modelverse/model/model.py

import sys
import time
import uuid
sys.path.append("kernel/")
sys.path.append("state/")
sys.path.append("interface/HUTN")
from modelverse_state.main import ModelverseState as MvS
from modelverse_kernel.main import ModelverseKernel as MvK
from modelverse_kernel.primitives import SleepKernel
from hutn_compiler.compiler import main as do_compile

from pypdevs.minimal import AtomicDEVS, CoupledDEVS, Simulator

PROFILE = False

import json
import random

random.seed(1)

COMPILER_PATH = "interface/HUTN"

sys.path.append(COMPILER_PATH)
from hutn_compiler.compiler import main as do_compile
import os

def clean_code(code):
    if code == "":
        return code

    code_fragments = code.split("\n")
    code_fragments = [i.rstrip() for i in code_fragments if i.strip() != ""]
    code_fragments = [i.replace("    ", "\t") for i in code_fragments]
    initial_tabs = min([len(i) - len(i.lstrip("\t")) for i in code_fragments])
    code_fragments = [i[initial_tabs:] for i in code_fragments]
    code_fragments.append("")
    code = "\n".join(code_fragments)
    return code.encode('ascii', 'replace')

def compile_model(temp_file):
    compiled = do_compile(temp_file, COMPILER_PATH + "/grammars/modelling.g", "M")
    return ["__LOCAL__"] + compiled

def translate(operation):
    return {
            "CN": "create_node",
            "CE": "create_edge",
            "CNV": "create_nodevalue",
            "CD": "create_dict",
            "RV": "read_value",
            "RO": "read_outgoing",
            "RI": "read_incoming",
            "RE": "read_edge",
            "RD": "read_dict",
            "RDN": "read_dict_node",
            "RDNE": "read_dict_node_edge",
            "RDE": "read_dict_edge",
            "RRD": "read_reverse_dict",
            "RR": "read_root",
            "RDK": "read_dict_keys",
            "DE": "delete_edge",
            "DN": "delete_node",
        }[operation]

class MvSState(object):
    def __init__(self):
        self.queue = []
        self.output = None
        self.mvs = MvS("bootstrap/bootstrap.m.gz")
        self.timer = float("inf")

class ModelverseState(AtomicDEVS):
    def __init__(self, 
                read_root,
                create_node,
                create_edge,
                create_nodevalue,
                create_dict,
                read_value,
                read_outgoing,
                read_incoming,
                read_edge,
                read_dict,
                read_dict_keys,
                read_dict_edge,
                read_dict_node,
                read_dict_node_edge,
                read_reverse_dict,
                delete_node,
                delete_edge):
        AtomicDEVS.__init__(self, "MvS")
        self.timings = {
                "read_root": read_root,
                "create_node": create_node,
                "create_edge": create_edge,
                "create_nodevalue": create_nodevalue,
                "create_dict": create_dict,
                "read_value": read_value,
                "read_outgoing": read_outgoing,
                "read_incoming": read_incoming,
                "read_edge": read_edge,
                "read_dict": read_dict,
                "read_dict_keys": read_dict_keys,
                "read_dict_edge": read_dict_edge,
                "read_dict_node": read_dict_node,
                "read_dict_node_edge": read_dict_node_edge,
                "read_reverse_dict": read_reverse_dict,
                "delete_node": delete_node,
                "delete_edge": delete_edge,
            }

        self.state = MvSState()

        self.from_mvk = self.addInPort("from_MvK")
        self.to_mvk = self.addOutPort("to_MvK")

    def extTransition(self, inputs):
        self.state.timer -= self.elapsed
        empty = len(self.state.queue) == 0
        self.state.queue.extend(inputs[self.from_mvk])
        if empty:
            # First message, so set the timer
            # And already compute the result so it is ready to output
            self.state.output = []
            self.state.timer = 0.0
            for v in self.state.queue[0]:
                f = getattr(self.state.mvs, translate(v[0]))
                start = time.time()
                self.state.output.append(f(*v[1]))
                if PROFILE:
                    print("%s: %.17f" % (translate(v[0]), time.time() - start))
                self.state.timer += self.timings[translate(v[0])]
        else:
            # Just append the message to process
            pass
        return self.state

