launchpad.add_wf(firework)

    #launch it locally
    #launch_rocket(launchpad)

    return 0

    def setUp(self, lpad=True):
        """
        Create scratch directory(removes the old one if there is one) and change to it.
        Also initialize launchpad.
        """
        if not SETTINGS.get("PMG_VASP_PSP_DIR"):
            SETTINGS["PMG_VASP_PSP_DIR"] = os.path.abspath(os.path.join(MODULE_DIR, "..", "vasp", "test_files"))
            print('This system is not set up to run VASP jobs. '
                  'Please set PMG_VASP_PSP_DIR variable in your ~/.pmgrc.yaml file.')

        self.scratch_dir = os.path.join(MODULE_DIR, "scratch")
        if os.path.exists(self.scratch_dir):
            shutil.rmtree(self.scratch_dir)
        os.makedirs(self.scratch_dir)
        os.chdir(self.scratch_dir)
        if lpad:
            try:
                self.lp = LaunchPad.from_file(os.path.join(DB_DIR, "my_launchpad.yaml"))
                self.lp.reset("", require_password=False)
            except:
                raise unittest.SkipTest('Cannot connect to MongoDB! Is the database server running? '
                                        'Are the credentials correct?')

from fireworks import Firework, Workflow, LaunchPad, ScriptTask
from fireworks.core.rocket_launcher import rapidfire

# set up the LaunchPad and reset it
launchpad = LaunchPad()
launchpad.reset('', require_password=False)

# create the individual FireWorks and Workflow
fw1 = Firework(ScriptTask.from_str('echo "hello"'), name="hello")
fw2 = Firework(ScriptTask.from_str('echo "goodbye"'), name="goodbye", parents=[fw1,])
wf = Workflow([fw1, fw2], name="test workflow")

# store workflow and launch it locally
launchpad.add_wf(wf)
rapidfire(launchpad)

"""
This code is described in the Introductory tutorial, https://materialsproject.github.io/fireworks/introduction.html
"""

from fireworks import Firework, LaunchPad, ScriptTask
from fireworks.core.rocket_launcher import launch_rocket

if __name__ == "__main__":
    # set up the LaunchPad and reset it
    launchpad = LaunchPad()
    # launchpad.reset('', require_password=False)

    # create the Firework consisting of a single task
    firetask = ScriptTask.from_str('echo "howdy, your job launched successfully!"')
    firework = Firework(firetask)

    # store workflow and launch it locally
    launchpad.add_wf(firework)
    launch_rocket(launchpad)

from fireworks.core.firework import FireTaskBase
from fireworks.scripts.rlaunch_run import launch_multiprocess
from fireworks.utilities.fw_utilities import explicit_serialize
from fw_tutorials.firetask.addition_task import AdditionTask

from rocketsled import OptTask, MissionControl
from rocketsled.utils import ExhaustedSpaceError

__author__ = "Alexander Dunn"
__email__ = "[email protected]"

lp_filedir = os.path.dirname(os.path.realpath(__file__))
with open(lp_filedir + '/tests_launchpad.yaml', 'r') as lp_file:
    yaml = YAML()
    lp_dict = dict(yaml.load(lp_file))
    launchpad = LaunchPad.from_dict(lp_dict)
opt_label = "test"
db_info = {"launchpad": launchpad, "opt_label": opt_label}
test_db_name = launchpad.db
common_kwargs = {"predictor": "RandomForestRegressor", "acq": None}


@explicit_serialize
class BasicTestTask(FireTaskBase):
    _fw_name = "BasicTestTask"

    def run_task(self, fw_spec):
        x = fw_spec['_x']
        y = np.sum(x[:-1])  # sum all except the final string element
        return FWAction(update_spec={'_y': y})

               'KPOINTS': [k for k in range(20, 30, 10)]
             }
job_dir = 'calBulk'
job_cmd = ['mpirun', '/home/km468/Software/VASP/vasp.5.3.5/vasp']
qparams= dict(nnodes='1', ppnode='16', 
              job_name='vasp_job', pmem='1000mb',
              walltime='24:00:00',
              rocket_launch=''.join(job_cmd))
# set qadapter to None to launch via qlaunch
# reserve and launch offline
# qlaunch -r singleshot
# lpad recover_offline
qadapter = None #CommonAdapter(q_type="PBS",**qparams)
cal = Calibrate(incar, poscar, potcar, kpoints,
                turn_knobs = turn_knobs,
                qadapter = qadapter,
                job_dir = job_dir, job_cmd=job_cmd)
caltask = MPINTCalibrateTask(cal.as_dict())

