westpa 2022.13__cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl

westpa/core/data_manager.py

@@ -0,0 +1,1761 @@
+"""
+HDF5 data manager for WEST.
+
+Original HDF5 implementation: Joseph W. Kaus
+Current implementation: Matthew C. Zwier
+
+WEST exclusively uses the cross-platform, self-describing file format HDF5
+for data storage. This ensures that data is stored efficiently and portably
+in a manner that is relatively straightforward for other analysis tools
+(perhaps written in C/C++/Fortran) to access.
+
+The data is laid out in HDF5 as follows:
+    - summary -- overall summary data for the simulation
+    - /iterations/ -- data for individual iterations, one group per iteration under /iterations
+        - iter_00000001/ -- data for iteration 1
+            - seg_index -- overall information about segments in the iteration, including weight
+            - pcoord -- progress coordinate data organized as [seg_id][time][dimension]
+            - wtg_parents -- data used to reconstruct the split/merge history of trajectories
+            - recycling -- flux and event count for recycled particles, on a per-target-state basis
+            - auxdata/ -- auxiliary datasets (data stored on the 'data' field of Segment objects)
+
+The file root object has an integer attribute 'west_file_format_version' which can be used to
+determine how to access data even as the file format (i.e. organization of data within HDF5 file)
+evolves.
+
+Version history:
+    Version 10
+        - BinMapper pickle, hash, and bin_target_count are now saved for iteration 1
+    Version 9
+        - Basis states are now saved as iter_segid instead of just segid as a pointer label.
+        - Initial states are also saved in the iteration 0 file, with a negative sign.
+    Version 8
+        - Added external links to trajectory files in iterations/iter_* groups, if the HDF5
+          framework was used.
+        - Added an iter group for the iteration 0 to store conformations of basis states.
+    Version 7
+        - Removed bin_assignments, bin_populations, and bin_rates from iteration group.
+        - Added new_segments subgroup to iteration group
+    Version 6
+        - ???
+    Version 5
+        - moved iter_* groups into a top-level iterations/ group,
+        - added in-HDF5 storage for basis states, target states, and generated states
+"""
+
+import logging
+import os
+import pickle
+import posixpath
+import sys
+import threading
+import time
+import re
+import builtins
+from operator import attrgetter
+from os.path import relpath, dirname, exists
+from os import remove
+from shutil import copyfile, move
+from subprocess import run, CalledProcessError
+
+import h5py
+from h5py import h5s
+import numpy as np
+
+from . import h5io
+from .segment import Segment
+from .states import BasisState, TargetState, InitialState
+from .we_driver import NewWeightEntry
+
+import westpa
+
+
+log = logging.getLogger(__name__)
+
+file_format_version = 10
+
+
+def makepath(template, template_args=None, expanduser=True, expandvars=True, abspath=False, realpath=False):
+    """Function for manipulating paths. Used in ExecutablePropagator as well."""
+    template_args = template_args or {}
+    path = template.format(**template_args)
+    if expandvars:
+        path = os.path.expandvars(path)
+    if expanduser:
+        path = os.path.expanduser(path)
+    if realpath:
+        path = os.path.realpath(path)
+    if abspath:
+        path = os.path.abspath(path)
+    path = os.path.normpath(path)
+    return path
+
+
+class flushing_lock:
+    def __init__(self, lock, fileobj):
+        self.lock = lock
+        self.fileobj = fileobj
+
+    def __enter__(self):
+        self.lock.acquire()
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.fileobj.flush()
+        self.lock.release()
+
+
+class expiring_flushing_lock:
+    def __init__(self, lock, flush_method, nextsync):
+        self.lock = lock
+        self.flush_method = flush_method
+        self.nextsync = nextsync
+
+    def __enter__(self):
+        self.lock.acquire()
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        if time.time() > self.nextsync:
+            self.flush_method()
+        self.lock.release()
+
+
+# Data types for use in the HDF5 file
+seg_id_dtype = np.int64  # Up to 9 quintillion segments per iteration; signed so that initial states can be stored negative
+n_iter_dtype = np.uint32  # Up to 4 billion iterations
+weight_dtype = np.float64  # about 15 digits of precision in weights
+utime_dtype = np.float64  # ("u" for Unix time) Up to ~10^300 cpu-seconds
+vstr_dtype = h5py.special_dtype(vlen=str)
+h5ref_dtype = h5py.special_dtype(ref=h5py.Reference)
+binhash_dtype = np.dtype('|S64')
+
+# seg_status_dtype    = h5py.special_dtype(enum=(np.uint8, Segment.statuses))
+# seg_initpoint_dtype = h5py.special_dtype(enum=(np.uint8, Segment.initpoint_types))
+# seg_endpoint_dtype  = h5py.special_dtype(enum=(np.uint8, Segment.endpoint_types))
+# istate_type_dtype   = h5py.special_dtype(enum=(np.uint8, InitialState.istate_types))
+# istate_status_dtype = h5py.special_dtype(enum=(np.uint8, InitialState.istate_statuses))
+
+seg_status_dtype = np.uint8
+seg_initpoint_dtype = np.uint8
+seg_endpoint_dtype = np.uint8
+istate_type_dtype = np.uint8
+istate_status_dtype = np.uint8
+
+summary_table_dtype = np.dtype(
+    [
+        ('n_particles', seg_id_dtype),  # Number of live trajectories in this iteration
+        ('norm', weight_dtype),  # Norm of probability, to watch for errors or drift
+        ('min_bin_prob', weight_dtype),  # Per-bin minimum probability
+        ('max_bin_prob', weight_dtype),  # Per-bin maximum probability
+        ('min_seg_prob', weight_dtype),  # Per-segment minimum probability
+        ('max_seg_prob', weight_dtype),  # Per-segment maximum probability
+        ('cputime', utime_dtype),  # Total CPU time for this iteration
+        ('walltime', utime_dtype),  # Total wallclock time for this iteration
+        ('binhash', binhash_dtype),
+    ]
+)
+
+
+# The HDF5 file tracks two distinct, but related, histories:
+#    (1) the evolution of the trajectory, which requires only an identifier
+#        of where a segment's initial state comes from (the "history graph");
+#        this is stored as the parent_id field of the seg index
+#    (2) the flow of probability due to splits, merges, and recycling events,
+#        which can be thought of as an adjacency list (the "weight graph")
+# segment ID is implied by the row in the index table, and so is not stored
+# initpoint_type remains implicitly stored as negative IDs (if parent_id < 0, then init_state_id = -(parent_id+1)
+seg_index_dtype = np.dtype(
+    [
+        ('weight', weight_dtype),  # Statistical weight of this segment
+        ('parent_id', seg_id_dtype),  # ID of parent (for trajectory history)
+        ('wtg_n_parents', np.uint),  # number of parents this segment has in the weight transfer graph
+        ('wtg_offset', np.uint),  # offset into the weight transfer graph dataset
+        ('cputime', utime_dtype),  # CPU time used in propagating this segment
+        ('walltime', utime_dtype),  # Wallclock time used in propagating this segment
+        ('endpoint_type', seg_endpoint_dtype),  # Endpoint type (will continue, merged, or recycled)
+        ('status', seg_status_dtype),  # Status of propagation of this segment
+    ]
+)
+
+# Index to basis/initial states
+ibstate_index_dtype = np.dtype([('iter_valid', np.uint), ('n_bstates', np.uint), ('group_ref', h5ref_dtype)])
+
+# Basis state index type
+bstate_dtype = np.dtype(
+    [
+        ('label', vstr_dtype),  # An optional descriptive label
+        ('probability', weight_dtype),  # Probability that this state will be selected
+        ('auxref', vstr_dtype),  # An optional auxiliar data reference
+    ]
+)
+
+# Even when initial state generation is off and basis states are passed through directly, an initial state entry
+# is created, as that allows precise tracing of the history of a given state in the most complex case of
+# a new initial state for every new trajectory.
+istate_dtype = np.dtype(
+    [
+        ('iter_created', np.uint),  # Iteration during which this state was generated (0 for at w_init)
+        ('iter_used', np.uint),  # When this state was used to start a new trajectory
+        ('basis_state_id', seg_id_dtype),  # Which basis state this state was generated from
+        ('istate_type', istate_type_dtype),  # What type this initial state is (generated or basis)
+        ('istate_status', istate_status_dtype),  # Whether this initial state is ready to go
+        ('basis_auxref', vstr_dtype),  # for start states to point back to their original location
+    ]
+)
+
+tstate_index_dtype = np.dtype(
+    [('iter_valid', np.uint), ('n_states', np.uint), ('group_ref', h5ref_dtype)]  # Iteration when this state list is valid
+)  # Reference to a group containing further data; this will be the
+# null reference if there is no target state for that timeframe.