    def outputFnc(self):
        return {self.to_mvk: [self.state.output]}

    def intTransition(self):
        self.state.queue.pop(0)
        self.state.output = []
        if len(self.state.queue) > 0:
            self.state.timer = 0.0
            # Value contains a list of operations to do
            # So do them and calculate how long it takes
            for v in self.state.queue[0]:
                f = getattr(self.state.mvs, translate(v[0]))
                start = time.time()
                self.state.output.append(f(*v[1]))
                if PROFILE:
                    print("%s: %.17f" % (translate(v[0]), time.time() - start))
                self.state.timer += self.timings[translate(v[0])]
        else:
            self.state.timer = float("inf")

        return self.state

    def timeAdvance(self):
        return self.state.timer

class MvKState(object):
    def __init__(self, rule_generation):
        self.mvk = None
        self.waiting = False
        self.inputs = {}
        self.outputs = {}
        self.tasks = []
        self.reply = None
        self.phase = None
        self.commands = None
        self.root = None
        self.current_task = None
        self.loaded_primitives = False
        self.execution_counter = 0
        self.rule_generation = rule_generation
        self.current_time = 0.0
        self.start_task_time = 0.0

    def __str__(self):
        return "\nMvK: %s\n" % self.mvk + \
                "waiting: %s\n" % self.waiting + \
                "inputs: %s\n" % self.inputs + \
                "outputs: %s\n" % self.outputs + \
                "tasks: %s\n" % self.tasks + \
                "reply: %s\n" % self.reply + \
                "phase: %s\n" % self.phase + \
                "commands: %s\n" % self.commands + \
                "root: %s\n" % self.root + \
                "current task: %s\n" % self.current_task + \
                "execution counter: %s\n"

class ModelverseKernel(AtomicDEVS):
    def __init__(self, time_per_phase, rule_generation):
        AtomicDEVS.__init__(self, "MvK")
        self.state = MvKState(rule_generation)

        self.from_mvi = self.addInPort("from_MvI")
        self.from_mvs = self.addInPort("from_MvS")
        self.to_mvi = self.addOutPort("to_MvI")
        self.to_mvs = self.addOutPort("to_MvS")

        self.time_per_phase = time_per_phase

    def extTransition(self, inputs):
        self.state.current_time += self.elapsed
        if self.from_mvi in inputs:
            # Got input from MvI, so we queue it
            for inp in inputs[self.from_mvi]:
                taskname = inp[0]
                data = inp[1]
                if data is not None:
                    self.state.inputs.setdefault(taskname, []).extend(data)
                else:
                    self.state.outputs.setdefault(taskname, []).append(None)

        if self.from_mvs in inputs:
            # Got input from MvS, so we can continue processing
            #print(" --> " + str(inputs[self.from_mvs]))
            for mvs_input in inputs[self.from_mvs]:
                if self.state.mvk is None:
                    # No MvK, so set it with the root we have just received (or should have received)
                    self.state.root = mvs_input[0]
                    self.state.mvk = MvK(self.state.root)
                else:
                    self.state.reply = mvs_input
            self.state.waiting = False

        return self.state

    def intTransition(self):
        self.state.current_time += self.timeAdvance()
        was_empty = len(self.state.tasks) == 0
        if self.state.commands is not None:
            self.state.commands = None
            return self.state

        if self.state.mvk is not None:
            self.state.mvk.returnvalue = None

        if self.state.mvk is None:
            # Initializing
            self.state.waiting = True
        elif not self.state.loaded_primitives:
            commands = self.state.mvk.execute_yields("", "load_primitives", [], self.state.reply)
            if commands is None:
                self.state.loaded_primitives = True
                self.state.reply = None
            else:
                self.state.waiting = True
            self.state.commands = commands
        else:
            # Are initialized and have work to do
            if len(self.state.tasks) == 0:
                # Read out new set of tasks first
                if self.state.reply is None:
                    commands = [("RDK", [self.state.root])]
                else:
                    self.state.tasks = self.state.reply[0]
                    commands = None
            elif self.state.phase == "init_task":
                if self.state.reply is None:
                    commands = [("RV", [self.state.tasks[0]])]
                else:
                    self.state.current_task = self.state.reply[0]
                    #print("Processing task %s at time %s" % (self.state.current_task, self.time_last))
                    self.state.start_task_time = self.state.current_time
                    if self.state.current_task.startswith("__"):
                        # Don't process this task and force termination of task
                        self.state.phase = "output"
                    commands = None
            elif self.state.phase == "input":
                # Process inputs
                if self.state.inputs.get(self.state.current_task, None):
                    value = self.state.inputs[self.state.current_task][0]
                    start = time.time()
                    commands = self.state.mvk.execute_yields(self.state.current_task, "set_input", [value], self.state.reply)
                    if PROFILE:
                        print("rule_generation: %.17f" % ((time.time() - start)))
                    #self.state.rule_generation = time.time() - start
                    self.state.mvk.returnvalue = None
                    if commands is None:
                        self.state.inputs[self.state.current_task].pop(0)
                else:
                    commands = None

