How to use _restore_vm method in lisa

Best Python code snippet using lisa_python

transformers.py

Source:transformers.py

...105        assert isinstance(node, RemoteNode)106        self._prepare_virtual_machine(node)107        virtual_machine = get_vm(platform, node)108        vhd_location = self._export_vhd(platform, virtual_machine)109        self._restore_vm(platform, virtual_machine, node)110        return {self.__url_name: vhd_location}111    def _prepare_virtual_machine(self, node: RemoteNode) -> None:112        runbook: VhdTransformerSchema = self.runbook113        if not runbook.public_address:114            runbook.public_address = node.public_address115        # prepare vm for exporting116        wa = node.tools[Waagent]117        node.execute("export HISTSIZE=0", shell=True)118        wa.deprovision()119        # stop the vm120        startstop = node.features[StartStop]121        startstop.stop()122    def _export_vhd(self, platform: AzurePlatform, virtual_machine: Any) -> str:123        runbook: VhdTransformerSchema = self.runbook124        compute_client = get_compute_client(platform)125        # generate sas url from os disk, so it can be copied.126        self._log.debug("generating sas url...")127        location = virtual_machine.location128        os_disk_name = virtual_machine.storage_profile.os_disk.name129        operation = compute_client.disks.begin_grant_access(130            resource_group_name=runbook.resource_group_name,131            disk_name=os_disk_name,132            grant_access_data=GrantAccessData(access="Read", duration_in_seconds=86400),133        )134        wait_operation(operation)135        sas_url = operation.result().access_sas136        assert sas_url, "cannot get sas_url from os disk"137        self._log.debug("getting or creating storage account and container...")138        # get vhd container139        if not runbook.storage_account_name:140            runbook.storage_account_name = get_storage_account_name(141                subscription_id=platform.subscription_id, location=location, type="t"142            )143        check_or_create_storage_account(144            credential=platform.credential,145            subscription_id=platform.subscription_id,146            account_name=runbook.storage_account_name,147            resource_group_name=runbook.shared_resource_group_name,148            location=location,149            log=self._log,150        )151        container_client = get_or_create_storage_container(152            credential=platform.credential,153            subscription_id=platform.subscription_id,154            account_name=runbook.storage_account_name,155            container_name=runbook.container_name,156            resource_group_name=runbook.shared_resource_group_name,157        )158        path = _generate_vhd_path(container_client, runbook.file_name_part)159        vhd_path = f"{container_client.url}/{path}"160        blob_client = container_client.get_blob_client(path)161        blob_client.start_copy_from_url(sas_url, metadata=None, incremental_copy=False)162        wait_copy_blob(blob_client, vhd_path, self._log)163        return vhd_path164    def _restore_vm(165        self, platform: AzurePlatform, virtual_machine: Any, node: Node166    ) -> None:167        runbook: VhdTransformerSchema = self.runbook168        self._log.debug("restoring vm...")169        # release the vhd export lock, so it can be started back170        compute_client = get_compute_client(platform)171        os_disk_name = virtual_machine.storage_profile.os_disk.name172        operation = compute_client.disks.begin_revoke_access(173            resource_group_name=runbook.resource_group_name,174            disk_name=os_disk_name,175        )176        wait_operation(operation)177        if runbook.restore:178            start_stop = node.features[StartStop]...