+tstate_dtype = np.dtype([('label', vstr_dtype)])  # An optional descriptive label for this state
+
+# Support for west.we_driver.NewWeightEntry
+nw_source_dtype = np.uint8
+nw_index_dtype = np.dtype(
+    [
+        ('source_type', nw_source_dtype),
+        ('weight', weight_dtype),
+        ('prev_seg_id', seg_id_dtype),
+        ('target_state_id', seg_id_dtype),
+        ('initial_state_id', seg_id_dtype),
+    ]
+)
+
+# Storage of bin identities
+binning_index_dtype = np.dtype([('hash', binhash_dtype), ('pickle_len', np.uint32)])
+
+
+class WESTDataManager:
+    """Data manager for assisiting the reading and writing of WEST data from/to HDF5 files."""
+
+    # defaults for various options
+    default_iter_prec = 8
+    default_we_h5filename = 'west.h5'
+    default_we_h5file_driver = None
+    default_flush_period = 60
+
+    # Compress any auxiliary dataset whose total size (across all segments) is more than 1MB
+    default_aux_compression_threshold = 1048576
+
+    # Bin data horizontal (second dimension) chunk size
+    binning_hchunksize = 4096
+
+    # Number of rows to retrieve during a table scan
+    table_scan_chunksize = 1024
+
+    def flushing_lock(self):
+        return flushing_lock(self.lock, self.we_h5file)
+
+    def expiring_flushing_lock(self):
+        next_flush = self.last_flush + self.flush_period
+        return expiring_flushing_lock(self.lock, self.flush_backing, next_flush)
+
+    def process_config(self):
+        config = self.rc.config
+
+        for entry, type_ in [('iter_prec', int)]:
+            config.require_type_if_present(['west', 'data', entry], type_)
+
+        self.we_h5filename = config.get_path(['west', 'data', 'west_data_file'], default=self.default_we_h5filename)
+        self.we_h5file_driver = config.get_choice(
+            ['west', 'data', 'west_data_file_driver'],
+            [None, 'sec2', 'family'],
+            default=self.default_we_h5file_driver,
+            value_transform=(lambda x: x.lower() if x else None),
+        )
+        self.iter_prec = config.get(['west', 'data', 'iter_prec'], self.default_iter_prec)
+        self.aux_compression_threshold = config.get(
+            ['west', 'data', 'aux_compression_threshold'], self.default_aux_compression_threshold
+        )
+        self.flush_period = config.get(['west', 'data', 'flush_period'], self.default_flush_period)
+
+        # Path to per-iter h5 file
+        self.iter_h5_path_template = config.get(['west', 'data', 'data_refs', 'iteration'], None)
+        try:
+            # Generating path to a template file for per-iter h5 file
+            self.iter_h5_template_file_path = re.sub(r'\{(.*?)\}', 'template', self.iter_h5_path_template)
+        except TypeError:
+            self.iter_h5_template_file_path = None
+
+        # If not provided, turn HDF5 Framework off.
+        self.store_h5 = self.iter_h5_path_template is not None
+
+        # Process dataset options
+        dsopts_list = config.get(['west', 'data', 'datasets']) or []
+        for dsopts in dsopts_list:
+            dsopts = normalize_dataset_options(dsopts, path_prefix='auxdata' if dsopts['name'] != 'pcoord' else '')
+            try:
+                self.dataset_options[dsopts['name']].update(dsopts)
+            except KeyError:
+                self.dataset_options[dsopts['name']] = dsopts
+
+        if 'pcoord' in self.dataset_options:
+            if self.dataset_options['pcoord']['h5path'] != 'pcoord':
+                raise ValueError('cannot override pcoord storage location')
+
+    def __init__(self, rc=None):
+        self.rc = rc or westpa.rc
+
+        self.we_h5filename = self.default_we_h5filename
+        self.we_h5file_driver = self.default_we_h5file_driver
+        self.we_h5file_version = None
+        self.h5_access_mode = 'r+'
+        self.iter_prec = self.default_iter_prec
+        self.aux_compression_threshold = self.default_aux_compression_threshold
+
+        self.we_h5file = None
+
+        self.lock = threading.RLock()
+        self.flush_period = None
+        self.last_flush = 0
+
+        self._system = None
+        self.iter_h5_path_template = None  # Template for per-iter H5 file Path
+        self.iter_h5_template_file_path = None  # Path to per-iter H5 template file
+        self.store_h5 = False  # Indicates HDF5 Framework is activated or not
+        self.template_copy_flag = False  # Flag indicating the template file was made this iteration
+
+        self.dataset_options = {}
+        self.process_config()
+
+    @property
+    def system(self):
+        if self._system is None:
+            self._system = self.rc.get_system_driver()
+        return self._system
+
+    @system.setter
+    def system(self, system):
+        self._system = system
+
+    @property
+    def closed(self):
+        return self.we_h5file is None
+
+    def iter_group_name(self, n_iter, absolute=True):
+        if absolute:
+            return '/iterations/iter_{:0{prec}d}'.format(int(n_iter), prec=self.iter_prec)
+        else:
+            return 'iter_{:0{prec}d}'.format(int(n_iter), prec=self.iter_prec)
+
+    def require_iter_group(self, n_iter):
+        '''Get the group associated with n_iter, creating it if necessary.'''
+        with self.lock:
+            iter_group = self.we_h5file.require_group('/iterations/iter_{:0{prec}d}'.format(int(n_iter), prec=self.iter_prec))
+            iter_group.attrs['n_iter'] = n_iter
+        return iter_group
+
+    def del_iter_group(self, n_iter):
+        with self.lock:
+            del self.we_h5file['/iterations/iter_{:0{prec}d}'.format(int(n_iter), prec=self.iter_prec)]
+
+    def get_iter_group(self, n_iter):
+        with self.lock:
+            try:
+                return self.we_h5file['/iterations/iter_{:0{prec}d}'.format(int(n_iter), prec=self.iter_prec)]
+            except KeyError:
+                return self.we_h5file['/iter_{:0{prec}d}'.format(int(n_iter), prec=self.iter_prec)]
+
+    def get_seg_index(self, n_iter):
+        with self.lock:
+            seg_index = self.get_iter_group(n_iter)['seg_index']
+            return seg_index
+
+    @property
+    def current_iteration(self):
+        with self.lock:
+            h5file_attrs = self.we_h5file['/'].attrs
+            h5file_attr_keys = list(h5file_attrs.keys())
+
+            if 'west_current_iteration' in h5file_attr_keys:
+                return int(self.we_h5file['/'].attrs['west_current_iteration'])
+            else:
+                return int(self.we_h5file['/'].attrs['wemd_current_iteration'])
+
+    @current_iteration.setter
+    def current_iteration(self, n_iter):
+        with self.lock:
+            self.we_h5file['/'].attrs['west_current_iteration'] = n_iter
+
+    def open_backing(self, mode=None):
+        '''Open the (already-created) HDF5 file named in self.west_h5filename.'''
+        mode = mode or self.h5_access_mode
+        if not self.we_h5file:
+            log.debug('attempting to open {} with mode {}'.format(self.we_h5filename, mode))
+            self.we_h5file = h5io.WESTPAH5File(self.we_h5filename, mode, driver=self.we_h5file_driver)
+
+            h5file_attrs = self.we_h5file['/'].attrs
+            h5file_attr_keys = list(h5file_attrs.keys())
+
+            if 'west_iter_prec' in h5file_attr_keys:
+                self.iter_prec = int(h5file_attrs['west_iter_prec'])
+            elif 'wemd_iter_prec' in h5file_attr_keys:
+                self.iter_prec = int(h5file_attrs['wemd_iter_prec'])
+            else:
+                log.info('iteration precision not stored in HDF5; using {:d}'.format(self.iter_prec))
+
+            if 'west_file_format_version' in h5file_attr_keys:
+                self.we_h5file_version = h5file_attrs['west_file_format_version']
+            elif 'wemd_file_format_version' in h5file_attr_keys:
+                self.we_h5file_version = h5file_attrs['wemd_file_format_version']
+            else:
+                log.info('WEST HDF5 file format version not stored, assuming 0')
+                self.we_h5file_version = 0
+
+            log.debug('opened WEST HDF5 file version {:d}'.format(self.we_h5file_version))
+
+    def prepare_backing(self):  # istates):
+        '''Create new HDF5 file'''
+        self.we_h5file = h5py.File(self.we_h5filename, 'w', driver=self.we_h5file_driver)
+
+        with self.flushing_lock():
+            self.we_h5file['/'].attrs['west_file_format_version'] = file_format_version
+            self.we_h5file['/'].attrs['west_iter_prec'] = self.iter_prec
+            self.we_h5file['/'].attrs['west_version'] = westpa.__version__
+            self.current_iteration = 0
+            self.we_h5file['/'].create_dataset('summary', shape=(1,), dtype=summary_table_dtype, maxshape=(None,))
+            self.we_h5file.create_group('/iterations')
+
+    def close_backing(self):
+        if self.we_h5file is not None:
+            with self.lock:
+                self.we_h5file.close()
+            self.we_h5file = None
+
+    def flush_backing(self):
+        if self.we_h5file is not None:
+            with self.lock:
+                self.we_h5file.flush()
+                self.last_flush = time.time()
+
+    def save_target_states(self, tstates, n_iter=None):
+        """
+        Save the given target states in the HDF5 file; they will be used for the next iteration to
+        be propagated.  A complete set is required, even if nominally appending to an existing set,
+        which simplifies the mapping of IDs to the table.