            elif self.state.phase == "computation":
                try:
                    start = time.time()
                    commands = self.state.mvk.execute_yields(self.state.current_task, "execute_rule", [], self.state.reply)
                    if PROFILE:
                        print("rule_generation: %.17f" % ((time.time() - start)))
                    #self.state.rule_generation = time.time() - start
                except SleepKernel:
                    commands = None
                    self.state.mvk.success = False
                else:
                    self.state.mvk.success = True
            elif self.state.phase == "output":
                start = time.time()
                commands = self.state.mvk.execute_yields(self.state.current_task, "get_output", [], self.state.reply)
                if PROFILE:
                    print("rule_generation: %.17f" % ((time.time() - start)))
                #self.state.rule_generation = time.time() - start
            else:
                raise Exception("Phase: " + str(self.state.phase))

            # Advance phase
            if commands is None:
                if was_empty:
                    self.state.phase = "init_task"
                elif self.state.phase == "init_task":
                    self.state.phase = "input"
                elif self.state.phase == "input":
                    self.state.phase = "computation"
                elif self.state.phase == "computation":
                    if not self.state.mvk.success or (self.state.current_time - self.state.start_task_time > self.time_per_phase):
                        self.state.phase = "output"
                elif self.state.phase == "output":
                    self.state.tasks.pop(0)
                    self.state.phase = "init_task"
                self.state.waiting = False
                self.state.reply = None
            else:
                self.state.waiting = True

            # Send the commands to the MvS
            self.state.commands = commands
            #print(" <-- " + str(commands))
        return self.state

    def outputFnc(self):
        outputs = {}
        if self.state.mvk is None:
            # Ask the root first
            outputs[self.to_mvs] = [[("RR", [])]]
        elif self.state.waiting:
            outputs[self.to_mvs] = [self.state.commands]

        if self.state.mvk and self.state.mvk.returnvalue is not None:
            outputs[self.to_mvi] = [(self.state.current_task, self.state.mvk.returnvalue)]

        return outputs

    def timeAdvance(self):
        if self.state.commands is not None:
            return self.state.rule_generation
        elif self.state.waiting:
            return float("inf")
        elif self.state.mvk is None:  
            return 0
        else:
            return 0

class MvIState():
    def __init__(self):
        self.operations = []
        self.additional_operations = []
        self.keyed_operations = {}
        self.task_to_spawner = {}
        self.task_to_operation = {}
        self.output = {}
        self.blocked = True
        self.finished = False
        self.send_operations = {}

class ModelverseInterface(AtomicDEVS):
    def __init__(self, taskname, operations, finish_on, additional_operations=[], keyed_operations={}):
        AtomicDEVS.__init__(self, "MvI_%s" % taskname)
        self.state = MvIState()
        if taskname == "task_manager":
            self.state.blocked = False
        self.state.operations = operations
        self.state.additional_operations = additional_operations
        self.state.keyed_operations = keyed_operations
        self.state.create_additional_task = []
        self.taskname = taskname
        self.finish_on = finish_on

        self.to_mvk = self.addOutPort("to_MvK")
        self.from_mvk = self.addInPort("from_MvK")

    def intTransition(self):
        self.state.create_additional_task = []
        if not self.state.send_operations:
            self.state.operations.pop(0)
        else:
            for k in self.state.send_operations.keys():
                if self.state.send_operations[k]:
                    self.state.send_operations[k].pop(0)

                    if not self.state.send_operations[k]:
                        del self.state.send_operations[k]

                        # At the end of these operations, so finish up!
                        if self.state.task_to_spawner[k] is not None:
                            self.state.keyed_operations.pop(self.state.task_to_operation[self.state.task_to_spawner[k]])
                            self.state.additional_operations.insert(0, [])
                            self.state.send_operations[self.state.task_to_spawner[k]] = ["__continue__"]
                        else:
                            self.state.additional_operations.pop(0)
                            self.state.operations.pop(0)
                            print("Clear up to the normal task!")

