def get_segments_by_id(self, n_iter, seg_ids, include_pcoords = True):
'''Get segments from the data manager, employing caching where possible'''
if len(seg_ids) == 0: return []
seg_index = self.get_seg_index(n_iter)
all_wtg_parent_ids = self.get_wtg_parent_array(n_iter)
segments = []
if include_pcoords:
pcoords = self.get_pcoords(n_iter, seg_ids)
for (isegid, seg_id) in enumerate(seg_ids):
row = seg_index[seg_id]
parents_offset = row['wtg_offset']
n_parents = row['wtg_n_parents']
segment = Segment(seg_id = seg_id,
n_iter = n_iter,
status = row['status'],
endpoint_type = row['endpoint_type'],
walltime = row['walltime'],
cputime = row['cputime'],
weight = row['weight'],
)
if include_pcoords:
segment.pcoord = pcoords[isegid]
parent_ids = all_wtg_parent_ids[parents_offset:parents_offset+n_parents]
segment.wtg_parent_ids = {long(parent_id) for parent_id in parent_ids}
segment.parent_id = long(parent_ids[0])
segments.append(segment)
return segments
def get_segments_by_id(self, n_iter, seg_ids, include_pcoords = True):
'''Get segments from the data manager, employing caching where possible'''
if len(seg_ids) == 0: return []
seg_index = self.get_seg_index(n_iter)
all_wtg_parent_ids = self.get_wtg_parent_array(n_iter)
segments = []
if include_pcoords:
pcoords = self.get_pcoords(n_iter, seg_ids)
for (isegid, seg_id) in enumerate(seg_ids):
row = seg_index[seg_id]
parents_offset = row['wtg_offset']
n_parents = row['wtg_n_parents']
segment = Segment(seg_id = seg_id,
n_iter = n_iter,
status = row['status'],
endpoint_type = row['endpoint_type'],
walltime = row['walltime'],
cputime = row['cputime'],
weight = row['weight'],
)
if include_pcoords:
segment.pcoord = pcoords[isegid]
parent_ids = all_wtg_parent_ids[parents_offset:parents_offset+n_parents]
segment.wtg_parent_ids = {int(parent_id) for parent_id in parent_ids}
segment.parent_id = int(parent_ids[0])
segments.append(segment)
return segments
for (iseg, (index_row, pcoord)) in enumerate(izip(old_index, old_final_pcoords)):
istate = istates[iseg]
istate.iter_created = 0
istate.iter_used = 1
#istate.istate_type = InitialState.ISTATE_TYPE_RESTART
istate.istate_type = InitialState.ISTATE_TYPE_BASIS
istate.istate_status = InitialState.ISTATE_STATUS_PREPARED
istate.pcoord = pcoord
segment = Segment(n_iter=1, seg_id=iseg, weight=index_row['weight'],
#parent_id =-(istate.state_id+1),
parent_id = (istate.state_id),
#wtg_parent_ids = [-(istate.state_id+1)],
wtg_parent_ids = [(istate.state_id)],
status=Segment.SEG_STATUS_PREPARED)
segment.pcoord = numpy.zeros((pcoord_len, pcoord_ndim), dtype=pcoord.dtype)
segment.pcoord[0] = pcoord
segments.append(segment)
state_map[iseg]['old_seg_id'] = iseg
state_map[iseg]['new_istate_id'] = istate.state_id
dm_new.update_initial_states(istates, n_iter=0)
dm_new.prepare_iteration(n_iter=1, segments=segments)
# Update current iteration and close both files
dm_new.current_iteration = 1
dm_new.close_backing()
dm_old.close_backing()
# Write state map
istate_map_file = open(args.istate_map, 'wt')
state_map['old_n_iter'] = n_iter
for (iseg, (index_row, pcoord)) in enumerate(zip(old_index, old_final_pcoords)):
istate = istates[iseg]
istate.iter_created = 0
istate.iter_used = 1
istate.istate_type = InitialState.ISTATE_TYPE_RESTART
istate.istate_status = InitialState.ISTATE_STATUS_PREPARED
istate.pcoord = pcoord
segment = Segment(n_iter=1, seg_id=iseg, weight=index_row['weight'],
parent_id =-(istate.state_id+1),
wtg_parent_ids = [-(istate.state_id+1)],
status=Segment.SEG_STATUS_PREPARED)
segment.pcoord = numpy.zeros((pcoord_len, pcoord_ndim), dtype=pcoord.dtype)
segment.pcoord[0] = pcoord
segments.append(segment)
state_map[iseg]['old_seg_id'] = iseg
state_map[iseg]['new_istate_id'] = istate.state_id
dm_new.update_initial_states(istates, n_iter=0)
dm_new.prepare_iteration(n_iter=1, segments=segments)
# Update current iteration and close both files
dm_new.current_iteration = 1
dm_new.close_backing()
dm_old.close_backing()
# Write state map
istate_map_file = open(args.istate_map, 'wt')