+        """
+
+        system = self.system
+
+        n_iter = n_iter or self.current_iteration
+
+        # Assemble all the important data before we start to modify the HDF5 file
+        tstates = list(tstates)
+        if tstates:
+            state_table = np.empty((len(tstates),), dtype=tstate_dtype)
+            state_pcoords = np.empty((len(tstates), system.pcoord_ndim), dtype=system.pcoord_dtype)
+            for i, state in enumerate(tstates):
+                state.state_id = i
+                state_table[i]['label'] = state.label
+                state_pcoords[i] = state.pcoord
+        else:
+            state_table = None
+            state_pcoords = None
+
+        # Commit changes to HDF5
+        with self.lock:
+            master_group = self.we_h5file.require_group('tstates')
+
+            try:
+                master_index = master_group['index']
+            except KeyError:
+                master_index = master_group.create_dataset('index', shape=(1,), maxshape=(None,), dtype=tstate_index_dtype)
+                n_sets = 1
+            else:
+                n_sets = len(master_index) + 1
+                master_index.resize((n_sets,))
+
+            set_id = n_sets - 1
+            master_index_row = master_index[set_id]
+            master_index_row['iter_valid'] = n_iter
+            master_index_row['n_states'] = len(tstates)
+
+            if tstates:
+                state_group = master_group.create_group(str(set_id))
+                master_index_row['group_ref'] = state_group.ref
+                state_group['index'] = state_table
+                state_group['pcoord'] = state_pcoords
+            else:
+                master_index_row['group_ref'] = None
+
+            master_index[set_id] = master_index_row
+
+    def _find_multi_iter_group(self, n_iter, master_group_name):
+        with self.lock:
+            master_group = self.we_h5file[master_group_name]
+            master_index = master_group['index'][...]
+            set_id = np.digitize([n_iter], master_index['iter_valid']) - 1
+            group_ref = master_index[set_id]['group_ref']
+
+            # Check if reference is Null
+            if not bool(group_ref):
+                return None
+
+            # This extra [0] is to work around a bug in h5py
+            try:
+                group = self.we_h5file[group_ref]
+            except (TypeError, AttributeError):
+                group = self.we_h5file[group_ref[0]]
+            else:
+                log.debug('h5py fixed; remove alternate code path')
+            log.debug('reference {!r} points to group {!r}'.format(group_ref, group))
+            return group
+
+    def find_tstate_group(self, n_iter):
+        return self._find_multi_iter_group(n_iter, 'tstates')
+
+    def find_ibstate_group(self, n_iter):
+        return self._find_multi_iter_group(n_iter, 'ibstates')
+
+    def get_target_states(self, n_iter):
+        '''Return a list of Target objects representing the target (sink) states that are in use for iteration n_iter.
+        Future iterations are assumed to continue from the most recent set of states.'''
+
+        with self.lock:
+            tstate_group = self.find_tstate_group(n_iter)
+
+            if tstate_group is not None:
+                tstate_index = tstate_group['index'][...]
+                tstate_pcoords = tstate_group['pcoord'][...]
+
+                tstates = [
+                    TargetState(state_id=i, label=h5io.tostr(row['label']), pcoord=pcoord.copy())
+                    for (i, (row, pcoord)) in enumerate(zip(tstate_index, tstate_pcoords))
+                ]
+            else:
+                tstates = []
+
+            return tstates
+
+    def create_ibstate_group(self, basis_states, n_iter=None):
+        '''Create the group used to store basis states and initial states (whose definitions are always
+        coupled).  This group is hard-linked into all iteration groups that use these basis and
+        initial states.'''
+
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            master_group = self.we_h5file.require_group('ibstates')
+
+            try:
+                master_index = master_group['index']
+            except KeyError:
+                master_index = master_group.create_dataset('index', dtype=ibstate_index_dtype, shape=(1,), maxshape=(None,))
+                n_sets = 1
+            else:
+                n_sets = len(master_index) + 1
+                master_index.resize((n_sets,))
+
+            set_id = n_sets - 1
+            master_index_row = master_index[set_id]
+            master_index_row['iter_valid'] = n_iter
+            master_index_row['n_bstates'] = len(basis_states)
+            state_group = master_group.create_group(str(set_id))
+            master_index_row['group_ref'] = state_group.ref
+
+            if basis_states:
+                system = self.system
+                state_table = np.empty((len(basis_states),), dtype=bstate_dtype)
+                state_pcoords = np.empty((len(basis_states), system.pcoord_ndim), dtype=system.pcoord_dtype)
+                for i, state in enumerate(basis_states):
+                    state.state_id = i
+                    state_table[i]['label'] = state.label
+                    state_table[i]['probability'] = state.probability
+                    state_table[i]['auxref'] = state.auxref or ''
+                    state_pcoords[i] = state.pcoord
+
+                state_group['bstate_index'] = state_table
+                state_group['bstate_pcoord'] = state_pcoords
+
+            master_index[set_id] = master_index_row
+            return state_group
+
+    def create_ibstate_iter_h5file(self, basis_states):
+        """
+        Create the per-iteration HDF5 file for the basis states (i.e., iteration 0).
+        This special treatment is needed so that the analysis tools can access basis states
+        more easily.
+        """
+
+        if not self.store_h5:
+            return
+
+        segments = []
+        for i, state in enumerate(basis_states):
+            dummy_segment = Segment(
+                n_iter=0,
+                seg_id=state.state_id,
+                parent_id=-(state.state_id + 1),
+                weight=state.probability,
+                wtg_parent_ids=None,
+                pcoord=state.pcoord,
+                status=Segment.SEG_STATUS_UNSET,
+                data=state.data,
+            )
+            segments.append(dummy_segment)
+
+        # # link the iteration file in west.h5
+        self.prepare_iteration(0, segments)
+        self.update_iter_h5file(0, segments)
+
+    def update_iter_h5file(self, n_iter, segments):
+        """Write out the per-iteration HDF5 file with given segments and add an external link to it
+        in the main HDF5 file (west.h5) if the link is not present."""
+
+        if not self.store_h5:
+            return
+
+        west_h5_file = makepath(self.we_h5filename)
+        iter_ref_h5_file = makepath(self.iter_h5_path_template, {'n_iter': n_iter})
+        iter_ref_rel_path = relpath(iter_ref_h5_file, dirname(west_h5_file))
+        if self.iter_h5_template_file_path:
+            # Make path to per-iter H5 File
+            iter_h5_template_file_path_expanded = makepath(self.iter_h5_template_file_path)
+
+            # Copy the template per-iter H5 file with topology
+            if exists(iter_h5_template_file_path_expanded) and not exists(iter_ref_h5_file):
+                copyfile(iter_h5_template_file_path_expanded, iter_ref_h5_file)
+
+        with h5io.WESTIterationFile(iter_ref_h5_file, 'a') as outf:
+            for segment in segments:
+                outf.write_segment(segment, True)
+
+        if self.iter_h5_template_file_path and not exists(iter_h5_template_file_path_expanded):
+            # If template per-iter H5 file does not exist, copy and scrub out old data
+            copyfile(iter_ref_h5_file, iter_h5_template_file_path_expanded)
+            with h5io.WESTIterationFile(iter_h5_template_file_path_expanded, 'a') as outf:
+                outf.scrub_data()
+
+            # Launch a subprocess to repack the file to reclaim space, replacing template with smaller file
+            try:
+                run(
+                    f'h5repack {iter_h5_template_file_path_expanded} {iter_h5_template_file_path_expanded}_repacked.h5', shell=True
+                ).check_returncode()
+                move(f'{iter_h5_template_file_path_expanded}_repacked.h5', iter_h5_template_file_path_expanded)
+            except CalledProcessError as e:  # Unsuccessful in repacking file
+                log.warning(f'Unable to repack into {iter_h5_template_file_path_expanded}_repacked.h5: {e}')
+                if exists(f'{iter_h5_template_file_path_expanded}_repacked.h5'):
+                    remove(f'{iter_h5_template_file_path_expanded}_repacked.h5')
+
+        iter_group = self.get_iter_group(n_iter)
+
+        if 'trajectories' not in iter_group:
+            iter_group['trajectories'] = h5py.ExternalLink(iter_ref_rel_path, '/')
+
+    def get_basis_states(self, n_iter=None):
+        """Return a list of BasisState objects representing the basis states that are in use for iteration n_iter."""
+
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            ibstate_group = self.find_ibstate_group(n_iter)
+            try:
+                bstate_index = ibstate_group['bstate_index'][...]