        self.state.blocked = True
        return self.state

    def extTransition(self, inputs):
        for inp in inputs[self.from_mvk]:
            print("Got input: " + str(inp))
            self.state.blocked = False

            self.state.output.setdefault(inp[0], []).append(inp[1])
            if inp[0] == self.taskname and inp[1] == self.finish_on:
                self.state.finished = True
            elif inp[0] == self.taskname and self.state.operations[0] is None:
                # We have to block for now, and modify a model first...
                print("Blocking for now...")
                prev_output = self.state.output[inp[0]][-1]
                if prev_output.startswith("Please edit this model before sending next input: "):
                    _, model_name = prev_output.split("Please edit this model before sending next input: ", 1)
                    new_taskname = str(uuid.uuid4())
                    self.state.send_operations[new_taskname] = [[], ["admin"], ["admin"], ["quiet"], ["model_modify", model_name, ""]] + self.state.additional_operations[0] + [["exit"]]
                    print("Modifying model " + str(model_name))
                    print("On taskname " + str(new_taskname))
                    self.state.create_additional_task.append(new_taskname)
                    self.state.task_to_operation[new_taskname] = None
                    self.state.task_to_spawner[new_taskname] = None
                elif prev_output.startswith("Spawned activity on task: "):
                    print("Spawned activity")
                    _, task_name = prev_output.split("Spawned activity on task: ", 1)
                    self.state.blocked = True
                    self.state.task_to_spawner[task_name] = None
                    # NOTE We now know that there is something to do on an other task, so we just wait for that event to come in
                    self.state.operations.insert(0, [])
                    self.state.operations.insert(0, [])
                elif prev_output.startswith("Finished task: "):
                    self.state.blocked = True
                else:
                    print("UNKNOWN: " + str(prev_output))

            elif inp[0] != self.taskname:
                # Got some output on another task
                if inp[1].startswith("Please edit this model before sending next input: "):
                    _, model_name = inp[1].split("Please edit this model before sending next input: ", 1)
                    new_taskname = str(uuid.uuid4())
                    self.state.send_operations[new_taskname] = [[], ["admin"], ["admin"], ["quiet"], ["model_modify", model_name, ""]] + self.state.keyed_operations[self.state.task_to_operation[inp[0]]] + [["exit"]]
                    print("Modifying model " + str(model_name))
                    print("On taskname " + str(new_taskname))
                    self.state.create_additional_task.append(new_taskname)
                    self.state.task_to_spawner[new_taskname] = inp[0]
                elif inp[1].startswith("Please perform manual operation "):
                    _, op_name = inp[1].split("Please perform manual operation ", 1)
                    self.state.task_to_operation[inp[0]] = op_name[1:-1]
                elif inp[1].startswith("Success: ready for "):
                    pass

        return self.state

    def outputFnc(self):
        if self.state.send_operations:
            outp = []
            if self.state.create_additional_task:
                outp.append(('task_manager', self.state.create_additional_task))
            for k, v in self.state.send_operations.items():
                outp.append((k, v[0]))
            print("REQUEST special: " + str(outp))
            return {self.to_mvk: outp}
        elif self.state.operations:
            print("REQUEST: " + str(self.state.operations[0]))
            return {self.to_mvk: [(self.taskname, self.state.operations[0])]}
        else:
            return {}

    def timeAdvance(self):
        if self.state.blocked:
            return float("inf")
        else:
            return 0.0

class NetworkState(object):
    def __init__(self):
        self.processing = []
        self.timer = float("inf")

class Network(AtomicDEVS):  
    def __init__(self, name, latency, bandwidth):
        AtomicDEVS.__init__(self, name)
        self.state = NetworkState()

        self.input_port = self.addInPort("input_port")
        self.output_port = self.addOutPort("output_port")

        self.latency = latency
        self.bandwidth = bandwidth

    def intTransition(self):
        self.state.processing.pop(0)
        if self.state.processing:
            self.state.timer = (len(self.state.processing[0]) * 8 / float(self.bandwidth) + self.latency)
        else:
            self.state.timer = float("inf")
        return self.state

