Source code for

"""Define the Group class."""
from __future__ import division

import os
from collections import Counter, OrderedDict, defaultdict

# note: this is a Python 3.3 change, clean this up for OpenMDAO 3.x
    from import Iterable
except ImportError:
    from collections import Iterable

from itertools import product, chain
from numbers import Number
import inspect
from fnmatch import fnmatchcase
import copy

from six import iteritems, string_types, itervalues
from six.moves import range

import numpy as np
import networkx as nx

from openmdao.jacobians.dictionary_jacobian import DictionaryJacobian
from openmdao.approximation_schemes.complex_step import ComplexStep
from openmdao.approximation_schemes.finite_difference import FiniteDifference
from openmdao.core.system import System, INT_DTYPE
from openmdao.core.component import Component, _DictValues, _full_slice
from openmdao.proc_allocators.default_allocator import DefaultAllocator, ProcAllocationError
from openmdao.jacobians.jacobian import SUBJAC_META_DEFAULTS
from openmdao.recorders.recording_iteration_stack import Recording
from openmdao.solvers.nonlinear.nonlinear_runonce import NonlinearRunOnce
from openmdao.solvers.linear.linear_runonce import LinearRunOnce
from openmdao.utils.array_utils import convert_neg, array_connection_compatible, \
from openmdao.utils.general_utils import warn_deprecation, ContainsAll, all_ancestors, \
from openmdao.utils.units import is_compatible, get_conversion
from openmdao.utils.mpi import MPI
from openmdao.utils.coloring import Coloring, _STD_COLORING_FNAME
import openmdao.utils.coloring as coloring_mod

# regex to check for valid names.
import re
namecheck_rgx = re.compile('[a-zA-Z][_a-zA-Z0-9]*')

[docs]class Group(System): """ Class used to group systems together; instantiate or inherit. Attributes ---------- _mpi_proc_allocator : ProcAllocator Object used to allocate MPI processes to subsystems. _proc_info : dict of subsys_name: (min_procs, max_procs, weight) Information used to determine MPI process allocation to subsystems. _local_system_set : set or None Set of pathnames of all fully local (not remote or distributed) direct or indirect subsystems. _subgroups_myproc : list List of local subgroups. _manual_connections : dict Dictionary of input_name: (output_name, src_indices) connections. _static_manual_connections : dict Dictionary that stores all explicit connections added outside of setup. _conn_abs_in2out : {'abs_in': 'abs_out'} Dictionary containing all explicit & implicit connections owned by this system only. The data is the same across all processors. _conn_discrete_in2out : {'abs_in': 'abs_out'} Dictionary containing all explicit & implicit discrete var connections owned by this system only. The data is the same across all processors. _transfers : dict of dict of Transfers First key is the vec_name, second key is (mode, isub) where mode is 'fwd' or 'rev' and isub is the subsystem index among allprocs subsystems or isub can be None for the full, simultaneous transfer. _discrete_transfers : dict of discrete transfer metadata Key is system pathname or None for the full, simultaneous transfer. _loc_subsys_map : dict Mapping of local subsystem names to their corresponding System. _approx_subjac_keys : list List of subjacobian keys used for approximated derivatives. _setup_procs_finished : bool Flag to check if setup_procs is complete _has_distrib_vars : bool If True, this Group contains distributed variables. """
[docs] def __init__(self, **kwargs): """ Set the solvers to nonlinear and linear block Gauss--Seidel by default. Parameters ---------- **kwargs : dict dict of arguments available here and in all descendants of this Group. """ self._mpi_proc_allocator = DefaultAllocator() self._proc_info = {} super(Group, self).__init__(**kwargs) self._local_system_set = None self._subgroups_myproc = None self._manual_connections = {} self._static_manual_connections = {} self._conn_abs_in2out = {} self._conn_discrete_in2out = {} self._transfers = {} self._discrete_transfers = {} self._approx_subjac_keys = None self._setup_procs_finished = False self._has_distrib_vars = False # TODO: we cannot set the solvers with property setters at the moment # because our lint check thinks that we are defining new attributes # called nonlinear_solver and linear_solver without documenting them. if not self._nonlinear_solver: self._nonlinear_solver = NonlinearRunOnce() if not self._linear_solver: self._linear_solver = LinearRunOnce()
[docs] def setup(self): """ Build this group. This method should be overidden by your Group's method. The reason for using this method to add subsystem is to save memory and setup time when using your Group while running under MPI. This avoids the creation of systems that will not be used in the current process. You may call 'add_subsystem' to add systems to this group. You may also issue connections, and set the linear and nonlinear solvers for this group level. You cannot safely change anything on children systems; use the 'configure' method instead. Available attributes: name pathname comm options """ pass
[docs] def configure(self): """ Configure this group to assign children settings. This method may optionally be overidden by your Group's method. You may only use this method to change settings on your children subsystems. This includes setting solvers in cases where you want to override the defaults. You can assume that the full hierarchy below your level has been instantiated and has already called its own configure methods. Available attributes: name pathname comm options system hieararchy with attribute access """ pass
def _get_scope(self, excl_sub=None): """ Find the input and output variables that are needed for a particular matvec product. Parameters ---------- excl_sub : <System> A subsystem whose variables should be excluded from the matvec product. Returns ------- (set, set) Sets of output and input variables. """ try: return self._scope_cache[excl_sub] except KeyError: pass if excl_sub is None: # All outputs scope_out = frozenset(self._var_allprocs_abs_names['output']) # All inputs connected to an output in this system scope_in = frozenset(self._conn_global_abs_in2out).intersection( self._var_allprocs_abs_names['input']) else: # Empty for the excl_sub scope_out = frozenset() # All inputs connected to an output in this system but not in excl_sub scope_in = set() for abs_in in self._var_allprocs_abs_names['input']: if abs_in in self._conn_global_abs_in2out: abs_out = self._conn_global_abs_in2out[abs_in] if abs_out not in excl_sub._var_allprocs_abs2idx['linear']: scope_in.add(abs_in) scope_in = frozenset(scope_in) self._scope_cache[excl_sub] = (scope_out, scope_in) return scope_out, scope_in def _compute_root_scale_factors(self): """ Compute scale factors for all variables. Returns ------- dict Mapping of each absolute var name to its corresponding scaling factor tuple. """ scale_factors = super(Group, self)._compute_root_scale_factors() if self._has_input_scaling: abs2meta_in = self._var_abs2meta allprocs_meta_out = self._var_allprocs_abs2meta for abs_in, abs_out in iteritems(self._conn_global_abs_in2out): if abs_in not in abs2meta_in: # we only perform scaling on local, non-discrete arrays, so skip continue meta_in = abs2meta_in[abs_in] meta_out = allprocs_meta_out[abs_out] ref = meta_out['ref'] ref0 = meta_out['ref0'] src_indices = meta_in['src_indices'] if src_indices is not None: if not (np.isscalar(ref) and np.isscalar(ref0)): # TODO: if either ref or ref0 are not scalar and the output is # distributed, we need to do a scatter # to obtain the values needed due to global src_indices if meta_out['distributed']: raise RuntimeError("{}: vector scalers with distrib vars " "not supported yet.".format(self.msginfo)) if src_indices.ndim != 1: src_indices = _flatten_src_indices(src_indices, meta_in['shape'], meta_out['global_shape'], meta_out['global_size']) ref = ref[src_indices] ref0 = ref0[src_indices] # Compute scaling arrays for inputs using a0 and a1 # Example: # Let x, x_src, x_tgt be the dimensionless variable, # variable in source units, and variable in target units, resp. # x_src = a0 + a1 x # x_tgt = b0 + b1 x # x_tgt = g(x_src) = d0 + d1 x_src # b0 + b1 x = d0 + d1 a0 + d1 a1 x # b0 = d0 + d1 a0 # b0 = g(a0) # b1 = d0 + d1 a1 - d0 # b1 = g(a1) - g(0) units_in = meta_in['units'] units_out = meta_out['units'] if units_in is None or units_out is None or units_in == units_out: a0 = ref0 a1 = ref - ref0 else: factor, offset = get_conversion(units_out, units_in) a0 = (ref0 + offset) * factor a1 = (ref - ref0) * factor scale_factors[abs_in] = { ('input', 'phys'): (a0, a1), ('input', 'norm'): (-a0 / a1, 1.0 / a1) } return scale_factors def _configure(self): """ Configure our model recursively to assign any children settings. Highest system's settings take precedence. """ for subsys in self._subsystems_myproc: subsys._configure() if subsys._has_guess: self._has_guess = True if subsys._has_bounds: self._has_bounds = True if subsys.matrix_free: self.matrix_free = True self.configure() def _setup_procs(self, pathname, comm, mode, prob_options): """ Execute first phase of the setup process. Distribute processors, assign pathnames, and call setup on the group. This method recurses downward through the model. Parameters ---------- pathname : str Global name of the system, including the path. comm : MPI.Comm or <FakeComm> MPI communicator object. mode : string Derivatives calculation mode, 'fwd' for forward, and 'rev' for reverse (adjoint). Default is 'rev'. prob_options : OptionsDictionary Problem level options. """ self.pathname = pathname self._problem_options = prob_options self.options._parent_name = self.msginfo self.recording_options._parent_name = self.msginfo self._setup_procs_finished = False if self._num_par_fd > 1: info = self._coloring_info if comm.size > 1: # if approx_totals has been declared, or there is an approx coloring, setup par FD if self._owns_approx_jac or info['dynamic'] or info['static'] is not None: comm = self._setup_par_fd_procs(comm) else: msg = "%s: num_par_fd = %d but FD is not active." % (self.msginfo, self._num_par_fd) raise RuntimeError(msg) elif not MPI: msg = ("%s: MPI is not active but num_par_fd = %d. No parallel finite difference " "will be performed." % (self.msginfo, self._num_par_fd)) simple_warning(msg) self.comm = comm self._mode = mode self._subsystems_allprocs = [] self._manual_connections = {} self._design_vars = OrderedDict() self._responses = OrderedDict() self._first_call_to_linearize = True self._approx_subjac_keys = None self._static_mode = False self._subsystems_allprocs.extend(self._static_subsystems_allprocs) self._manual_connections.update(self._static_manual_connections) self._design_vars.update(self._static_design_vars) self._responses.update(self._static_responses) # Call setup function for this group. self.setup() self._static_mode = True if MPI: proc_info = [self._proc_info[] for s in self._subsystems_allprocs] # Call the load balancing algorithm try: sub_inds, sub_comm, sub_proc_range = self._mpi_proc_allocator( proc_info, len(self._subsystems_allprocs), comm) except ProcAllocationError as err: subs = self._subsystems_allprocs if err.sub_inds is None: raise RuntimeError("%s: %s" % (self.msginfo, err.msg)) else: raise RuntimeError("%s: MPI process allocation failed: %s for the following " "subsystems: %s" % (self.msginfo, err.msg, [subs[i].name for i in err.sub_inds])) self._subsystems_myproc = [self._subsystems_allprocs[ind] for ind in sub_inds] # Define local subsystems if not (np.sum([minp for minp, _, _ in proc_info]) <= comm.size): # reorder the subsystems_allprocs based on which procs they live on. If we don't # do this, we can get ordering mismatches in some of our data structures. new_allsubs = [] seen = set() gathered = self.comm.allgather(sub_inds) for rank, inds in enumerate(gathered): for ind in inds: if ind not in seen: new_allsubs.append(self._subsystems_allprocs[ind]) seen.add(ind) self._subsystems_allprocs = new_allsubs else: sub_comm = comm self._subsystems_myproc = self._subsystems_allprocs sub_proc_range = (0, 1) # Compute _subsystems_proc_range self._subsystems_proc_range = [sub_proc_range] * len(self._subsystems_myproc) self._subsystems_inds = inds = {} # need to set pathname correctly even for non-local subsystems for i, s in enumerate(self._subsystems_allprocs): inds[] = i s.pathname = '.'.join((self.pathname, if self.pathname else self._local_system_set = set() # Perform recursion for subsys in self._subsystems_myproc: subsys._local_vector_class = self._local_vector_class subsys._distributed_vector_class = self._distributed_vector_class subsys.force_alloc_complex = self.force_alloc_complex subsys._use_derivatives = self._use_derivatives subsys._solver_info = self._solver_info subsys._recording_iter = self._recording_iter subsys._setup_procs(subsys.pathname, sub_comm, mode, prob_options) # build a list of local subgroups to speed up later loops self._subgroups_myproc = [s for s in self._subsystems_myproc if isinstance(s, Group)] self._loc_subsys_map = { s for s in self._subsystems_myproc} self._setup_procs_finished = True def _post_configure(self): """ Do any remaining setup that had to wait until after final user configuration. """ for subsys in self._subsystems_myproc: subsys._post_configure() super(Group, self)._post_configure() def _check_child_reconf(self, subsys=None): """ Check if any subsystem has reconfigured and if so, perform the necessary update setup. Parameters ---------- subsys : System or None If not None, check only if the given subsystem has reconfigured. """ if subsys is None: # See if any local subsystem has reconfigured for subsys in self._subgroups_myproc: if subsys._reconfigured: reconf = 1 break else: reconf = 0 else: reconf = int(subsys._reconfigured) if in self._loc_subsys_map else 0 # See if any subsystem on this or any other processor has configured if self.comm.size > 1: reconf = self.comm.allreduce(reconf) > 0 if reconf: # Perform an update setup with self._unscaled_context_all(): self.resetup('update') # Reset the _reconfigured attribute to False for subsys in self._subsystems_myproc: subsys._reconfigured = False self._reconfigured = True def _list_states(self): """ Return list of all local states at and below this system. Returns ------- list List of all states. """ states = [] for subsys in self._subsystems_myproc: states.extend(subsys._list_states()) return sorted(states) def _list_states_allprocs(self): """ Return list of all states at and below this system across all procs. Returns ------- list List of all states. """ if MPI: all_states = set() byproc = self.comm.allgather(self._list_states()) for proc_states in byproc: all_states.update(proc_states) return sorted(all_states) else: return self._list_states() def _setup_var_index_ranges(self, recurse=True): """ Compute the division of variables by subsystem. Parameters ---------- recurse : bool Whether to call this method in subsystems. """ nsub_allprocs = len(self._subsystems_allprocs) subsystems_var_range = self._subsystems_var_range = {} vec_names = self._lin_rel_vec_name_list if self._use_derivatives else self._vec_names # First compute these on one processor for each subsystem for vec_name in vec_names: # Here, we count the number of variables in each subsystem. # We do this so that we can compute the offset when we recurse into each subsystem. allprocs_counters = {} for type_ in ['input', 'output']: allprocs_counters[type_] = np.zeros(nsub_allprocs, INT_DTYPE) for subsys in self._subsystems_myproc: comm = subsys.comm if subsys._full_comm is None else subsys._full_comm if comm.rank == 0 and vec_name in subsys._rel_vec_names: isub = self._subsystems_inds[] allprocs_counters[type_][isub] = \ len(subsys._var_allprocs_relevant_names[vec_name][type_]) # If running in parallel, allgather if self.comm.size > 1: gathered = self.comm.allgather(allprocs_counters) allprocs_counters = { type_: np.zeros(nsub_allprocs, INT_DTYPE) for type_ in ['input', 'output'] } for myproc_counters in gathered: for type_ in ['input', 'output']: allprocs_counters[type_] += myproc_counters[type_] # Compute _subsystems_var_range subsystems_var_range[vec_name] = {} for type_ in ['input', 'output']: subsystems_var_range[vec_name][type_] = {} for subsys in self._subsystems_myproc: if vec_name not in subsys._rel_vec_names: continue isub = self._subsystems_inds[] start = np.sum(allprocs_counters[type_][:isub]) subsystems_var_range[vec_name][type_][] = ( start, start + allprocs_counters[type_][isub] ) if self._use_derivatives: subsystems_var_range['nonlinear'] = subsystems_var_range['linear'] self._setup_var_index_maps(recurse=recurse) # Recursion if recurse: for subsys in self._subsystems_myproc: subsys._setup_var_index_ranges(recurse) def _setup_var_data(self, recurse=True): """ Compute the list of abs var names, abs/prom name maps, and metadata dictionaries. Parameters ---------- recurse : bool Whether to call this method in subsystems. """ super(Group, self)._setup_var_data() abs_names = self._var_abs_names abs_names_discrete = self._var_abs_names_discrete allprocs_abs_names = self._var_allprocs_abs_names allprocs_abs_names_discrete = self._var_allprocs_abs_names_discrete var_discrete = self._var_discrete allprocs_discrete = self._var_allprocs_discrete abs2meta = self._var_abs2meta abs2prom = self._var_abs2prom allprocs_abs2meta = self._var_allprocs_abs2meta allprocs_abs2prom = self._var_allprocs_abs2prom allprocs_prom2abs_list = self._var_allprocs_prom2abs_list for subsys in self._subsystems_myproc: if recurse: subsys._setup_var_data(recurse) self._has_output_scaling |= subsys._has_output_scaling self._has_resid_scaling |= subsys._has_resid_scaling var_maps = subsys._get_maps(subsys._var_allprocs_prom2abs_list) # Assemble allprocs_abs2meta and abs2meta allprocs_abs2meta.update(subsys._var_allprocs_abs2meta) abs2meta.update(subsys._var_abs2meta) sub_prefix = + '.' for type_ in ['input', 'output']: # Assemble abs_names and allprocs_abs_names allprocs_abs_names[type_].extend( subsys._var_allprocs_abs_names[type_]) allprocs_abs_names_discrete[type_].extend( subsys._var_allprocs_abs_names_discrete[type_]) abs_names[type_].extend(subsys._var_abs_names[type_]) abs_names_discrete[type_].extend(subsys._var_abs_names_discrete[type_]) allprocs_discrete[type_].update({k: v for k, v in iteritems(subsys._var_allprocs_discrete[type_])}) var_discrete[type_].update({sub_prefix + k: v for k, v in iteritems(subsys._var_discrete[type_])}) # Assemble abs2prom sub_loc_proms = subsys._var_abs2prom[type_] sub_proms = subsys._var_allprocs_abs2prom[type_] for abs_name in chain(subsys._var_allprocs_abs_names[type_], subsys._var_allprocs_abs_names_discrete[type_]): if abs_name in sub_loc_proms: abs2prom[type_][abs_name] = var_maps[type_][sub_loc_proms[abs_name]] allprocs_abs2prom[type_][abs_name] = var_maps[type_][sub_proms[abs_name]] # Assemble allprocs_prom2abs_list for sub_prom, sub_abs in iteritems(subsys._var_allprocs_prom2abs_list[type_]): prom_name = var_maps[type_][sub_prom] if prom_name not in allprocs_prom2abs_list[type_]: allprocs_prom2abs_list[type_][prom_name] = [] allprocs_prom2abs_list[type_][prom_name].extend(sub_abs) for prom_name, abs_list in iteritems(allprocs_prom2abs_list['output']): if len(abs_list) > 1: raise RuntimeError("{}: Output name '{}' refers to " "multiple outputs: {}.".format(self.msginfo, prom_name, sorted(abs_list))) # If running in parallel, allgather if self.comm.size > 1: mysub = self._subsystems_myproc[0] if self._subsystems_myproc else False if (mysub and mysub.comm.rank == 0 and (mysub._full_comm is None or mysub._full_comm.rank == 0)): raw = (allprocs_abs_names, allprocs_discrete, allprocs_prom2abs_list, allprocs_abs2prom, allprocs_abs2meta, self._has_output_scaling, self._has_resid_scaling) else: raw = ( {'input': [], 'output': []}, {'input': {}, 'output': {}}, {'input': {}, 'output': {}}, {'input': {}, 'output': {}}, {}, False, False ) gathered = self.comm.allgather(raw) for type_ in ['input', 'output']: allprocs_abs_names[type_] = [] allprocs_abs2prom[type_] = {} allprocs_prom2abs_list[type_] = OrderedDict() for (myproc_abs_names, myproc_discrete, myproc_prom2abs_list, all_abs2prom, myproc_abs2meta, oscale, rscale) in gathered: self._has_output_scaling |= oscale self._has_resid_scaling |= rscale # Assemble in parallel allprocs_abs2meta for n in myproc_abs2meta: if n not in allprocs_abs2meta: allprocs_abs2meta[n] = myproc_abs2meta[n] for type_ in ['input', 'output']: # Assemble in parallel allprocs_abs_names allprocs_abs_names[type_].extend(myproc_abs_names[type_]) allprocs_discrete[type_].update(myproc_discrete[type_]) allprocs_abs2prom[type_].update(all_abs2prom[type_]) # Assemble in parallel allprocs_prom2abs_list for prom_name, abs_names_list in iteritems(myproc_prom2abs_list[type_]): if prom_name not in allprocs_prom2abs_list[type_]: allprocs_prom2abs_list[type_][prom_name] = [] allprocs_prom2abs_list[type_][prom_name].extend(abs_names_list) if self._var_discrete['input'] or self._var_discrete['output']: self._discrete_inputs = _DictValues(self._var_discrete['input']) self._discrete_outputs = _DictValues(self._var_discrete['output']) else: self._discrete_inputs = self._discrete_outputs = () def _setup_var_sizes(self, recurse=True): """ Compute the arrays of local variable sizes for all variables/procs on this system. Parameters ---------- recurse : bool Whether to call this method in subsystems. """ super(Group, self)._setup_var_sizes() self._var_offsets = None iproc = self.comm.rank nproc = self.comm.size subsystems_proc_range = self._subsystems_proc_range # Recursion if recurse: for subsys in self._subsystems_myproc: subsys._setup_var_sizes(recurse) sizes = self._var_sizes relnames = self._var_allprocs_relevant_names vec_names = self._lin_rel_vec_name_list if self._use_derivatives else self._vec_names n_distrib_vars = 0 # Compute _var_sizes for vec_name in vec_names: sizes[vec_name] = {} subsystems_var_range = self._subsystems_var_range[vec_name] for type_ in ['input', 'output']: sizes[vec_name][type_] = sz = np.zeros((nproc, len(relnames[vec_name][type_])), INT_DTYPE) for ind, subsys in enumerate(self._subsystems_myproc): if isinstance(subsys, Component) and subsys.options['distributed']: n_distrib_vars += 1 if vec_name not in subsys._rel_vec_names: continue proc_slice = slice(*subsystems_proc_range[ind]) var_slice = slice(*subsystems_var_range[type_][]) if proc_slice.stop - proc_slice.start > subsys.comm.size: # in this case, we've split the proc for parallel FD, so subsys doesn't # have var_sizes for all the ranks we need. Since each parallel FD comm # has the same size distribution (since all are identical), just 'tile' # the var_sizes from the subsystem to fill in the full rank range we need # at this level. assert (proc_slice.stop - proc_slice.start) % subsys.comm.size == 0, \ "%s comm size (%d) is not an exact multiple of %s comm size (%d)" % ( self.pathname, self.comm.size, subsys.pathname, subsys.comm.size) proc_i = proc_slice.start while proc_i < proc_slice.stop: sz[proc_i:proc_i + subsys.comm.size, var_slice] = \ subsys._var_sizes[vec_name][type_] proc_i += subsys.comm.size else: sz[proc_slice, var_slice] = subsys._var_sizes[vec_name][type_] # If parallel, all gather if self.comm.size > 1: for vec_name in self._lin_rel_vec_name_list: sizes = self._var_sizes[vec_name] for type_ in ['input', 'output']: sizes_in = sizes[type_][iproc, :].copy() self.comm.Allgather(sizes_in, sizes[type_]) self._has_distrib_vars = self.comm.allreduce(n_distrib_vars) > 0 if (self._has_distrib_vars or not np.all(self._var_sizes[vec_names[0]]['output']) or not np.all(self._var_sizes[vec_names[0]]['input'])): if self._distributed_vector_class is not None: self._vector_class = self._distributed_vector_class else: raise RuntimeError("{}: Distributed vectors are required but no distributed " "vector type has been set.".format(self.msginfo)) # compute owning ranks and owned sizes abs2meta = self._var_allprocs_abs2meta owns = self._owning_rank self._owned_sizes = self._var_sizes[vec_names[0]]['output'].copy() for type_ in ('input', 'output'): sizes = self._var_sizes[vec_names[0]][type_] for i, name in enumerate(self._var_allprocs_abs_names[type_]): for rank in range(self.comm.size): if sizes[rank, i] > 0: owns[name] = rank if type_ == 'output' and not abs2meta[name]['distributed']: self._owned_sizes[rank + 1:, i] = 0 # zero out all dups break if self._var_allprocs_discrete[type_]: local = list(self._var_discrete[type_]) for i, names in enumerate(self.comm.allgather(local)): for n in names: if n not in owns: owns[n] = i else: self._owned_sizes = self._var_sizes[vec_names[0]]['output'] self._vector_class = self._local_vector_class if self._use_derivatives: self._var_sizes['nonlinear'] = self._var_sizes['linear'] if self.comm.size > 1: self._setup_global_shapes() def _setup_global_connections(self, recurse=True, conns=None): """ Compute dict of all connections between this system's inputs and outputs. The connections come from 4 sources: 1. Implicit connections owned by the current system 2. Explicit connections declared by the current system 3. Explicit connections declared by parent systems 4. Implicit / explicit from subsystems Parameters ---------- recurse : bool Whether to call this method in subsystems. conns : dict Dictionary of connections passed down from parent group. """ global_abs_in2out = self._conn_global_abs_in2out = {} allprocs_prom2abs_list_in = self._var_allprocs_prom2abs_list['input'] allprocs_prom2abs_list_out = self._var_allprocs_prom2abs_list['output'] abs2meta = self._var_abs2meta pathname = self.pathname abs_in2out = {} if pathname == '': path_len = 0 nparts = 0 else: path_len = len(pathname) + 1 nparts = len(pathname.split('.')) new_conns = defaultdict(dict) if conns is not None: for abs_in, abs_out in iteritems(conns): inparts = abs_in.split('.') outparts = abs_out.split('.') if inparts[:nparts] == outparts[:nparts]: global_abs_in2out[abs_in] = abs_out # if connection is contained in a subgroup, add to conns # to pass down to subsystems. if inparts[:nparts + 1] == outparts[:nparts + 1]: new_conns[inparts[nparts]][abs_in] = abs_out # Add implicit connections (only ones owned by this group) for prom_name in allprocs_prom2abs_list_out: if prom_name in allprocs_prom2abs_list_in: abs_out = allprocs_prom2abs_list_out[prom_name][0] out_subsys = abs_out[path_len:].split('.', 1)[0] for abs_in in allprocs_prom2abs_list_in[prom_name]: in_subsys = abs_in[path_len:].split('.', 1)[0] if