+            except KeyError:
+                return []
+            bstate_pcoords = ibstate_group['bstate_pcoord'][...]
+            bstates = [
+                BasisState(
+                    state_id=i,
+                    label=h5io.tostr(row['label']),
+                    probability=row['probability'],
+                    auxref=h5io.tostr(row['auxref']) or None,
+                    pcoord=pcoord.copy(),
+                )
+                for (i, (row, pcoord)) in enumerate(zip(bstate_index, bstate_pcoords))
+            ]
+
+            bstate_total_prob = sum(bstate.probability for bstate in bstates)
+
+            # This should run once in the second iteration, and only if start-states are specified,
+            # but is necessary to re-normalize (i.e. normalize without start-state probabilities included)
+            for i, bstate in enumerate(bstates):
+                bstate.probability /= bstate_total_prob
+                bstates[i] = bstate
+            return bstates
+
+    def create_initial_states(self, n_states, n_iter=None):
+        """Create storage for ``n_states`` initial states associated with iteration ``n_iter``, and
+        return bare InitialState objects with only state_id set."""
+
+        system = self.system
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            ibstate_group = self.find_ibstate_group(n_iter)
+
+            try:
+                istate_index = ibstate_group['istate_index']
+            except KeyError:
+                istate_index = ibstate_group.create_dataset('istate_index', dtype=istate_dtype, shape=(n_states,), maxshape=(None,))
+                istate_pcoords = ibstate_group.create_dataset(
+                    'istate_pcoord',
+                    dtype=system.pcoord_dtype,
+                    shape=(n_states, system.pcoord_ndim),
+                    maxshape=(None, system.pcoord_ndim),
+                )
+                len_index = len(istate_index)
+                first_id = 0
+            else:
+                first_id = len(istate_index)
+                len_index = len(istate_index) + n_states
+                istate_index.resize((len_index,))
+                istate_pcoords = ibstate_group['istate_pcoord']
+                istate_pcoords.resize((len_index, system.pcoord_ndim))
+
+        index_entries = istate_index[first_id:len_index]
+        new_istates = []
+        for irow, row in enumerate(index_entries):
+            row['iter_created'] = n_iter
+            row['istate_status'] = InitialState.ISTATE_STATUS_PENDING
+            new_istates.append(
+                InitialState(
+                    state_id=first_id + irow,
+                    basis_state_id=None,
+                    iter_created=n_iter,
+                    istate_status=InitialState.ISTATE_STATUS_PENDING,
+                )
+            )
+        istate_index[first_id:len_index] = index_entries
+        return new_istates
+
+    def update_initial_states(self, initial_states, n_iter=None):
+        """Save the given initial states in the HDF5 file"""
+
+        system = self.system
+        initial_states = sorted(initial_states, key=attrgetter('state_id'))
+        if not initial_states:
+            return
+
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            ibstate_group = self.find_ibstate_group(n_iter)
+            state_ids = [state.state_id for state in initial_states]
+            index_entries = ibstate_group['istate_index'][state_ids]
+            pcoord_vals = np.empty((len(initial_states), system.pcoord_ndim), dtype=system.pcoord_dtype)
+            for i, initial_state in enumerate(initial_states):
+                index_entries[i]['iter_created'] = initial_state.iter_created
+                index_entries[i]['iter_used'] = initial_state.iter_used or InitialState.ISTATE_UNUSED
+                index_entries[i]['basis_state_id'] = (
+                    initial_state.basis_state_id if initial_state.basis_state_id is not None else -1
+                )
+                index_entries[i]['istate_type'] = initial_state.istate_type or InitialState.ISTATE_TYPE_UNSET
+                index_entries[i]['istate_status'] = initial_state.istate_status or InitialState.ISTATE_STATUS_PENDING
+                pcoord_vals[i] = initial_state.pcoord
+
+                index_entries[i]['basis_auxref'] = initial_state.basis_auxref or ""
+
+            ibstate_group['istate_index'][state_ids] = index_entries
+            ibstate_group['istate_pcoord'][state_ids] = pcoord_vals
+
+            if self.store_h5:
+                segments = []
+                for i, state in enumerate(initial_states):
+                    dummy_segment = Segment(
+                        n_iter=-state.iter_created,
+                        seg_id=state.state_id,
+                        parent_id=state.basis_state_id,
+                        wtg_parent_ids=None,
+                        pcoord=state.pcoord,
+                        status=Segment.SEG_STATUS_PREPARED,
+                        data=state.data,
+                    )
+                    segments.append(dummy_segment)
+                self.update_iter_h5file(0, segments)
+
+    def get_initial_states(self, n_iter=None):
+        states = []
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            ibstate_group = self.find_ibstate_group(n_iter)
+            try:
+                istate_index = ibstate_group['istate_index'][...]
+            except KeyError:
+                return []
+            istate_pcoords = ibstate_group['istate_pcoord'][...]
+
+            for state_id, (state, pcoord) in enumerate(zip(istate_index, istate_pcoords)):
+                states.append(
+                    InitialState(
+                        state_id=state_id,
+                        basis_state_id=int(state['basis_state_id']),
+                        iter_created=int(state['iter_created']),
+                        iter_used=int(state['iter_used']),
+                        istate_type=int(state['istate_type']),
+                        basis_auxref=h5io.tostr(state['basis_auxref']),
+                        pcoord=pcoord.copy(),
+                    )
+                )
+            return states
+
+    def get_segment_initial_states(self, segments, n_iter=None):
+        '''Retrieve all initial states referenced by the given segments.'''
+
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            ibstate_group = self.get_iter_group(n_iter)['ibstates']
+
+            istate_ids = {-int(segment.parent_id + 1) for segment in segments if segment.parent_id < 0}
+            sorted_istate_ids = sorted(istate_ids)
+            if not sorted_istate_ids:
+                return []
+
+            istate_rows = ibstate_group['istate_index'][sorted_istate_ids][...]
+            istate_pcoords = ibstate_group['istate_pcoord'][sorted_istate_ids][...]
+            istates = []
+
+            for state_id, state, pcoord in zip(sorted_istate_ids, istate_rows, istate_pcoords):
+                try:
+                    b_auxref = h5io.tostr(state['basis_auxref'])
+                except ValueError:
+                    b_auxref = ''
+                istate = InitialState(
+                    state_id=state_id,
+                    basis_state_id=int(state['basis_state_id']),
+                    iter_created=int(state['iter_created']),
+                    iter_used=int(state['iter_used']),
+                    istate_type=int(state['istate_type']),
+                    basis_auxref=b_auxref,
+                    pcoord=pcoord.copy(),
+                )
+                istates.append(istate)
+            return istates
+
+    def get_unused_initial_states(self, n_states=None, n_iter=None):
+        """Retrieve any prepared but unused initial states applicable to the given iteration.
+        Up to ``n_states`` states are returned; if ``n_states`` is None, then all unused states
+        are returned."""
+
+        n_states = n_states or sys.maxsize
+        ISTATE_UNUSED = InitialState.ISTATE_UNUSED
+        ISTATE_STATUS_PREPARED = InitialState.ISTATE_STATUS_PREPARED
+        with self.lock:
+            n_iter = n_iter or self.current_iteration
+            ibstate_group = self.find_ibstate_group(n_iter)
+            istate_index = ibstate_group['istate_index']
+            istate_pcoords = ibstate_group['istate_pcoord']
+            n_index_entries = istate_index.len()
+            chunksize = self.table_scan_chunksize
+
+            states = []
+            istart = 0
+            while istart < n_index_entries and len(states) < n_states:
+                istop = min(istart + chunksize, n_index_entries)
+                istate_chunk = istate_index[istart:istop]
+                pcoord_chunk = istate_pcoords[istart:istop]
+                # state_ids = np.arange(istart,istop,dtype=np.uint)
+
+                for ci in range(len(istate_chunk)):
+                    row = istate_chunk[ci]
+                    pcoord = pcoord_chunk[ci]
+                    state_id = istart + ci
+                    if row['iter_used'] == ISTATE_UNUSED and row['istate_status'] == ISTATE_STATUS_PREPARED:
+                        istate = InitialState(
+                            state_id=state_id,
+                            basis_state_id=int(row['basis_state_id']),
+                            iter_created=int(row['iter_created']),
+                            iter_used=0,
+                            istate_type=int(row['istate_type']),
+                            pcoord=pcoord.copy(),
+                            istate_status=ISTATE_STATUS_PREPARED,
+                        )
+                        states.append(istate)
+                    del row, pcoord, state_id
+                istart += chunksize
+                del istate_chunk, pcoord_chunk  # , state_ids, unused, ids_of_unused
+            log.debug('found {:d} unused states'.format(len(states)))
+            return states[:n_states]
+
+    def prepare_iteration(self, n_iter, segments):
+        """Prepare for a new iteration by creating space to store the new iteration's data.