    def extTransition(self, inputs):
        self.state.timer -= self.elapsed
        if self.state.timer == float("inf"):
            self.state.timer = 0
        for v in inputs[self.input_port]:
            self.state.processing.append(json.dumps(v))
            # NOTE data is in bytes, while bandwidth is in bits, so multiply by 8
        if len(self.state.processing) > 0:
            self.state.timer = (len(self.state.processing[0]) * 8 / float(self.bandwidth) + self.latency)
        return self.state

    def outputFnc(self):
        return {self.output_port: [json.loads(self.state.processing[0])]}

    def timeAdvance(self):
        #print("Timer: " + str(self.state.timer))
        return self.state.timer

class System(CoupledDEVS):
    def __init__(self,
                taskname,
                operations,
                mvi_additional,
                mvi_keyed,
                finish_on,
                rule_generation,
                time_per_phase,
                mvi2mvk_latency,
                mvi2mvk_bandwidth,
                mvk2mvs_latency,
                mvk2mvs_bandwidth,
                mvs2mvk_latency,
                mvs2mvk_bandwidth,
                mvk2mvi_latency,
                mvk2mvi_bandwidth,
                read_root,
                create_node,
                create_edge,
                create_nodevalue,
                create_dict,
                read_value,
                read_outgoing,
                read_incoming,
                read_edge,
                read_dict,
                read_dict_keys,
                read_dict_edge,
                read_dict_node,
                read_dict_node_edge,
                read_reverse_dict,
                delete_node,
                delete_edge):
        CoupledDEVS.__init__(self, "System")

        self.mvi_manager = self.addSubModel(ModelverseInterface(\
                            taskname            = "task_manager",
                            operations          = [[taskname]],
                            finish_on           = None,
                        ))
        self.mvi = self.addSubModel(ModelverseInterface(\
                            taskname            = taskname,
                            operations          = operations,
                            finish_on           = finish_on,
                            additional_operations = mvi_additional,
                            keyed_operations    = mvi_keyed,
                        ))
        self.mvk = self.addSubModel(ModelverseKernel(\
                            time_per_phase     = time_per_phase,
                            rule_generation     = rule_generation,
                        ))
        self.mvs = self.addSubModel(ModelverseState(\
                            read_root           = read_root,
                            create_node         = create_node,
                            create_edge         = create_edge,
                            create_nodevalue    = create_nodevalue,
                            create_dict         = create_dict,
                            read_value          = read_value,
                            read_outgoing       = read_outgoing,
                            read_incoming       = read_incoming,
                            read_edge           = read_edge,
                            read_dict           = read_dict,
                            read_dict_keys      = read_dict_keys,
                            read_dict_edge      = read_dict_edge,
                            read_dict_node      = read_dict_node,
                            read_dict_node_edge = read_dict_node_edge,
                            read_reverse_dict   = read_reverse_dict,
                            delete_node         = delete_node,
                            delete_edge         = delete_edge,
                        ))
        self.mvi2mvk = self.addSubModel(Network(\
                            name        = "mvi2mvk",
                            latency     = mvi2mvk_latency,
                            bandwidth   = mvi2mvk_bandwidth,
                        ))
        self.mvk2mvs = self.addSubModel(Network(\
                            name        = "mvk2mvs",
                            latency     = mvk2mvs_latency,
                            bandwidth   = mvk2mvs_bandwidth,
                        ))
        self.mvs2mvk = self.addSubModel(Network(\
                            name        = "mvs2mvk",
                            latency     = mvs2mvk_latency,
                            bandwidth   = mvs2mvk_bandwidth,
                        ))
        self.mvk2mvi = self.addSubModel(Network(\
                            name        = "mvk2mvi",
                            latency     = mvk2mvi_latency,
                            bandwidth   = mvk2mvi_bandwidth,
                        ))

        self.connectPorts(self.mvi_manager.to_mvk, self.mvk.from_mvi)
        self.connectPorts(self.mvi.to_mvk, self.mvi2mvk.input_port)
        self.connectPorts(self.mvi2mvk.output_port, self.mvk.from_mvi)
        self.connectPorts(self.mvk.to_mvs, self.mvk2mvs.input_port)
        self.connectPorts(self.mvk2mvs.output_port, self.mvs.from_mvk)
        self.connectPorts(self.mvs.to_mvk, self.mvs2mvk.input_port)
        self.connectPorts(self.mvs2mvk.output_port, self.mvk.from_mvs)
        self.connectPorts(self.mvk.to_mvi, self.mvk2mvi.input_port)
        self.connectPorts(self.mvk2mvi.output_port, self.mvi.from_mvk)