openmm.py

Source:openmm.py

1# SPDX-License-Identifier: MIT2# Copyright (c) 2020-2021: PySAGES contributors3# See LICENSE.md and CONTRIBUTORS.md at https://github.com/SSAGESLabs/PySAGES4from functools import partial5from typing import Callable6from jax import jit, numpy as np7from jax.dlpack import from_dlpack as asarray8from jax.lax import cond9from openmm_dlext import ContextView, DeviceType, Force10from pysages.backends.core import ContextWrapper11from pysages.backends.snapshot import (12    Box,13    HelperMethods,14    Snapshot,15    SnapshotMethods,16    build_data_querier,17    restore as _restore,18    restore_vm as _restore_vm,19)20from pysages.methods import SamplingMethod21from pysages.utils import copy, try_import22import importlib23import jax24import openmm_dlext as dlext25openmm = try_import("openmm", "simtk.openmm")26unit = try_import("openmm.unit", "simtk.unit")27class Sampler:28    def __init__(self, method_bundle, bias, callback: Callable, restore):29        snapshot, initialize, method_update = method_bundle30        self.snapshot = snapshot31        self.state = initialize()32        self._update = method_update33        self._restore = restore34        self.bias = bias35        self.callback = callback36    def update(self, timestep=0):37        self.state = self._update(self.snapshot, self.state)38        self.bias(self.snapshot, self.state)39        if self.callback:40            self.callback(self.snapshot, self.state, timestep)41    def restore(self, prev_snapshot):42        self._restore(self.snapshot, prev_snapshot)43    def take_snapshot(self):44        return copy(self.snapshot)45def is_on_gpu(view: ContextView):46    return view.device_type() == DeviceType.GPU47def take_snapshot(wrapped_context):48    #49    context = wrapped_context.context.context  # extra indirection for OpenMM50    context_view = wrapped_context.view51    #52    positions = asarray(dlext.positions(context_view))53    forces = asarray(dlext.forces(context_view))54    ids = asarray(dlext.atom_ids(context_view))55    #56    velocities = asarray(dlext.velocities(context_view))57    if is_on_gpu(context_view):58        vel_mass = velocities59    else:60        inverse_masses = asarray(dlext.inverse_masses(context_view))61        vel_mass = (velocities, inverse_masses.reshape((-1, 1)))62    #63    box_vectors = context.getSystem().getDefaultPeriodicBoxVectors()64    a = box_vectors[0].value_in_unit(unit.nanometer)65    b = box_vectors[1].value_in_unit(unit.nanometer)66    c = box_vectors[2].value_in_unit(unit.nanometer)67    H = ((a[0], b[0], c[0]), (a[1], b[1], c[1]), (a[2], b[2], c[2]))68    origin = (0.0, 0.0, 0.0)69    dt = context.getIntegrator().getStepSize() / unit.picosecond70    # OpenMM doesn't have images71    return Snapshot(positions, vel_mass, forces, ids, None, Box(H, origin), dt)72def identity(x):73    return x74def safe_divide(v, invm):75    return cond(invm[0] == 0, lambda x: v, lambda x: np.divide(v, x), invm)76def build_snapshot_methods(context, sampling_method):77    if is_on_gpu(context):78        def unpack(vel_mass):79            return vel_mass[:, :3], vel_mass[:, 3:]80        def indices(snapshot):81            return snapshot.ids.argsort()82        def masses(snapshot):83            return snapshot.vel_mass[:, 3:]84    else:85        unpack = identity86        def indices(snapshot):87            return snapshot.ids88        def masses(snapshot):89            _, invM = snapshot.vel_mass90            return jax.vmap(safe_divide)(1, invM)91    def positions(snapshot):92        return snapshot.positions93    def momenta(snapshot):94        V, invM = unpack(snapshot.vel_mass)95        return jax.vmap(safe_divide)(V, invM).flatten()96    return SnapshotMethods(jit(positions), jit(indices), jit(momenta), jit(masses))97def build_helpers(context, sampling_method):98    # Depending on the device being used we need to use either cupy or numpy99    # (or numba) to generate a view of jax's DeviceArrays100    if is_on_gpu(context):101        cupy = importlib.import_module("cupy")102        view = cupy.asarray103        restore_vm = _restore_vm104        def sync_forces():105            cupy.cuda.get_current_stream().synchronize()106        @jit107        def adapt(biases):108            return np.int64(2**32 * biases.T)109    else:110        utils = importlib.import_module(".utils", package="pysages.backends")111        view = utils.view112        adapt = identity113        def sync_forces():114            pass115        def restore_vm(view, snapshot, prev_snapshot):116            # TODO: Check if we can omit modifying the masses117            # (in general the masses are unlikely to change)118            velocities = view(snapshot.vel_mass[0])119            masses = view(snapshot.vel_mass[1])120            velocities[:] = view(prev_snapshot.vel_mass[0])121            masses[:] = view(prev_snapshot.vel_mass[1])122    def bias(snapshot, state, sync_backend):123        """Adds the computed bias to the forces."""124        if state.bias is None:125            return126        biases = adapt(state.bias)127        # Forces may be computed asynchronously on the GPU, so we need to128        # synchronize them before applying the bias.129        sync_backend()130        forces = view(snapshot.forces)131        biases = view(biases.block_until_ready())132        forces += biases133        sync_forces()134    snapshot_methods = build_snapshot_methods(context, sampling_method)135    flags = sampling_method.snapshot_flags136    restore = partial(_restore, view, restore_vm=restore_vm)137    helpers = HelperMethods(build_data_querier(snapshot_methods, flags))138    return helpers, restore, bias139def check_integrator(context):140    integrator = context.getIntegrator()141    if isinstance(integrator, openmm.VariableLangevinIntegrator) or isinstance(142        integrator, openmm.VariableVerletIntegrator143    ):144        raise ValueError("Variable step size integrators are not supported")145def bind(146    wrapped_context: ContextWrapper, sampling_method: SamplingMethod, callback: Callable, **kwargs147):148    # For OpenMM we need to store a Simulation object as the context,149    simulation = wrapped_context.context150    context = simulation.context151    check_integrator(context)152    force = Force()153    force.add_to(context)  # OpenMM will handle the lifetime of the force154    wrapped_context.view = force.view(context)155    wrapped_context.run = simulation.step156    helpers, restore, bias = build_helpers(wrapped_context.view, sampling_method)157    snapshot = take_snapshot(wrapped_context)158    method_bundle = sampling_method.build(snapshot, helpers)159    sync_and_bias = partial(bias, sync_backend=wrapped_context.view.synchronize)160    sampler = Sampler(method_bundle, sync_and_bias, callback, restore)161    force.set_callback_in(context, sampler.update)...

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