+        The number of segments, their IDs, and their lineage must be determined and included
+        in the set of segments passed in."""
+
+        log.debug('preparing HDF5 group for iteration %d (%d segments)' % (n_iter, len(segments)))
+
+        # Ensure we have a list for guaranteed ordering
+        init = n_iter == 0
+        segments = list(segments)
+        n_particles = len(segments)
+        system = self.system
+        pcoord_ndim = system.pcoord_ndim
+        pcoord_len = 2 if init else system.pcoord_len
+        pcoord_dtype = system.pcoord_dtype
+
+        with self.lock:
+            if not init:
+                # Create a table of summary information about each iteration
+                summary_table = self.we_h5file['summary']
+                if len(summary_table) < n_iter:
+                    summary_table.resize((n_iter + 1,))
+
+            iter_group = self.require_iter_group(n_iter)
+
+            for linkname in ('seg_index', 'pcoord', 'wtgraph'):
+                try:
+                    del iter_group[linkname]
+                except KeyError:
+                    pass
+
+            # everything indexed by [particle] goes in an index table
+            seg_index_table_ds = iter_group.create_dataset('seg_index', shape=(n_particles,), dtype=seg_index_dtype)
+            # unfortunately, h5py doesn't like in-place modification of individual fields; it expects
+            # tuples. So, construct everything in a numpy array and then dump the whole thing into hdf5
+            # In fact, this appears to be an h5py best practice (collect as much in ram as possible and then dump)
+            seg_index_table = seg_index_table_ds[...]
+
+            if not init:
+                summary_row = np.zeros((1,), dtype=summary_table_dtype)
+                summary_row['n_particles'] = n_particles
+                summary_row['norm'] = np.add.reduce(list(map(attrgetter('weight'), segments)))
+                summary_table[n_iter - 1] = summary_row
+
+            # pcoord is indexed as [particle, time, dimension]
+            pcoord_opts = self.dataset_options.get('pcoord', {'name': 'pcoord', 'h5path': 'pcoord', 'compression': False})
+            shape = (n_particles, pcoord_len, pcoord_ndim)
+            pcoord_ds = create_dataset_from_dsopts(iter_group, pcoord_opts, shape, pcoord_dtype)
+            pcoord = np.empty((n_particles, pcoord_len, pcoord_ndim), pcoord_dtype)
+
+            total_parents = 0
+            for seg_id, segment in enumerate(segments):
+                if segment.seg_id is not None:
+                    assert segment.seg_id == seg_id
+                else:
+                    segment.seg_id = seg_id
+                # Parent must be set, though what it means depends on initpoint_type
+                assert segment.parent_id is not None
+                segment.seg_id = seg_id
+                seg_index_table[seg_id]['status'] = segment.status
+                seg_index_table[seg_id]['weight'] = segment.weight
+                seg_index_table[seg_id]['parent_id'] = segment.parent_id
+                seg_index_table[seg_id]['wtg_n_parents'] = len(segment.wtg_parent_ids)
+                seg_index_table[seg_id]['wtg_offset'] = total_parents
+                total_parents += len(segment.wtg_parent_ids)
+
+                # Assign progress coordinate if any exists
+                if segment.pcoord is not None:
+                    if init:
+                        if segment.pcoord.shape != pcoord.shape[2:]:
+                            raise ValueError(
+                                'basis state pcoord shape [%r] does not match expected shape [%r]'
+                                % (segment.pcoord.shape, pcoord.shape[2:])
+                            )
+                        # Initial pcoord
+                        pcoord[seg_id, 1, :] = segment.pcoord[:]
+                    else:
+                        if len(segment.pcoord) == 1:
+                            # Initial pcoord
+                            pcoord[seg_id, 0, :] = segment.pcoord[0, :]
+                        elif segment.pcoord.shape != pcoord.shape[1:]:
+                            raise ValueError(
+                                'segment pcoord shape [%r] does not match expected shape [%r]'
+                                % (segment.pcoord.shape, pcoord.shape[1:])
+                            )
+                        else:
+                            pcoord[seg_id, ...] = segment.pcoord
+
+            if total_parents > 0:
+                wtgraph_ds = iter_group.create_dataset('wtgraph', (total_parents,), seg_id_dtype, compression='gzip', shuffle=True)
+                parents = np.empty((total_parents,), seg_id_dtype)
+
+                for seg_id, segment in enumerate(segments):
+                    offset = seg_index_table[seg_id]['wtg_offset']
+                    extent = seg_index_table[seg_id]['wtg_n_parents']
+                    parent_list = list(segment.wtg_parent_ids)
+                    parents[offset : offset + extent] = parent_list[:]
+
+                    assert set(parents[offset : offset + extent]) == set(segment.wtg_parent_ids)
+
+                wtgraph_ds[:] = parents
+
+            # Create convenient hard links
+            self.update_iter_group_links(n_iter)
+
+            # Since we accumulated many of these changes in RAM (and not directly in HDF5), propagate
+            # the changes out to HDF5
+            seg_index_table_ds[:] = seg_index_table
+            pcoord_ds[...] = pcoord
+
+    def update_iter_group_links(self, n_iter):
+        """Update the per-iteration hard links pointing to the tables of target and initial/basis states for the
+        given iteration.  These links are not used by this class, but are remarkably convenient for third-party
+        analysis tools and hdfview."""
+
+        with self.lock:
+            iter_group = self.require_iter_group(n_iter)
+
+            for linkname in ('ibstates', 'tstates'):
+                try:
+                    del iter_group[linkname]
+                except KeyError:
+                    pass
+
+            iter_group['ibstates'] = self.find_ibstate_group(n_iter)
+
+            tstate_group = self.find_tstate_group(n_iter)
+            if tstate_group is not None:
+                iter_group['tstates'] = tstate_group
+
+    def get_iter_summary(self, n_iter=None):
+        n_iter = n_iter or self.current_iteration
+        with self.lock:
+            return self.we_h5file['summary'][n_iter - 1]
+
+    def update_iter_summary(self, summary, n_iter=None):
+        n_iter = n_iter or self.current_iteration
+        with self.lock:
+            self.we_h5file['summary'][n_iter - 1] = summary
+
+    def del_iter_summary(self, min_iter):  # delete the iterations starting at min_iter
+        with self.lock:
+            self.we_h5file['summary'].resize((min_iter - 1,))
+
+    def update_segments(self, n_iter, segments):
+        """Update segment information in the HDF5 file; all prior information for each
+        ``segment`` is overwritten, except for parent and weight transfer information."""
+
+        segments = sorted(segments, key=attrgetter('seg_id'))
+
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+
+            pc_dsid = iter_group['pcoord'].id
+            si_dsid = iter_group['seg_index'].id
+
+            seg_ids = [segment.seg_id for segment in segments]
+            n_segments = len(segments)
+            n_total_segments = si_dsid.shape[0]
+            system = self.system
+            pcoord_ndim = system.pcoord_ndim
+            pcoord_len = system.pcoord_len
+            pcoord_dtype = system.pcoord_dtype
+
+            seg_index_entries = np.empty((n_segments,), dtype=seg_index_dtype)
+            pcoord_entries = np.empty((n_segments, pcoord_len, pcoord_ndim), dtype=pcoord_dtype)
+
+            pc_msel = h5s.create_simple(pcoord_entries.shape, (h5s.UNLIMITED,) * pcoord_entries.ndim)
+            pc_msel.select_all()
+            si_msel = h5s.create_simple(seg_index_entries.shape, (h5s.UNLIMITED,))
+            si_msel.select_all()
+            pc_fsel = pc_dsid.get_space()
+            si_fsel = si_dsid.get_space()
+
+            for iseg in range(n_segments):
+                seg_id = seg_ids[iseg]
+                op = h5s.SELECT_OR if iseg != 0 else h5s.SELECT_SET
+                si_fsel.select_hyperslab((seg_id,), (1,), op=op)
+                pc_fsel.select_hyperslab((seg_id, 0, 0), (1, pcoord_len, pcoord_ndim), op=op)
+
+            # read summary data so that we have value, parent and weight transfer information
+            si_dsid.read(si_msel, si_fsel, seg_index_entries)
+
+            for iseg, (segment, ientry) in enumerate(zip(segments, seg_index_entries)):
+                ientry['status'] = segment.status
+                ientry['endpoint_type'] = segment.endpoint_type or Segment.SEG_ENDPOINT_UNSET
+                ientry['cputime'] = segment.cputime
+                ientry['walltime'] = segment.walltime
+                ientry['weight'] = segment.weight
+
+                pcoord_entries[iseg] = segment.pcoord
+
+            # write progress coordinates and index using low level HDF5 functions for efficiency
+            si_dsid.write(si_msel, si_fsel, seg_index_entries)
+            pc_dsid.write(pc_msel, pc_fsel, pcoord_entries)
+
+            # Now, to deal with auxiliary data
+            # If any segment has any auxiliary data, then the aux dataset must spring into
+            # existence. Each is named according to the name in segment.data, and has shape
+            # (n_total_segs, ...) where the ... is the shape of the data in segment.data (and may be empty
+            # in the case of scalar data) and dtype is taken from the data type of the data entry
+            # compression is on by default for datasets that will be more than 1MiB
+
+            # a mapping of data set name to (per-segment shape, data type) tuples
+            dsets = {}
+
+            # First we scan for presence, shape, and data type of auxiliary data sets
+            for segment in segments:
+                if segment.data:
+                    for dsname in segment.data:
+                        if dsname.startswith('iterh5/'):
+                            continue
+                        data = np.asarray(segment.data[dsname], order='C')
+                        segment.data[dsname] = data
+                        dsets[dsname] = (data.shape, data.dtype)
+
+            # Then we iterate over data sets and store data
+            if dsets:
+                for dsname, (shape, dtype) in dsets.items():
+                    # dset = self._require_aux_dataset(iter_group, dsname, n_total_segments, shape, dtype)
+                    try:
+                        dsopts = self.dataset_options[dsname]
+                    except KeyError:
+                        dsopts = normalize_dataset_options({'name': dsname}, path_prefix='auxdata')
+
+                    shape = (n_total_segments,) + shape
+                    dset = require_dataset_from_dsopts(
+                        iter_group, dsopts, shape, dtype, autocompress_threshold=self.aux_compression_threshold, n_iter=n_iter
+                    )
+                    if dset is None:
+                        # storage is suppressed
+                        continue
+                    for segment in segments:
+                        try:
+                            auxdataset = segment.data[dsname]
+                        except KeyError:
+                            pass
+                        else:
+                            source_rank = len(auxdataset.shape)
+                            source_sel = h5s.create_simple(auxdataset.shape, (h5s.UNLIMITED,) * source_rank)
+                            source_sel.select_all()
+                            dest_sel = dset.id.get_space()
+                            dest_sel.select_hyperslab((segment.seg_id,) + (0,) * source_rank, (1,) + auxdataset.shape)
+                            dset.id.write(source_sel, dest_sel, auxdataset)
+                    if 'delram' in list(dsopts.keys()):
+                        del dsets[dsname]
+
+            self.update_iter_h5file(n_iter, segments)
+
+    def get_segments(self, n_iter=None, seg_ids=None, load_pcoords=True):
+        """
+        Return the given (or all) segments from a given iteration.