taskname = "test_task"

operations = json.loads(open("model/operations", 'r').read())
#operations = json.loads(open("model/operations_simple", 'r').read())
additional_operations = [[], # revise_req
                         [], # revise_environment
                         [], # revise_plant
                         [], # revise_control
                         [], # revise_query
                         [], # revise_architecture
                         [], # make_initial_models
                         [["instantiate_edge", "Association", "PLANT2EPN_link", "PW_Plant/State", "Encapsulated_PetriNet/Place"], ["instantiate_edge", "Association", "PLANT2EPN_tlink", "PW_Plant/Transition", "Encapsulated_PetriNet/Transition"]], # plant_to_EPN
                         [["instantiate_edge", "Association", "CTRL2EPN_link", "PW_Control/State", "Encapsulated_PetriNet/Place"], ["instantiate_edge", "Association", "CTRL2EPN_tlink", "PW_Control/Transition", "Encapsulated_PetriNet/Transition"]], # control_to_EPN
                         [["instantiate_edge", "Association", "ENV2EPN_link", "PW_Environment/Event", "Encapsulated_PetriNet/Place"]], # environment_to_EPN
                         [["instantiate_edge", "Association", "EPN2PN_place_link", "Encapsulated_PetriNet/Place", "PetriNet/Place"], ["instantiate_edge", "Association", "EPN2PN_transition_link", "Encapsulated_PetriNet/Transition", "PetriNet/Transition"]], # EPN_to_PN
                         [], # match
                         [], # reachability
                         [], # bfs
                         [], # merge
                        ]

#additional_operations = [[]]
keyed_operations = {"models/revise_req": [["model_overwrite"] + compile_model("models/requirements_model.mvc")],
                    "models/revise_plant": [["model_overwrite"] + compile_model("models/plant_model.mvc")],
                    "models/revise_environment": [["model_overwrite"] + compile_model("models/environment_model.mvc")],
                    "models/revise_control": [["model_overwrite"] + compile_model("models/control_model.mvc")],
                    "models/revise_query": [["model_overwrite"] + compile_model("models/query_model.mvc")],
                    "models/revise_architecture": [["model_overwrite"] + compile_model("models/architecture_model.mvc")],
                    }
#keyed_operations = {"models/modify_lang": [["instantiate_node", "PN/Class", ""]]}
finish_on = "FINISHED"

args = {
        "taskname":             taskname,
        "operations":           operations,
        "finish_on":            finish_on,
        "mvi_additional":       additional_operations,
        "mvi_keyed":            keyed_operations,
        "mvi2mvk_latency":      0.0000001,
        "mvi2mvk_bandwidth":    50000000000,
        "mvk2mvs_latency":      0.0000001,
        "mvk2mvs_bandwidth":    50000000000,
        "mvs2mvk_latency":      0.0000001,
        "mvs2mvk_bandwidth":    50000000000,
        "mvk2mvi_latency":      0.0000001,
        "mvk2mvi_bandwidth":    50000000000,
        "time_per_phase":       0.05,
        # Automatically filled in from calibration results, just here to prevent crashes (results for my UA desktop)
        "read_root":            0.00001406669616699,
        "create_node":          0.00000379181167487,
        "create_edge":          0.00000601282282066,
        "create_nodevalue":     0.00000501364247391,
        "create_dict":          0.00001028065706205,
        "read_value":           0.00000388661630500,
        "read_outgoing":        0.00000520600098073,
        "read_incoming":        0.00000645903181994,
        "read_edge":            0.00000449162172644,
        "read_dict":            0.00000460127038355,
        "read_dict_keys":       0.00001678063432883,
        "read_dict_node":       0.00001020808859528,
        "read_dict_edge":       0.00000642558526942,
        "read_dict_node_edge":  0.0,
        "read_reverse_dict":    0.00002557890755790,
        "delete_node":          0.00004755891187096,
        "delete_edge":          0.00000683382081240,
        "rule_generation":      0.00001543215873893,
    }

with open("calibration/averages", 'r') as param_file:
    for l in param_file:
        op, t = l.split(": ")
        op = op.strip()
        args[op] = float(t)

model = System(**args)
sim = Simulator(model)
sim.setTerminationCondition(lambda t, m: m.mvi.state.finished)
#sim.setVerbose()
tn = sim.simulate()

print("Simulation finished at time %s" % tn)