#firework with launch directory set to $FW_JOB_DIR, an environment variable
#spec={'_launch_dir':'$FW_JOB_DIR'}, 
fw_calibrate = Firework([caltask], 
                        name="fw_test")
wf = Workflow([fw_calibrate], name="mpint_wf_test")
lp = LaunchPad.from_file(LAUNCHPAD_LOC)
print('fireworks in the database before adding the workflow: \n',
      lp.get_fw_ids())
lp.add_wf(wf)
print('fireworks in the database: \n', lp.get_fw_ids())

objective function is multi-objective. Additionally, the objective function
has dimensions of differing data types (int, float, categorical), which is
automatically handled by rocketsled as long as the dimensions are passed into
MissionControl.configure(...).

Finally, we add some arguments to the MissionControl configuration before
launching.
"""

from fireworks.utilities.fw_utilities import explicit_serialize
from fireworks.core.rocket_launcher import rapidfire
from fireworks import Workflow, Firework, LaunchPad, FireTaskBase, FWAction

from rocketsled import OptTask, MissionControl

launchpad = LaunchPad(name='rsled')
opt_label = "opt_complex"
db_info = {"launchpad": launchpad, "opt_label": opt_label}
x_dim = [(16, 145), (0.0, 90.0),
         ["industry standard", "shark fin", "dolphin fin"]]


@explicit_serialize
class ComplexMultiObjTask(FireTaskBase):
    """
    An example of a complex, multiobjective task with directly competing
    objectives. The input vector is defined on a search space with numerical
    and categorical inputs.

    This task accepts a 3-vector of the form [int, float, str].
    """

"""

# Parameters:
box_scale = 8.9 # edge length of MD box in Angstroms, can also be a numpy array that scales the lattice
packmol_path = "~/packmol/packmol/packmol" # Revise as appropriate
structure = {'H2O':20} # "structure" in this context can be a dict of number of atoms or molecules.
temperature = 320

# Note one can use a pymatgen Structure object also
# E.g. p = Poscar.from_file("POSCAR")
#      structure = p.structure

copy_calcs = True # MD runs can be backed up in a desired location
calc_home = '~/test_H2O_wflows' # This is the location to copy the calculations if copy_calcs=True

# Since we specified a molecule, we must also give the path to xyz
# file of a single sample molecule.
xyz_paths = ['H2O.xyz']
name = 'H2O_df_'+str(temperature)


from mpmorph.workflow.workflows import get_wf_density
from fireworks import LaunchPad

amorphous_maker_params = {'box_scale':box_scale, 'packmol_path':packmol_path, 'xyz_paths': xyz_paths, 'tol': 2.0}

wf = get_wf_density(structure, temperature=temperature, pressure_threshold=0.5, nsteps=1000, wall_time=19200, max_rescales=5,
                    amorphous_maker_params=amorphous_maker_params, copy_calcs=copy_calcs, calc_home=calc_home, name=name)

lp = LaunchPad.auto_load()
lp.add_wf(wf)

@explicit_serialize
class TaskB(FireTaskBase):

    def run_task(self, fw_spec):
        print("This is task B")
        return FWAction(update_spec={"param_B": 20})

@explicit_serialize
class TaskC(FireTaskBase):

    def run_task(self, fw_spec):
        print("This is task C.")
        print("Task A gave me: {}".format(fw_spec["param_A"]))
        print("Task B gave me: {}".format(fw_spec["param_B"]))

if __name__ == "__main__":
    # set up the LaunchPad and reset it
    launchpad = LaunchPad()
    # launchpad.reset('', require_password=False)

    fw_A = Firework([TaskA()])
    fw_B = Firework([TaskB()])
    fw_C = Firework([TaskC()], parents=[fw_A, fw_B])

    # assemble Workflow from FireWorks and their connections by id
    workflow = Workflow([fw_A, fw_B, fw_C])

    # store workflow and launch it locally
    launchpad.add_wf(workflow)
    rapidfire(launchpad)