out_subsys != in_subsys: abs_in2out[abs_in] = abs_out # Add explicit connections (only ones declared by this group) for prom_in, (prom_out, src_indices, flat_src_indices) in \ iteritems(self._manual_connections): # throw an exception if either output or input doesn't exist # (not traceable to a connect statement, so provide context) if (prom_out not in allprocs_prom2abs_list_out and prom_out not in self._var_allprocs_discrete['output']): if (prom_out in allprocs_prom2abs_list_in or prom_out in self._var_allprocs_discrete['input']): raise NameError( "%s: Attempted to connect from '%s' to '%s', but '%s' is an input. " "All connections must be from an output to an input." % (self.msginfo, prom_out, prom_in, prom_out)) else: raise NameError( "%s: Attempted to connect from '%s' to '%s', but '%s' doesn't exist." % (self.msginfo, prom_out, prom_in, prom_out)) if (prom_in not in allprocs_prom2abs_list_in and prom_in not in self._var_allprocs_discrete['input']): if (prom_in in allprocs_prom2abs_list_out or prom_in in self._var_allprocs_discrete['output']): raise NameError( "%s: Attempted to connect from '%s' to '%s', but '%s' is an output. " "All connections must be from an output to an input." % (self.msginfo, prom_out, prom_in, prom_in)) else: raise NameError( "%s: Attempted to connect from '%s' to '%s', but '%s' doesn't exist." % (self.msginfo, prom_out, prom_in, prom_in)) # Throw an exception if output and input are in the same system # (not traceable to a connect statement, so provide context) # and check if src_indices is defined in both connect and add_input. abs_out = allprocs_prom2abs_list_out[prom_out][0] outparts = abs_out.split('.') out_subsys = outparts[:-1] for abs_in in allprocs_prom2abs_list_in[prom_in]: inparts = abs_in.split('.') in_subsys = inparts[:-1] if out_subsys == in_subsys: raise RuntimeError("{}: Output and input are in the same System " "for connection from '{}' to '{}'.".format(self.msginfo, prom_out, prom_in)) if src_indices is not None and abs_in in abs2meta: meta = abs2meta[abs_in] if meta['src_indices'] is not None: raise RuntimeError("{}: src_indices has been defined " "in both connect('{}', '{}') " "and add_input('{}', ...).".format(self.msginfo, prom_out, prom_in, prom_in)) meta['src_indices'] = np.atleast_1d(src_indices) meta['flat_src_indices'] = flat_src_indices if abs_in in abs_in2out: raise RuntimeError("%s: Input '%s' cannot be connected to '%s' because it's " "already connected to '%s'" % (self.msginfo, abs_in, abs_out, abs_in2out[abs_in])) abs_in2out[abs_in] = abs_out # if connection is contained in a subgroup, add to conns to pass down to subsystems. if inparts[:nparts + 1] == outparts[:nparts + 1]: new_conns[inparts[nparts]][abs_in] = abs_out # Recursion if recurse: for subsys in self._subgroups_myproc: if in new_conns: subsys._setup_global_connections(recurse=recurse, conns=new_conns[]) else: subsys._setup_global_connections(recurse=recurse) # Compute global_abs_in2out by first adding this group's contributions, # then adding contributions from systems above/below, then allgathering. conn_list = list(iteritems(global_abs_in2out)) conn_list.extend(iteritems(abs_in2out)) global_abs_in2out.update(abs_in2out) for subsys in self._subgroups_myproc: global_abs_in2out.update(subsys._conn_global_abs_in2out) conn_list.extend(iteritems(subsys._conn_global_abs_in2out)) if len(conn_list) > len(global_abs_in2out): dupes = [n for n, val in iteritems(Counter(tgt for tgt, src in conn_list)) if val > 1] dup_info = defaultdict(set) for tgt, src in conn_list: for dup in dupes: if tgt == dup: dup_info[tgt].add(src) dup_info = [(n, srcs) for n, srcs in iteritems(dup_info) if len(srcs) > 1] if dup_info: msg = ["%s from %s" % (tgt, sorted(srcs)) for tgt, srcs in dup_info] raise RuntimeError("%s: The following inputs have multiple connections: %s" % (self.msginfo, ", ".join(msg))) # If running in parallel, allgather if self.comm.size > 1: if self._subsystems_myproc and self._subsystems_myproc[0].comm.rank == 0: raw = global_abs_in2out else: raw = {} gathered = self.comm.allgather(raw) for myproc_global_abs_in2out in gathered: global_abs_in2out.update(myproc_global_abs_in2out) def _setup_connections(self, recurse=True): """ Compute dict of all connections owned by this Group. Parameters ---------- recurse : bool Whether to call this method in subsystems. """ abs_in2out = self._conn_abs_in2out = {} global_abs_in2out = self._conn_global_abs_in2out pathname = self.pathname allprocs_discrete_in = self._var_allprocs_discrete['input'] allprocs_discrete_out = self._var_allprocs_discrete['output'] # Recursion if recurse: for subsys in self._subsystems_myproc: subsys._setup_connections(recurse) if MPI: # collect set of local (not remote, not distributed) subsystems so we can # identify cross-process connections, which require the use of distributed # instead of purely local vector and transfer objects. self._local_system_set = set() for s in self._subsystems_myproc: if isinstance(s, Group): self._local_system_set.update(s._local_system_set) elif not s.options['distributed']: self._local_system_set.add(s.pathname) path_dot = pathname + '.' if pathname else '' path_len = len(path_dot) allprocs_abs2meta = self._var_allprocs_abs2meta nproc = self.comm.size # Check input/output units here, and set _has_input_scaling # to True for this Group if units are defined and different, or if # ref or ref0 are defined for the output. for abs_in, abs_out in iteritems(global_abs_in2out): # First, check that this system owns both the input and output. if abs_in[:path_len] == path_dot and abs_out[:path_len] == path_dot: # Second, check that they are in different subsystems of this system. out_subsys = abs_out[path_len:].split('.', 1)[0] in_subsys = abs_in[path_len:].split('.', 1)[0] if out_subsys != in_subsys: if abs_in in allprocs_discrete_in: self._conn_discrete_in2out[abs_in] = abs_out elif abs_out in allprocs_discrete_out: raise RuntimeError("%s: Can't connect discrete output '%s' to continuous " "input '%s'." % (self.msginfo, abs_out, abs_in)) else: abs_in2out[abs_in] = abs_out if nproc > 1 and self._vector_class is None: # check for any cross-process data transfer. If found, use # self._distributed_vector_class as our vector class. in_path = abs_in.rsplit('.', 1)[0] if in_path not in self._local_system_set: self._vector_class = self._distributed_vector_class else: out_path = abs_out.rsplit('.', 1)[0] if out_path not in self._local_system_set: self._vector_class = self._distributed_vector_class # if connected output has scaling then we need input scaling if not self._has_input_scaling and not (abs_in in allprocs_discrete_in or abs_out in allprocs_discrete_out): out_units = allprocs_abs2meta[abs_out]['units'] in_units = allprocs_abs2meta[abs_in]['units'] # if units are defined and different, we need input scaling. needs_input_scaling = (in_units and out_units and in_units != out_units) # we also need it if a connected output has any scaling. if not needs_input_scaling: out_meta = allprocs_abs2meta[abs_out] ref = out_meta['ref'] if np.isscalar(ref): needs_input_scaling = ref != 1.0 else: needs_input_scaling = np.any(ref != 1.0) if not needs_input_scaling: ref0 = out_meta['ref0'] if np.isscalar(ref0): needs_input_scaling = ref0 != 0.0 else: needs_input_scaling = np.any(ref0) if not needs_input_scaling: res_ref = out_meta['res_ref'] if np.isscalar(res_ref): needs_input_scaling = res_ref != 1.0 else: needs_input_scaling = np.any(res_ref != 1.0) self._has_input_scaling = needs_input_scaling # check compatability for any discrete connections for abs_in, abs_out in iteritems(self._conn_discrete_in2out): in_type = self._var_allprocs_discrete['input'][abs_in]['type'] try: out_type = self._var_allprocs_discrete['output'][abs_out]['type'] except KeyError: raise RuntimeError("%s: Can't connect continuous output '%s' to discrete " "input '%s'." % (self.msginfo, abs_out, abs_in)) if not issubclass(in_type, out_type): raise RuntimeError("%s: Type '%s' of output '%s' is" " incompatible with type '%s' of input '%s'." % (self.msginfo, out_type.__name__, abs_out, in_type.