+
+        If the optional parameter ``load_auxdata`` is true, then all auxiliary datasets
+        available are loaded and mapped onto the ``data`` dictionary of each segment. If
+        ``load_auxdata`` is None, then use the default ``self.auto_load_auxdata``, which can
+        be set by the option ``load_auxdata`` in the ``[data]`` section of ``west.cfg``. This
+        essentially requires as much RAM as there is per-iteration auxiliary data, so this
+        behavior is not on by default.
+        """
+
+        n_iter = n_iter or self.current_iteration
+        file_version = self.we_h5file_version
+
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+            seg_index_ds = iter_group['seg_index']
+
+            if file_version < 5:
+                all_parent_ids = iter_group['parents'][...]
+            else:
+                all_parent_ids = iter_group['wtgraph'][...]
+
+            if seg_ids is not None:
+                seg_ids = list(sorted(seg_ids))
+                seg_index_entries = seg_index_ds[seg_ids]
+                if load_pcoords:
+                    pcoord_entries = iter_group['pcoord'][seg_ids]
+            else:
+                seg_ids = list(range(len(seg_index_ds)))
+                seg_index_entries = seg_index_ds[...]
+                if load_pcoords:
+                    pcoord_entries = iter_group['pcoord'][...]
+
+            segments = []
+
+            for iseg, (seg_id, row) in enumerate(zip(seg_ids, seg_index_entries)):
+                segment = Segment(
+                    seg_id=seg_id,
+                    n_iter=n_iter,
+                    status=int(row['status']),
+                    endpoint_type=int(row['endpoint_type']),
+                    walltime=float(row['walltime']),
+                    cputime=float(row['cputime']),
+                    weight=float(row['weight']),
+                )
+
+                if load_pcoords:
+                    segment.pcoord = pcoord_entries[iseg]
+
+                if file_version < 5:
+                    wtg_n_parents = row['n_parents']
+                    wtg_offset = row['parents_offset']
+                    wtg_parent_ids = all_parent_ids[wtg_offset : wtg_offset + wtg_n_parents]
+                    segment.parent_id = int(wtg_parent_ids[0])
+                else:
+                    wtg_n_parents = row['wtg_n_parents']
+                    wtg_offset = row['wtg_offset']
+                    wtg_parent_ids = all_parent_ids[wtg_offset : wtg_offset + wtg_n_parents]
+                    segment.parent_id = int(row['parent_id'])
+                segment.wtg_parent_ids = set(map(int, wtg_parent_ids))
+                assert len(segment.wtg_parent_ids) == wtg_n_parents
+                segments.append(segment)
+            del all_parent_ids
+            if load_pcoords:
+                del pcoord_entries
+
+            # If any other data sets are requested, load them as well
+            for dsinfo in self.dataset_options.values():
+                if dsinfo.get('load', False):
+                    dsname = dsinfo['name']
+                    try:
+                        ds = iter_group[dsinfo['h5path']]
+                    except KeyError:
+                        ds = None
+
+                    if ds is not None:
+                        for segment in segments:
+                            seg_id = segment.seg_id
+                            segment.data[dsname] = ds[seg_id]
+
+        return segments
+
+    def prepare_segment_restarts(self, segments, basis_states=None, initial_states=None):
+        """
+        Prepare the necessary folder and files given the data stored in parent per-iteration HDF5 file
+        for propagating the simulation. ``basis_states`` and ``initial_states`` should be provided if the
+        segments are newly created
+        """
+
+        if not self.store_h5:
+            return
+
+        for segment in segments:
+            if segment.parent_id < 0:
+                if initial_states is None or basis_states is None:
+                    raise ValueError('initial and basis states required for preparing the segments')
+                initial_state = initial_states[segment.initial_state_id]
+                # Check if it's a start state
+                if initial_state.istate_type == InitialState.ISTATE_TYPE_START:
+                    log.debug(
+                        f'Skip reading start state file from per-iteration HDF5 file for initial state {segment.initial_state_id}'
+                    )
+                    continue
+                else:
+                    basis_state = basis_states[initial_state.basis_state_id]
+
+                parent = Segment(n_iter=0, seg_id=basis_state.state_id)
+            else:
+                parent = Segment(n_iter=segment.n_iter - 1, seg_id=segment.parent_id)
+
+            try:
+                parent_iter_ref_h5_file = makepath(self.iter_h5_path_template, {'n_iter': parent.n_iter})
+
+                with h5io.WESTIterationFile(parent_iter_ref_h5_file, 'r') as outf:
+                    outf.read_restart(parent)
+
+                segment.data['iterh5/restart'] = parent.data['iterh5/restart']
+            except Exception as e:
+                print('could not prepare restart data for segment {}/{}: {}'.format(segment.n_iter, segment.seg_id, str(e)))
+
+    def get_all_parent_ids(self, n_iter):
+        file_version = self.we_h5file_version
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+            seg_index = iter_group['seg_index']
+
+            if file_version < 5:
+                offsets = seg_index['parents_offset']
+                all_parents = iter_group['parents'][...]
+                return all_parents.take(offsets)
+            else:
+                return seg_index['parent_id']
+
+    def get_parent_ids(self, n_iter, seg_ids=None):
+        '''Return a sequence of the parent IDs of the given seg_ids.'''
+
+        file_version = self.we_h5file_version
+
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+            seg_index = iter_group['seg_index']
+
+            if seg_ids is None:
+                seg_ids = range(len(seg_index))
+
+            if file_version < 5:
+                offsets = seg_index['parents_offset']
+                all_parents = iter_group['parents'][...]
+                return [all_parents[offsets[seg_id]] for seg_id in seg_ids]
+            else:
+                all_parents = seg_index['parent_id']
+                return [all_parents[seg_id] for seg_id in seg_ids]
+
+    def get_weights(self, n_iter, seg_ids):
+        '''Return the weights associated with the given seg_ids'''
+
+        unique_ids = sorted(set(seg_ids))
+        if not unique_ids:
+            return []
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+            index_subset = iter_group['seg_index'][unique_ids]
+            weight_map = dict(zip(unique_ids, index_subset['weight']))
+            return [weight_map[seg_id] for seg_id in seg_ids]
+
+    def get_child_ids(self, n_iter, seg_id):
+        """Return the seg_ids of segments who have the given segment as a parent."""
+
+        with self.lock:
+            if n_iter == self.current_iteration:
+                return []
+
+            iter_group = self.get_iter_group(n_iter + 1)
+            seg_index = iter_group['seg_index']
+            seg_ids = np.arange(len(seg_index), dtype=seg_id_dtype)
+
+            if self.we_h5file_version < 5:
+                offsets = seg_index['parents_offset']
+                all_parent_ids = iter_group['parents'][...]