__name__, abs_in)) # check unit/shape compatibility, but only for connections that are # either owned by (implicit) or declared by (explicit) this Group. # This way, we don't repeat the error checking in multiple groups. abs2meta = self._var_abs2meta for abs_in, abs_out in iteritems(abs_in2out): # check unit compatibility out_units = allprocs_abs2meta[abs_out]['units'] in_units = allprocs_abs2meta[abs_in]['units'] if out_units: if not in_units: simple_warning("%s: Output '%s' with units of '%s' is " "connected to input '%s' which has no" " units." % (self.msginfo, abs_out, out_units, abs_in)) elif not is_compatible(in_units, out_units): raise RuntimeError("%s: Output units of '%s' for '%s' are" " incompatible with input units of " "'%s' for '%s'." % (self.msginfo, out_units, abs_out, in_units, abs_in)) elif in_units is not None: simple_warning("%s: Input '%s' with units of '%s' is " "connected to output '%s' which has " "no units." % (self.msginfo, abs_in, in_units, abs_out)) # check shape compatibility if abs_in in abs2meta and abs_out in abs2meta: # get output shape from allprocs meta dict, since it may # be distributed (we want global shape) out_shape = allprocs_abs2meta[abs_out]['global_shape'] # get input shape and src_indices from the local meta dict # (input is always local) in_shape = abs2meta[abs_in]['shape'] src_indices = abs2meta[abs_in]['src_indices'] flat = abs2meta[abs_in]['flat_src_indices'] if src_indices is None and out_shape != in_shape: # out_shape != in_shape is allowed if # there's no ambiguity in storage order if not array_connection_compatible(in_shape, out_shape): msg = ("%s: The source and target shapes do not match or are ambiguous" " for the connection '%s' to '%s'. " "The source shape is %s but the target shape is %s.") raise ValueError(msg % (self.msginfo, abs_out, abs_in, tuple([int(s) for s in out_shape]), tuple([int(s) for s in in_shape]), )) if src_indices is not None: src_indices = np.atleast_1d(src_indices) # initial dimensions of indices shape must be same shape as target for idx_d, inp_d in zip(src_indices.shape, in_shape): if idx_d != inp_d: msg = ("%s: The source indices %s do not specify a " "valid shape for the connection '%s' to " "'%s'. The target shape is " "%s but indices are %s.") raise ValueError(msg % (self.msginfo, str(src_indices).replace('\n', ''), abs_out, abs_in, in_shape, src_indices.shape)) # any remaining dimension of indices must match shape of source if len(src_indices.shape) > len(in_shape): source_dimensions = src_indices.shape[len(in_shape)] if source_dimensions != len(out_shape): msg = ("%s: The source indices %s do not specify a " "valid shape for the connection '%s' to " "'%s'. The source has %d " "dimensions but the indices expect %d.") raise ValueError(msg % (self.msginfo, str(src_indices).replace('\n', ''), abs_out, abs_in, len(out_shape), source_dimensions)) else: source_dimensions = 1 # check all indices are in range of the source dimensions if flat: out_size = mx = np.max(src_indices) mn = np.min(src_indices) if mx >= out_size: bad_idx = mx elif mn < -out_size: bad_idx = mn else: bad_idx = None if bad_idx is not None: msg = ("%s: The source indices do not specify " "a valid index for the connection " "'%s' to '%s'. Index " "'%d' is out of range for a flat source " "of size %d.") raise ValueError(msg % (self.msginfo, abs_out, abs_in, bad_idx, out_size)) if src_indices.ndim > 1: abs2meta[abs_in]['src_indices'] = \ abs2meta[abs_in]['src_indices'].flatten() else: for d in range(source_dimensions): # when running under MPI, there is a value for each proc d_size = out_shape[d] * self.comm.size if src_indices.size > 0: for i in src_indices[..., d].flat: if abs(i) >= d_size: msg = ("%s: The source indices do not specify " "a valid index for the connection " "'%s' to '%s'. Index " "'%d' is out of range for source " "dimension of size %d.") raise ValueError(msg % (self.msginfo, abs_out, abs_in, i, d_size)) def _transfer(self, vec_name, mode, isub=None): """ Perform a vector transfer. Parameters ---------- vec_name : str Name of the vector RHS on which to perform a transfer. mode : str Either 'fwd' or 'rev' isub : None or int If None, perform a full transfer. If int, perform a partial transfer for linear Gauss--Seidel. """ vec_inputs = self._vectors['input'][vec_name] xfer = self._transfers[vec_name][mode, isub] if mode == 'fwd': if xfer is not None: if self._has_input_scaling: vec_inputs.scale('norm') xfer._transfer(vec_inputs, self._vectors['output'][vec_name], mode) vec_inputs.scale('phys') else: xfer._transfer(vec_inputs, self._vectors['output'][vec_name], mode) if self._conn_discrete_in2out and vec_name == 'nonlinear': self._discrete_transfer(isub) else: # rev if xfer is not None: if self._has_input_scaling: vec_inputs.scale('phys') xfer._transfer(vec_inputs, self._vectors['output'][vec_name], mode) vec_inputs.scale('norm') else: xfer._transfer(vec_inputs, self._vectors['output'][vec_name], mode) def _discrete_transfer(self, isub): """ Transfer discrete variables between components. This only occurs in fwd mode. Parameters ---------- isub : None or int If None, perform a full transfer. If int, perform a partial transfer for linear Gauss--Seidel. """ comm = self.comm key = None if isub is None else self._subsystems_allprocs[isub].name if comm.size == 1: for src_sys_name, src, tgt_sys_name, tgt in self._discrete_transfers[key]: tgt_sys = self._loc_subsys_map[tgt_sys_name] src_sys = self._loc_subsys_map[src_sys_name] # note that we are not copying the discrete value here, so if the # discrete value is some mutable object, for example not an int or str, # the downstream system will have a reference to the same object # as the source, allowing the downstream system to modify the value as # seen by the source system. tgt_sys._discrete_inputs[tgt] = src_sys._discrete_outputs[src] else: # MPI allprocs_recv = self._allprocs_discrete_recv[key] discrete_out = self._var_discrete['output'] if key in self._discrete_transfers: xfers, remote_send = self._discrete_transfers[key] if allprocs_recv: sendvars = [(n, discrete_out[n]['value']) for n in remote_send] allprocs_send = comm.gather(sendvars, root=0) if comm.rank == 0: allprocs_dict = {} for i in range(comm.size): allprocs_dict.update(allprocs_send[i]) recvs = [{} for i in range(comm.size)] for rname, ranks in iteritems(allprocs_recv): val = allprocs_dict[rname] for i in ranks: recvs[i][rname] = val data = comm.scatter(recvs, root=0) else: data = comm.scatter(None, root=0) else: data = None for src_sys_name, src, tgt_sys_name, tgt in xfers: if tgt_sys_name in self._loc_subsys_map: tgt_sys = self._loc_subsys_map[tgt_sys_name] if tgt in tgt_sys._discrete_inputs: abs_src = '.'.join((src_sys_name, src)) if data is not None and abs_src in data: src_val = data[abs_src] else: src_val = self._loc_subsys_map[src_sys_name]._discrete_outputs[src] tgt_sys._discrete_inputs[tgt] = src_val def _setup_global(self, ext_num_vars, ext_sizes): """ Compute total number and total size of variables in systems before / after this system. Parameters ---------- ext_num_vars : {'input': (int, int), 'output': (int, int)} Total number of allprocs variables in system before/after this one. ext_sizes : {'input': (int, int), 'output': (int, int)} Total size of local variables in system before/after this one. """ super(Group, self)._setup_global(ext_num_vars, ext_sizes) iproc = self.comm.rank relnames = self._var_allprocs_relevant_names for subsys in self._subsystems_myproc: sub_ext_num_vars = {} sub_ext_sizes = {} if subsys._use_derivatives: vec_names = subsys._lin_rel_vec_name_list else: vec_names = subsys._vec_names for vec_name in vec_names: subsystems_var_range = self._subsystems_var_range[vec_name] sizes = self._var_sizes[vec_name] sub_ext_num_vars[vec_name] = {} sub_ext_sizes[vec_name] = {} for type_ in ['input', 'output']: idx1, idx2 = subsystems_var_range[type_][] sub_ext_num_vars[vec_name][type_] = ( ext_num_vars[vec_name][type_][0] + idx1, ext_num_vars[vec_name][type_][1] + len(relnames[vec_name][type_]) - idx2, ) sub_ext_sizes[vec_name][type_] = ( ext_sizes[vec_name][type_][0] + np.sum(sizes[type_][iproc, :idx1]), ext_sizes[vec_name][type_][1] + np.sum(sizes[type_][iproc, idx2:]), ) if subsys._use_derivatives: sub_ext_num_vars['nonlinear'] = sub_ext_num_vars['linear'] sub_ext_sizes['nonlinear'] = sub_ext_sizes['linear'] subsys._setup_global(sub_ext_num_vars, sub_ext_sizes) def _setup_transfers(self, recurse=True): """ Compute all transfers that are owned by this system. Parameters ---------- recurse : bool Whether to call this method in subsystems. """ self._vector_class.TRANSFER._setup_transfers(self, recurse=recurse) if self._conn_discrete_in2out: self._vector_class.TRANSFER._setup_discrete_transfers(self, recurse=recurse)
[docs] def promotes(self, subsys_name, any=None, inputs=None, outputs=None): """ Promote a variable in the model tree. Parameters ---------- subsys_name : str The name of the child subsystem whose inputs/outputs are being promoted. any : Sequence of str or tuple A Sequence of variable names (or tuples) to be promoted, regardless of if they are inputs or outputs. This is equivalent to the items passed via the `promotes=` argument to add_subsystem. If given as a tuple, we use the "promote as" standard of ('real name', 'promoted name')*[]: inputs : Sequence of str or tuple A Sequence of input names (or tuples) to be promoted. Tuples are used for the "promote as" capability. outputs : Sequence of str or tuple A Sequence of output names (or tuples) to be promoted. Tuples are used for the "promote as" capability. """ subsys = getattr(self, subsys_name) if any: subsys._var_promotes['any'].extend(any) if inputs: subsys._var_promotes['input'].extend(inputs) if outputs: subsys._var_promotes['output'].extend(outputs) list_comp = [i if isinstance(i, tuple) else (i, i) for i in subsys._var_promotes['input']] for original, new in list_comp: for original_inside, new_inside in list_comp: if original == original_inside and new != new_inside: raise RuntimeError("%s: Trying to promote '%s' when it has been aliased to " "'%s'." % (self.msginfo, original_inside, new))