+                parent_ids = np.array([all_parent_ids[offset] for offset in offsets])
+            else:
+                parent_ids = seg_index['parent_id']
+
+            return seg_ids[parent_ids == seg_id]
+
+    def get_children(self, segment):
+        """Return all segments which have the given segment as a parent"""
+
+        if segment.n_iter == self.current_iteration:
+            return []
+
+        # Examine the segment index from the following iteration to see who has this segment
+        # as a parent.  We don't need to worry about the number of parents each segment
+        # has, since each has at least one, and indexing on the offset into the parents array
+        # gives the primary parent ID
+
+        with self.lock:
+            iter_group = self.get_iter_group(segment.n_iter + 1)
+            seg_index = iter_group['seg_index'][...]
+
+            # This is one of the slowest pieces of code I've ever written...
+            # seg_index = iter_group['seg_index'][...]
+            # seg_ids = [seg_id for (seg_id,row) in enumerate(seg_index)
+            #           if all_parent_ids[row['parents_offset']] == segment.seg_id]
+            # return self.get_segments_by_id(segment.n_iter+1, seg_ids)
+            if self.we_h5file_version < 5:
+                parents = iter_group['parents'][seg_index['parent_offsets']]
+            else:
+                parents = seg_index['parent_id']
+            all_seg_ids = np.arange(seg_index.len(), dtype=np.uintp)
+            seg_ids = all_seg_ids[parents == segment.seg_id]
+            # the above will return a scalar if only one is found, so convert
+            # to a list if necessary
+            try:
+                len(seg_ids)
+            except TypeError:
+                seg_ids = [seg_ids]
+
+            return self.get_segments(segment.n_iter + 1, seg_ids)
+
+    # The following are dictated by the SimManager interface
+    def prepare_run(self):
+        self.open_backing()
+
+    def finalize_run(self):
+        self.flush_backing()
+        self.close_backing()
+
+    def save_new_weight_data(self, n_iter, new_weights):
+        """
+        Save a set of NewWeightEntry objects to HDF5. Note that this should
+        be called for the iteration in which the weights appear in their
+        new locations (e.g. for recycled walkers, the iteration following
+        recycling).
+        """
+
+        if not new_weights:
+            return
+
+        system = self.system
+
+        index = np.empty(len(new_weights), dtype=nw_index_dtype)
+        prev_init_pcoords = system.new_pcoord_array(len(new_weights))
+        prev_final_pcoords = system.new_pcoord_array(len(new_weights))
+        new_init_pcoords = system.new_pcoord_array(len(new_weights))
+
+        for ientry, nwentry in enumerate(new_weights):
+            row = index[ientry]
+            row['source_type'] = nwentry.source_type
+            row['weight'] = nwentry.weight
+            row['prev_seg_id'] = nwentry.prev_seg_id
+            # the following use -1 as a sentinel for a missing value
+            row['target_state_id'] = nwentry.target_state_id if nwentry.target_state_id is not None else -1
+            row['initial_state_id'] = nwentry.initial_state_id if nwentry.initial_state_id is not None else -1
+
+            index[ientry] = row
+
+            if nwentry.prev_init_pcoord is not None:
+                prev_init_pcoords[ientry] = nwentry.prev_init_pcoord
+
+            if nwentry.prev_final_pcoord is not None:
+                prev_final_pcoords[ientry] = nwentry.prev_final_pcoord
+
+            if nwentry.new_init_pcoord is not None:
+                new_init_pcoords[ientry] = nwentry.new_init_pcoord
+
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+            try:
+                del iter_group['new_weights']
+            except KeyError:
+                pass
+
+            nwgroup = iter_group.create_group('new_weights')
+            nwgroup['index'] = index
+            nwgroup['prev_init_pcoord'] = prev_init_pcoords
+            nwgroup['prev_final_pcoord'] = prev_final_pcoords
+            nwgroup['new_init_pcoord'] = new_init_pcoords
+
+    def get_new_weight_data(self, n_iter):
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+
+            try:
+                nwgroup = iter_group['new_weights']
+            except KeyError:
+                return []
+
+            try:
+                index = nwgroup['index'][...]
+                prev_init_pcoords = nwgroup['prev_init_pcoord'][...]
+                prev_final_pcoords = nwgroup['prev_final_pcoord'][...]
+                new_init_pcoords = nwgroup['new_init_pcoord'][...]
+            except (KeyError, ValueError):  # zero-length selections raise ValueError
+                return []
+
+        entries = []
+        for i in range(len(index)):
+            irow = index[i]
+
+            prev_seg_id = irow['prev_seg_id']
+            if prev_seg_id == -1:
+                prev_seg_id = None
+
+            initial_state_id = irow['initial_state_id']
+            if initial_state_id == -1:
+                initial_state_id = None
+
+            target_state_id = irow['target_state_id']
+            if target_state_id == -1:
+                target_state_id = None
+
+            entry = NewWeightEntry(
+                source_type=irow['source_type'],
+                weight=irow['weight'],
+                prev_seg_id=prev_seg_id,
+                prev_init_pcoord=prev_init_pcoords[i].copy(),
+                prev_final_pcoord=prev_final_pcoords[i].copy(),
+                new_init_pcoord=new_init_pcoords[i].copy(),
+                target_state_id=target_state_id,
+                initial_state_id=initial_state_id,
+            )
+
+            entries.append(entry)
+        return entries
+
+    def find_bin_mapper(self, hashval):
+        """
+        Check to see if the given has value is in the binning table. Returns the index in the
+        bin data tables if found, or raises KeyError if not.
+        """
+
+        try:
+            hashval = hashval.hexdigest()
+        except AttributeError:
+            pass
+
+        with self.lock:
+            # these will raise KeyError if the group doesn't exist, which also means
+            # that bin data is not available, so no special treatment here
+            try:
+                binning_group = self.we_h5file['/bin_topologies']
+                index = binning_group['index']
+            except KeyError:
+                raise KeyError('hash {} not found'.format(hashval))
+
+            n_entries = len(index)
+            if n_entries == 0:
+                raise KeyError('hash {} not found'.format(hashval))
+
+            chunksize = self.table_scan_chunksize
+            for istart in range(0, n_entries, chunksize):
+                chunk = index[istart : min(istart + chunksize, n_entries)]
+                for i in range(len(chunk)):
+                    if chunk[i]['hash'] == bytes(hashval, 'utf-8'):
+                        return istart + i
+
+            raise KeyError('hash {} not found'.format(hashval))
+
+    def get_bin_mapper(self, hashval):
+        """Look up the given hash value in the binning table, unpickling and returning the corresponding
+        bin mapper if available, or raising KeyError if not."""
+
+        # Convert to a hex digest if we need to
+        try:
+            hashval = hashval.hexdigest()
+        except AttributeError:
+            pass
+
+        with self.lock:
+            # these will raise KeyError if the group doesn't exist, which also means
+            # that bin data is not available, so no special treatment here
+            try:
+                binning_group = self.we_h5file['/bin_topologies']
+                index = binning_group['index']
+                pkl = binning_group['pickles']
+            except KeyError:
+                raise KeyError('hash {} not found. Could not retrieve binning group'.format(hashval))
+
+            n_entries = len(index)
+            if n_entries == 0:
+                raise KeyError('hash {} not found. No entries in index'.format(hashval))
+
+            chunksize = self.table_scan_chunksize
+
+            for istart in range(0, n_entries, chunksize):
+                chunk = index[istart : min(istart + chunksize, n_entries)]
+                for i in range(len(chunk)):
+                    if chunk[i]['hash'] == bytes(hashval, 'utf-8'):
+                        pkldat = bytes(pkl[istart + i, 0 : chunk[i]['pickle_len']].data)
+                        mapper = pickle.loads(pkldat)
+                        log.debug('loaded {!r} from {!r}'.format(mapper, binning_group))
+                        log.debug('hash value {!r}'.format(hashval))
+                        return mapper
+
+            raise KeyError('hash {} not found'.format(hashval))
+
+    def save_bin_mapper(self, hashval, pickle_data):
+        """Store the given mapper in the table of saved mappers. If the mapper cannot be stored,
+        PickleError will be raised. Returns the index in the bin data tables where the mapper is stored."""
+
+        try:
+            hashval = hashval.hexdigest()
+        except AttributeError:
+            pass
+        pickle_data = bytes(pickle_data)
+
+        # First, scan to see if the mapper already is in the HDF5 file
+        try:
+            return self.find_bin_mapper(hashval)
+        except KeyError:
+            pass
+
+        # At this point, we have a valid pickle and know it's not stored
+        with self.lock:
+            binning_group = self.we_h5file.require_group('/bin_topologies')
+
+            try:
+                index = binning_group['index']
+                pickle_ds = binning_group['pickles']
+            except KeyError:
+                index = binning_group.create_dataset('index', shape=(1,), maxshape=(None,), dtype=binning_index_dtype)
+                pickle_ds = binning_group.create_dataset(
+                    'pickles',
+                    dtype=np.uint8,
+                    shape=(1, len(pickle_data)),
+                    maxshape=(None, None),
+                    chunks=(1, 4096),
+                    compression='gzip',
+                    compression_opts=9,
+                )
+                n_entries = 1
+            else:
+                n_entries = len(index) + 1
+                index.resize((n_entries,))
+                new_hsize = max(pickle_ds.shape[1], len(pickle_data))
+                pickle_ds.resize((n_entries, new_hsize))
+
+            index_row = index[n_entries - 1]
+            index_row['hash'] = hashval
+            index_row['pickle_len'] = len(pickle_data)
+            index[n_entries - 1] = index_row
+            pickle_ds[n_entries - 1, : len(pickle_data)] = memoryview(pickle_data)
+            return n_entries - 1
+
+    def save_iter_binning(self, n_iter, hashval, pickled_mapper, target_counts):
+        """Save information about the binning used to generate segments for iteration n_iter."""
+
+        with self.lock:
+            iter_group = self.get_iter_group(n_iter)
+
+            try:
+                del iter_group['bin_target_counts']
+            except KeyError:
+                pass
+
+            iter_group['bin_target_counts'] = target_counts
+
+            if hashval and pickled_mapper:
+                self.save_bin_mapper(hashval, pickled_mapper)
+                iter_group.attrs['binhash'] = hashval
+            else:
+                iter_group.attrs['binhash'] = ''
+
+
+def normalize_dataset_options(dsopts, path_prefix='', n_iter=0):
+    dsopts = dict(dsopts)
+
+    ds_name = dsopts['name']
+    if path_prefix:
+        default_h5path = '{}/{}'.format(path_prefix, ds_name)
+    else:
+        default_h5path = ds_name
+
+    dsopts.setdefault('h5path', default_h5path)
+    dtype = dsopts.get('dtype')
+    if dtype:
+        if isinstance(dtype, str):
+            try:
+                dsopts['dtype'] = np.dtype(getattr(np, dtype))
+            except AttributeError:
+                dsopts['dtype'] = np.dtype(getattr(builtins, dtype))
+        else:
+            dsopts['dtype'] = np.dtype(dtype)
+
+    dsopts['store'] = bool(dsopts['store']) if 'store' in dsopts else True
+    dsopts['load'] = bool(dsopts['load']) if 'load' in dsopts else False
+
+    return dsopts
+
+
+def create_dataset_from_dsopts(group, dsopts, shape=None, dtype=None, data=None, autocompress_threshold=None, n_iter=None):
+    # log.debug('create_dataset_from_dsopts(group={!r}, dsopts={!r}, shape={!r}, dtype={!r}, data={!r}, autocompress_threshold={!r})'
+    #          .format(group,dsopts,shape,dtype,data,autocompress_threshold))
+    if not dsopts.get('store', True):
+        return None
+
+    if 'file' in list(dsopts.keys()):
+        import h5py
+
+        #        dsopts['file'] = str(dsopts['file']).format(n_iter=n_iter)
+        h5_auxfile = h5io.WESTPAH5File(dsopts['file'].format(n_iter=n_iter))
+        h5group = group
+        if ("iter_" + str(n_iter).zfill(8)) not in h5_auxfile:
+            h5_auxfile.create_group("iter_" + str(n_iter).zfill(8))
+        group = h5_auxfile[('/' + "iter_" + str(n_iter).zfill(8))]
+
+    h5path = dsopts['h5path']
+    containing_group_name = posixpath.dirname(h5path)
+    h5_dsname = posixpath.basename(h5path)
+
+    # ensure arguments are sane
+    if not shape and data is None:
+        raise ValueError('either shape or data must be provided')
+    elif data is None and (shape and dtype is None):
+        raise ValueError('both shape and dtype must be provided when data is not provided')
+    elif shape and data is not None and not data.shape == shape:
+        raise ValueError('explicit shape {!r} does not match data shape {!r}'.format(shape, data.shape))
+
+    if data is not None:
+        shape = data.shape
+        if dtype is None:
+            dtype = data.dtype
+    # end argument sanity checks
+
+    # figure out where to store this data
+    if containing_group_name:
+        containing_group = group.require_group(containing_group_name)
+    else:
+        containing_group = group
+
+    # has user requested an explicit data type?
+    # the extra np.dtype is an idempotent operation on true dtype
+    # objects, but ensures that things like np.float32, which are
+    # actually NOT dtype objects, become dtype objects
+    h5_dtype = np.dtype(dsopts.get('dtype', dtype))
+
+    compression = None
+    scaleoffset = None
+    shuffle = False
+
+    # compress if 1) explicitly requested, or 2) dataset size exceeds threshold and
+    # compression not explicitly prohibited
+    compression_directive = dsopts.get('compression')
+    if compression_directive is None:
+        # No directive
+        nbytes = np.multiply.reduce(shape) * h5_dtype.itemsize
+        if autocompress_threshold and nbytes > autocompress_threshold:
+            compression = 9
+    elif compression_directive == 0:  # includes False
+        # Compression prohibited
+        compression = None
+    else:  # compression explicitly requested
+        compression = compression_directive
+
+    # Is scale/offset requested?
+    scaleoffset = dsopts.get('scaleoffset', None)
+    if scaleoffset is not None:
+        scaleoffset = int(scaleoffset)
+
+    # We always shuffle if we compress (losslessly)
+    if compression:
+        shuffle = True
+    else:
+        shuffle = False
+
+    need_chunks = any([compression, scaleoffset is not None, shuffle])
+
+    # We use user-provided chunks if available
+    chunks_directive = dsopts.get('chunks')
+    if chunks_directive is None:
+        chunks = None
+    elif chunks_directive is True:
+        chunks = calc_chunksize(shape, h5_dtype)
+    elif chunks_directive is False:
+        chunks = None
+    else:
+        chunks = tuple(chunks_directive[i] if chunks_directive[i] <= shape[i] else shape[i] for i in range(len(shape)))
+
+    if not chunks and need_chunks:
+        chunks = calc_chunksize(shape, h5_dtype)
+
+    opts = {'shape': shape, 'dtype': h5_dtype, 'compression': compression, 'shuffle': shuffle, 'chunks': chunks}
+
+    try:
+        import h5py._hl.filters
+
+        h5py._hl.filters._COMP_FILTERS['scaleoffset']
+    except (ImportError, KeyError, AttributeError):
+        # filter not available, or an unexpected version of h5py
+        # use lossless compression instead
+        opts['compression'] = True
+    else:
+        opts['scaleoffset'] = scaleoffset
+
+    if log.isEnabledFor(logging.DEBUG):
+        log.debug('requiring aux dataset {!r}, shape={!r}, opts={!r}'.format(h5_dsname, shape, opts))
+
+    dset = containing_group.require_dataset(h5_dsname, **opts)
+
+    if data is not None:
+        dset[...] = data
+
+    if 'file' in list(dsopts.keys()):
+        import h5py
+
+        if dsopts['h5path'] not in h5group:
+            h5group[dsopts['h5path']] = h5py.ExternalLink(
+                dsopts['file'].format(n_iter=n_iter), ("/" + "iter_" + str(n_iter).zfill(8) + "/" + dsopts['h5path'])
+            )
+
+    return dset
+
+
+def require_dataset_from_dsopts(group, dsopts, shape=None, dtype=None, data=None, autocompress_threshold=None, n_iter=None):
+    if not dsopts.get('store', True):
+        return None
+    try:
+        return group[dsopts['h5path']]
+    except KeyError:
+        return create_dataset_from_dsopts(
+            group, dsopts, shape=shape, dtype=dtype, data=data, autocompress_threshold=autocompress_threshold, n_iter=n_iter
+        )
+
+
+def calc_chunksize(shape, dtype, max_chunksize=262144):
+    """Calculate a chunk size for HDF5 data, anticipating that access will slice
+    along lower dimensions sooner than higher dimensions."""
+
+    chunk_shape = list(shape)
+    for idim in range(len(shape)):
+        chunk_nbytes = np.multiply.reduce(chunk_shape) * dtype.itemsize
+        while chunk_shape[idim] > 1 and chunk_nbytes > max_chunksize:
+            chunk_shape[idim] >>= 1  # divide by 2
+            chunk_nbytes = np.multiply.reduce(chunk_shape) * dtype.itemsize
+
+        if chunk_nbytes <= max_chunksize:
+            break
+
+    chunk_shape = tuple(chunk_shape)
+    log.debug(
+        'selected chunk shape {} for data set of type {} shaped {} (chunk size = {} bytes)'.format(
+            chunk_shape, dtype, shape, chunk_nbytes
+        )
+    )
+    return chunk_shape