[docs] def add(self, name, subsys, promotes=None): """ Add a subsystem (deprecated version of <Group.add_subsystem>). Parameters ---------- name : str Name of the subsystem being added subsys : System An instantiated, but not-yet-set up system object. promotes : iter of str, optional A list of variable names specifying which subsystem variables to 'promote' up to this group. This is for backwards compatibility with older versions of OpenMDAO. Returns ------- System The System that was passed in. """ warn_deprecation("The 'add' method provides backwards compatibility with " "OpenMDAO <= 1.x ; use 'add_subsystem' instead.") return self.add_subsystem(name, subsys, promotes=promotes)
[docs] def add_subsystem(self, name, subsys, promotes=None, promotes_inputs=None, promotes_outputs=None, min_procs=1, max_procs=None, proc_weight=1.0): """ Add a subsystem. Parameters ---------- name : str Name of the subsystem being added subsys : <System> An instantiated, but not-yet-set up system object. promotes : iter of (str or tuple), optional A list of variable names specifying which subsystem variables to 'promote' up to this group. If an entry is a tuple of the form (old_name, new_name), this will rename the variable in the parent group. promotes_inputs : iter of (str or tuple), optional A list of input variable names specifying which subsystem input variables to 'promote' up to this group. If an entry is a tuple of the form (old_name, new_name), this will rename the variable in the parent group. promotes_outputs : iter of (str or tuple), optional A list of output variable names specifying which subsystem output variables to 'promote' up to this group. If an entry is a tuple of the form (old_name, new_name), this will rename the variable in the parent group. min_procs : int Minimum number of MPI processes usable by the subsystem. Defaults to 1. max_procs : int or None Maximum number of MPI processes usable by the subsystem. A value of None (the default) indicates there is no maximum limit. proc_weight : float Weight given to the subsystem when allocating available MPI processes to all subsystems. Default is 1.0. Returns ------- <System> the subsystem that was passed in. This is returned to enable users to instantiate and add a subsystem at the same time, and get the reference back. """ if self._setup_procs_finished: raise RuntimeError("%s: Cannot call add_subsystem in " "the configure method" % (self.msginfo)) if inspect.isclass(subsys): raise TypeError("%s: Subsystem '%s' should be an instance, but a %s class object was " "found." % (self.msginfo, name, subsys.__name__)) for sub in chain(self._subsystems_allprocs, self._static_subsystems_allprocs): if name == raise RuntimeError("%s: Subsystem name '%s' is already used." % (self.msginfo, name)) if hasattr(self, name) and not isinstance(getattr(self, name), System): # replacing a subsystem is ok (e.g. resetup) but no other attribute raise RuntimeError("%s: Can't add subsystem '%s' because an attribute with that name " "already exits." % (self.msginfo, name)) match = namecheck_rgx.match(name) if match is None or != name: raise NameError("%s: '%s' is not a valid sub-system name." % (self.msginfo, name)) = subsys.pathname = name if isinstance(promotes, string_types) or \ isinstance(promotes_inputs, string_types) or \ isinstance(promotes_outputs, string_types): raise RuntimeError("%s: promotes must be an iterator of strings and/or tuples." % self.msginfo) if promotes: subsys._var_promotes['any'] = promotes if promotes_inputs: subsys._var_promotes['input'] = promotes_inputs if promotes_outputs: subsys._var_promotes['output'] = promotes_outputs if self._static_mode: subsystems_allprocs = self._static_subsystems_allprocs else: subsystems_allprocs = self._subsystems_allprocs subsystems_allprocs.append(subsys) if not isinstance(min_procs, int) or min_procs < 1: raise TypeError("%s: min_procs must be an int > 0 but (%s) was given." % (self.msginfo, min_procs)) if max_procs is not None and (not isinstance(max_procs, int) or max_procs < min_procs): raise TypeError("%s: max_procs must be None or an int >= min_procs but (%s) was given." % (self.msginfo, max_procs)) if isinstance(proc_weight, Number) and proc_weight < 0: raise TypeError("%s: proc_weight must be a float > 0. but (%s) was given." % (self.msginfo, proc_weight)) self._proc_info[name] = (min_procs, max_procs, proc_weight) setattr(self, name, subsys) return subsys
[docs] def connect(self, src_name, tgt_name, src_indices=None, flat_src_indices=None): """ Connect source src_name to target tgt_name in this namespace. Parameters ---------- src_name : str name of the source variable to connect tgt_name : str or [str, ... ] or (str, ...) name of the target variable(s) to connect src_indices : int or list of ints or tuple of ints or int ndarray or Iterable or None The global indices of the source variable to transfer data from. The shapes of the target and src_indices must match, and form of the entries within is determined by the value of 'flat_src_indices'. flat_src_indices : bool If True, each entry of src_indices is assumed to be an index into the flattened source. Otherwise it must be a tuple or list of size equal to the number of dimensions of the source. """ # if src_indices argument is given, it should be valid if isinstance(src_indices, string_types): if isinstance(tgt_name, string_types): tgt_name = [tgt_name] tgt_name.append(src_indices) raise TypeError("%s: src_indices must be an index array, did you mean" " connect('%s', %s)?" % (self.msginfo, src_name, tgt_name)) if isinstance(src_indices, Iterable): src_indices = np.atleast_1d(src_indices) if isinstance(src_indices, np.ndarray): if not np.issubdtype(src_indices.dtype, np.integer): raise TypeError("%s: src_indices must contain integers, but src_indices for " "connection from '%s' to '%s' is %s." % (self.msginfo, src_name, tgt_name, src_indices.dtype.type)) # if multiple targets are given, recursively connect to each if not isinstance(tgt_name, string_types) and isinstance(tgt_name, Iterable): for name in tgt_name: self.connect(src_name, name, src_indices, flat_src_indices=flat_src_indices) return # target should not already be connected for manual_connections in [self._manual_connections, self._static_manual_connections]: if tgt_name in manual_connections: srcname = manual_connections[tgt_name][0] raise RuntimeError("%s: Input '%s' is already connected to '%s'." % (self.msginfo, tgt_name, srcname)) # source and target should not be in the same system if src_name.rsplit('.', 1)[0] == tgt_name.rsplit('.', 1)[0]: raise RuntimeError("{}: Output and input are in the same System for " "connection from '{}' to '{}'.".format(self.msginfo, src_name, tgt_name)) if self._static_mode: manual_connections = self._static_manual_connections else: manual_connections = self._manual_connections manual_connections[tgt_name] = (src_name, src_indices, flat_src_indices)
[docs] def set_order(self, new_order): """ Specify a new execution order for this system. Parameters ---------- new_order : list of str List of system names in desired new execution order. """ # Make sure the new_order is valid. It must contain all subsystems # in this model. newset = set(new_order) if self._static_mode: subsystems = self._static_subsystems_allprocs else: subsystems = self._subsystems_allprocs olddict = { s for s in subsystems} oldset = set(olddict) if oldset != newset: msg = [] missing = oldset - newset if missing: msg.append("%s: %s expected in subsystem order and not found." % (self.msginfo, sorted(missing))) extra = newset - oldset if extra: msg.append("%s: subsystem(s) %s found in subsystem order but don't exist." % (self.msginfo, sorted(extra))) raise ValueError('\n'.join(msg)) # Don't allow duplicates either. if len(newset) < len(new_order): dupes = [key for key, val in iteritems(Counter(new_order)) if val > 1] raise ValueError("%s: Duplicate name(s) found in subsystem order list: %s" % (self.msginfo, sorted(dupes))) subsystems[:] = [olddict[name] for name in new_order]
def _get_subsystem(self, name): """ Return the system called 'name' in the current namespace. Parameters ---------- name : str name of the desired system in the current namespace. Returns ------- System or None System if found else None. """ system = self for subname in name.split('.'): for sub in chain(system._static_subsystems_allprocs, system._subsystems_allprocs): if == subname: system = sub break else: return None return system def _apply_nonlinear(self): """ Compute residuals. The model is assumed to be in a scaled state. """ name = self.pathname if self.pathname else 'root' self._transfer('nonlinear', 'fwd') # Apply recursion with Recording(name + '._apply_nonlinear', self.iter_count, self): for subsys in self._subsystems_myproc: subsys._apply_nonlinear() def _solve_nonlinear(self): """ Compute outputs. The model is assumed to be in a scaled state. """ super(Group, self)._solve_nonlinear() name = self.pathname if self.pathname else 'root' with Recording(name + '._solve_nonlinear', self.iter_count, self): self._nonlinear_solver.solve() def _guess_nonlinear(self): """ Provide initial guess for states. """ # let any lower level systems do their guessing first if self._has_guess: for isub, (sub, loc)in enumerate(self._all_subsystem_iter()): # TODO: could gather 'has_guess' information during setup and be able to # skip transfer for subs that don't have guesses... self._transfer('nonlinear', 'fwd', isub) if loc and sub._has_guess: sub._guess_nonlinear() # call our own guess_nonlinear method, after the recursion is done to # all the lower level systems and the data transfers have happened complex_step = self._inputs._under_complex_step if complex_step: self._inputs.set_complex_step_mode(False, keep_real=True) self._residuals.set_complex_step_mode(False, keep_real=True) # The Group outputs vector contains imaginary numbers from other components, so we need # to save a cache and restore it later. imag_cache = np.empty(len(self._outputs._data)) imag_cache[:] = self._outputs._data.imag self._outputs.set_complex_step_mode(False, keep_real=True) if self._discrete_inputs or self._discrete_outputs: self.guess_nonlinear(self._inputs, self._outputs, self._residuals, self._discrete_inputs, self._discrete_outputs) else: self.guess_nonlinear(self._inputs, self._outputs, self._residuals) if complex_step: # Note: passing in False swaps back to the complex vector, which is valid since # the inputs and residuals value cannot be edited by guess_nonlinear. self._inputs.set_complex_step_mode(False) self._residuals.set_complex_step_mode(False) self._inputs._under_complex_step = True self._residuals._under_complex_step = True self._outputs.set_complex_step_mode(True) self._outputs._data[:] += imag_cache * 1j
[docs] def guess_nonlinear(self, inputs, outputs, residuals, discrete_inputs=None, discrete_outputs=None): """ Provide initial guess for states. Override this method to set the initial guess for states. Parameters ---------- inputs : Vector unscaled, dimensional input variables read via inputs[key] outputs : Vector unscaled, dimensional output variables read via outputs[key] residuals : Vector unscaled, dimensional residuals written to via residuals[key] discrete_inputs : dict or None If not None, dict containing discrete input values. discrete_outputs : dict or None If not None, dict containing discrete output values. """ pass
def _apply_linear(self, jac, vec_names, rel_systems, mode, scope_out=None, scope_in=None): """ Compute jac-vec product. The model is assumed to be in a scaled state. Parameters ---------- jac : Jacobian or None If None, use local jacobian, else use assembled jacobian jac. vec_names : [str, ...] list of names of the right-hand-side vectors. rel_systems : set of str Set of names of relevant systems based on the current linear solve. mode : str 'fwd' or 'rev'. scope_out : set or None Set of absolute output names in the scope of this mat-vec product. If None, all are in the scope. scope_in : set or None Set of absolute input names in the scope of this mat-vec product. If None, all are in the scope. """ vec_names = [v for v in vec_names if v in self._rel_vec_names] if self._owns_approx_jac: jac = self._jacobian elif jac is None and self._assembled_jac is not None: jac = self._assembled_jac if jac is not None: for vec_name in vec_names: with self._matvec_context(vec_name, scope_out, scope_in, mode) as vecs: d_inputs, d_outputs, d_residuals = vecs jac._apply(self, d_inputs, d_outputs, d_residuals, mode) # Apply recursion else: if rel_systems is not None: irrelevant_subs = [s for s in self._subsystems_myproc if s.pathname not in rel_systems] if mode == 'fwd': for vec_name in vec_names: self._transfer(vec_name, mode) if rel_systems is not None: for s in irrelevant_subs: # zero out dvecs of irrelevant subsystems s._vectors['residual']['linear'].set_const(0.0) for subsys in self._subsystems_myproc: if rel_systems is None or subsys.pathname in rel_systems: subsys._apply_linear(jac, vec_names, rel_systems, mode, scope_out, scope_in) if mode == 'rev': for vec_name in vec_names: self._transfer(vec_name, mode) if rel_systems is not None: for s in irrelevant_subs: # zero out dvecs of irrelevant subsystems s._vectors['output']['linear'].set_const(0.0) def _solve_linear(self, vec_names, mode, rel_systems): """ Apply inverse jac product. The model is assumed to be in a scaled state. Parameters ---------- vec_names : [str, ...] list of names of the right-hand-side vectors. mode : str 'fwd' or 'rev'. rel_systems : set of str Set of names of relevant systems based on the current linear solve. """ vec_names = [v for v in vec_names if v in self._rel_vec_names] self._linear_solver.solve(vec_names, mode, rel_systems) def _linearize(self, jac, sub_do_ln=True): """ Compute jacobian / factorization. The model is assumed to be in a scaled state. Parameters ---------- jac : Jacobian or None If None, use local jacobian, else use assembled jacobian jac. sub_do_ln : boolean Flag indicating if the children should call linearize on their linear solvers. """ if self._jacobian is None: self._jacobian = DictionaryJacobian(self) self._check_first_linearize() # Group finite difference if self._owns_approx_jac: jac = self._jacobian if self.pathname == "": for approximation in itervalues(self._approx_schemes): approximation.compute_approximations(self, jac=jac, total=True) else: # When an approximation exists in a submodel (instead of in root), the model is # in a scaled state. with self._unscaled_context(outputs=[self._outputs]): for approximation in itervalues(self._approx_schemes): approximation.compute_approximations(self, jac=jac, total=True) else: if self._assembled_jac is not None: jac = self._assembled_jac # Only linearize subsystems if we aren't approximating the derivs at this level. for subsys in self._subsystems_myproc: do_ln = sub_do_ln and (subsys._linear_solver is not None and subsys._linear_solver._linearize_children()) subsys._linearize(jac, sub_do_ln=do_ln) # Update jacobian if self._assembled_jac is not None: self._assembled_jac._update(self) if sub_do_ln: for subsys in self._subsystems_myproc: if subsys._linear_solver is not None: subsys._linear_solver._linearize() def _check_first_linearize(self): if self._first_call_to_linearize: self._first_call_to_linearize = False # only do this once coloring = self._get_coloring() if coloring_mod._use_partial_sparsity else None if coloring is not None: if not self._coloring_info['dynamic']: coloring._check_config_partial(self) self._setup_approx_coloring() # TODO: for top level FD, call below is unnecessary, but we need this # for some tests that just call run_linearize directily without calling # compute_totals. elif self._approx_schemes: self._setup_approx_partials()
[docs] def approx_totals(self, method='fd', step=None, form=None, step_calc=None): """ Approximate derivatives for a Group using the specified approximation method. Parameters ---------- method : str The type of approximation that should be used. Valid options include: 'fd': Finite Difference, 'cs': Complex Step step : float Step size for approximation. Defaults to None, in which case, the approximation method provides its default value. form : string Form for finite difference, can be 'forward', 'backward', or 'central'. Defaults to None, in which case, the approximation method provides its default value. step_calc : string Step type for finite difference, can be 'abs' for absolute', or 'rel' for relative. Defaults to None, in which case, the approximation method provides its default value. """ self._has_approx = True self._approx_schemes = OrderedDict() approx_scheme = self._get_approx_scheme(method) default_opts = approx_scheme.DEFAULT_OPTIONS kwargs = {} for name, attr in (('step', step), ('form', form), ('step_calc', step_calc)): if attr is not None: if name in default_opts: kwargs[name] = attr else: raise RuntimeError("%s: '%s' is not a valid option for '%s'" % (self.msginfo, name, method)) self._owns_approx_jac = True self._owns_approx_jac_meta = kwargs
def _setup_partials(self, recurse=True): """ Call setup_partials in components. Parameters ---------- recurse : bool Whether to call this method in subsystems. """ self._subjacs_info = info = {} if recurse: for subsys in self._subsystems_myproc: subsys._setup_partials(recurse) info.update(subsys._subjacs_info) def _get_approx_subjac_keys(self): """ Return a list of (of, wrt) keys needed for approx derivs for this group. Returns ------- list List of approx derivative subjacobian keys. """ if self._approx_subjac_keys is None: self._approx_subjac_keys = list(self._approx_subjac_keys_iter()) return self._approx_subjac_keys def _approx_subjac_keys_iter(self): pro2abs = self._var_allprocs_prom2abs_list if self._owns_approx_wrt and not self.pathname: candidate_wrt = self._owns_approx_wrt else: candidate_wrt = list(var[0] for var in pro2abs['input'].values()) from openmdao.core.indepvarcomp import IndepVarComp wrt = set() ivc = set() if self.pathname: # get rid of any old stuff in here self._owns_approx_of = self._owns_approx_wrt = None for var in candidate_wrt: # Weed out inputs connected to anything inside our system unless the source is an # indepvarcomp. if var in self._conn_abs_in2out: src = self._conn_abs_in2out[var] compname = src.rsplit('.', 1)[0] comp = self._get_subsystem(compname) if isinstance(comp, IndepVarComp): wrt.add(src) ivc.add(src) else: wrt.add(var) if self._owns_approx_of: of = set(self._owns_approx_of) else: of = set(var[0] for var in pro2abs['output'].values()) # Skip indepvarcomp res wrt other srcs of -= ivc for key in product(of, wrt.union(of)): # Create approximations for the ones we need. # Skip explicit res wrt outputs if key[1] in of and key[1] not in ivc: # Support for specifying a desvar as an obj/con. if key[1] not in wrt or key[0] == key[1]: continue yield key def _jacobian_of_iter(self): """ Iterate over (name, offset, end, idxs) for each row var in the systems's jacobian. idxs will usually be a full slice, except in cases where _owns_approx__idx has a value for that variable. """ abs2meta = self._var_allprocs_abs2meta approx_of_idx = self._owns_approx_of_idx if self._owns_approx_of: # we're computing totals/semi-totals offset = end = 0 for of in self._owns_approx_of: if of in approx_of_idx: sub_of_idx = approx_of_idx[of] size = len(sub_of_idx) else: size = abs2meta[of]['size'] sub_of_idx = _full_slice end += size yield of, offset, end, sub_of_idx offset = end else: for tup in super(Group, self)._jacobian_of_iter(): yield tup def _jacobian_wrt_iter(self, wrt_matches=None): """ Iterate over (name, offset, end, idxs) for each column var in the systems's jacobian. idxs will usually be a full slice, except in cases where _owns_approx_wrt_idx has a value for that variable. Parameters ---------- wrt_matches : set or None Only include row vars that are contained in this set. This will determine what the actual offsets are, i.e. the offsets will be into a reduced jacobian containing only the matching columns. """ if self._owns_approx_wrt: if wrt_matches is None: wrt_matches = ContainsAll() abs2meta = self._var_allprocs_abs2meta approx_of_idx = self._owns_approx_of_idx approx_wrt_idx = self._owns_approx_wrt_idx offset = end = 0 if self.pathname: # doing semitotals, so include output columns for of, _offset, _end, sub_of_idx in self._jacobian_of_iter(): if of in wrt_matches: end += (_end - _offset) yield of, offset, end, sub_of_idx offset = end for wrt in self._owns_approx_wrt: if wrt in wrt_matches: if wrt in approx_wrt_idx: sub_wrt_idx = approx_wrt_idx[wrt] size = len(sub_wrt_idx) else: size = abs2meta[wrt]['size'] sub_wrt_idx = _full_slice end += size yield wrt, offset, end, sub_wrt_idx offset = end else: for tup in super(Group, self)._jacobian_wrt_iter(wrt_matches): yield tup def _update_wrt_matches(self, info): """ Determine the list of wrt variables that match the wildcard(s) given in declare_coloring. Parameters ---------- info : dict Coloring metadata dict. """ if not (self._owns_approx_of or self.pathname): return abs2prom = self._var_allprocs_abs2prom abs_outs = self._var_allprocs_abs_names['output'] abs_ins = self._var_allprocs_abs_names['input'] info['wrt_matches'] = wrt_colors_matched = set() wrt_color_patterns = info['wrt_patterns'] for key in self._get_approx_subjac_keys(): if wrt_color_patterns: if key[1] in abs2prom['output']: wrtprom = abs2prom['output'][key[1]] else: wrtprom = abs2prom['input'][key[1]] for patt in wrt_color_patterns: if patt == '*' or fnmatchcase(wrtprom, patt): wrt_colors_matched.add(key[1]) break baselen = len(self.pathname) + 1 if self.pathname else 0 info['wrt_matches_prom'] = [n[baselen:] for n in wrt_colors_matched] if info.get('dynamic') and info['coloring'] is None and self._owns_approx_of: if not wrt_colors_matched: raise ValueError("{}: Invalid 'wrt' variable(s) specified for colored approx " "partial options: {}.".format(self.msginfo, wrt_color_patterns)) def _setup_approx_partials(self): """ Add approximations for all approx derivs. """ self._jacobian = DictionaryJacobian(system=self) pro2abs = self._var_allprocs_prom2abs_list abs2prom = self._var_allprocs_abs2prom abs2meta = self._var_allprocs_abs2meta abs_outs = self._var_allprocs_abs_names['output'] abs_ins = self._var_allprocs_abs_names['input'] info = self._coloring_info if info['coloring'] is not None and (self._owns_approx_of is None or self._owns_approx_wrt is None): method = info['method'] else: method = list(self._approx_schemes)[0] wrt_matches = self._get_static_wrt_matches() approx = self._get_approx_scheme(method) # reset the approx if necessary approx._exec_dict = defaultdict(list) approx._reset() approx_keys = self._get_approx_subjac_keys() for key in approx_keys: if key in self._subjacs_info: meta = self._subjacs_info[key] else: meta = SUBJAC_META_DEFAULTS.copy() if key[0] == key[1]: size = self._var_allprocs_abs2meta[key[0]]['size'] meta['rows'] = meta['cols'] = np.arange(size) # All group approximations are treated as explicit components, so we # have a -1 on the diagonal. meta['value'] = np.full(size, -1.0) self._subjacs_info[key] = meta meta['method'] = method meta.update(self._owns_approx_jac_meta) if key[1] in wrt_matches: self._update_approx_coloring_meta(meta) if meta['value'] is None: shape = (abs2meta[key[0]]['size'], abs2meta[key[1]]['size']) meta['shape'] = shape meta['value'] = np.zeros(shape) approx.add_approximation(key, self, meta) if self.pathname: # we're taking semi-total derivs for this group. Update _owns_approx_of # and _owns_approx_wrt so we can use the same approx code for totals and # semi-totals. Also, the order must match order of vars in the output and # input vectors. wrtset = set([k[1] for k in approx_keys]) self._owns_approx_of = list(abs_outs) self._owns_approx_wrt = [n for n in chain(abs_outs, abs_ins) if n in wrtset] def _setup_approx_coloring(self): """ Ensure that if coloring is declared, approximations will be set up. """ if self._coloring_info['coloring'] is not None: meta = self._coloring_info self.approx_totals(meta['method'], meta.get('step'), meta.get('form')) self._setup_approx_partials() def _update_approx_coloring_meta(self, meta): """ Update metadata for a subjac based on coloring metadata. Parameters ---------- meta : dict Metadata for a subjac. """ info = self._coloring_info meta['coloring'] = True for name in ('method', 'step', 'form'): if name in info: meta[name] = info[name]
[docs] def compute_sys_graph(self, comps_only=False): """ Compute a dependency graph for subsystems in this group. Variable connection information is stored in each edge of the system graph. Parameters ---------- comps_only : bool (False) If True, return a graph of all components within this group or any of its descendants. No sub-groups will be included. Otherwise, a graph containing only direct children (both Components and Groups) of this group will be returned. Returns ------- DiGraph A directed graph containing names of subsystems and their connections. """ input_srcs = self._conn_global_abs_in2out glen = len(self.pathname.split('.')) if self.pathname else 0 graph = nx.DiGraph() # add all systems as nodes in the graph so they'll be there even if # unconnected. if comps_only: systems = [s.pathname for s in self.system_iter(recurse=True, typ=Component)] else: systems = [ for s in self._subsystems_myproc] if MPI: sysbyproc = self.comm.allgather(systems) systems = set() for slist in sysbyproc: systems.update(slist) graph.add_nodes_from(systems) edge_data = defaultdict(lambda: defaultdict(list)) for in_abs, src_abs in iteritems(input_srcs): if src_abs is not None: if comps_only: src = src_abs.rsplit('.', 1)[0] tgt = in_abs.rsplit('.', 1)[0] else: src = src_abs.split('.')[glen] tgt = in_abs.split('.')[glen] # store var connection data in each system to system edge for later # use in relevance calculation. edge_data[(src, tgt)][src_abs].append(in_abs) for key in edge_data: src_sys, tgt_sys = key if comps_only or src_sys != tgt_sys: graph.add_edge(src_sys, tgt_sys, conns=edge_data[key]) return graph