public release 2.2.0 - see README.md and CHANGES.md for details
This commit is contained in:
@ -21,6 +21,8 @@ import signal
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import collections
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import copy
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import logging
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import math
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from attrdict import AttrDict
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from mpi4py import MPI
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from pmsco.helpers import BraceMessage as BMsg
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@ -53,7 +55,7 @@ TAG_ERROR_ABORTING = 4
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## levels of calculation tasks
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#
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CALC_LEVELS = ('model', 'scan', 'sym', 'emit', 'region')
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CALC_LEVELS = ('model', 'scan', 'domain', 'emit', 'region')
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## intermediate sub-class of CalcID
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#
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@ -159,13 +161,13 @@ class CalculationTask(object):
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@arg @c id.model structure number or iteration (handled by the mode module)
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@arg @c id.scan scan number (handled by the project)
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@arg @c id.sym symmetry number (handled by the project)
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@arg @c id.domain domain number (handled by the project)
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@arg @c id.emit emitter number (handled by the project)
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@arg @c id.region region number (handled by the region handler)
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specified members must be greater or equal to zero.
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-1 is the wildcard which is used in parent tasks,
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where, e.g., no specific symmetry is chosen.
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where, e.g., no specific domain is chosen.
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the root task has the ID (-1, -1, -1, -1, -1).
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"""
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@ -311,7 +313,8 @@ class CalculationTask(object):
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format input or output file name including calculation index.
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@param overrides optional keyword arguments override object fields.
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the following keywords are handled: @c root, @c model, @c scan, @c sym, @c emit, @c region, @c ext.
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the following keywords are handled:
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`root`, `model`, `scan`, `domain`, `emit`, `region`, `ext`.
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@return a string consisting of the concatenation of the base name, the ID, and the extension.
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"""
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@ -322,7 +325,7 @@ class CalculationTask(object):
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for key in overrides.keys():
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parts[key] = overrides[key]
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filename = "{root}_{model}_{scan}_{sym}_{emit}_{region}{ext}".format(**parts)
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filename = "{root}_{model}_{scan}_{domain}_{emit}_{region}{ext}".format(**parts)
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return filename
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def copy(self):
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@ -462,7 +465,7 @@ class CachedCalculationMethod(object):
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def wrapped_func(inst, model, index):
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# note: _replace returns a new instance of the namedtuple
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index = index._replace(emit=-1, region=-1)
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cache_index = (id(inst), index.model, index.scan, index.sym)
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cache_index = (id(inst), index.model, index.scan, index.domain)
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try:
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result = self._cache[cache_index]
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except KeyError:
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@ -565,6 +568,8 @@ class MscoProcess(object):
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"""
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clean up after all calculations.
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this method must be called after run() has finished.
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@return: None
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"""
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pass
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@ -693,7 +698,7 @@ class MscoProcess(object):
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parameters generation is delegated to the project's create_params method.
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@param task: CalculationTask with all attributes set for the calculation.
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@return: pmsco.project.Params object for the calculator.
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@return: pmsco.project.CalculatorParams object for the calculator.
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"""
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par = self._project.create_params(task.model, task.id)
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@ -711,7 +716,7 @@ class MscoProcess(object):
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@param task: CalculationTask with all attributes set for the calculation.
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@param par: pmsco.project.Params object for the calculator.
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@param par: pmsco.project.CalculatorParams object for the calculator.
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its phase_files attribute is updated with the created scattering files.
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the radial matrix elements are not changed (but may be in a future version).
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@ -740,7 +745,7 @@ class MscoProcess(object):
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calculate the multiple scattering intensity.
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@param task: CalculationTask with all attributes set for the calculation.
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@param par: pmsco.project.Params object for the calculator.
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@param par: pmsco.project.CalculatorParams object for the calculator.
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@param clu: pmsco.cluster.Cluster object for the calculator.
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@return: None
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"""
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@ -820,7 +825,7 @@ class MscoMaster(MscoProcess):
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## @var task_handlers
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# (AttrDict) dictionary of task handler objects
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#
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# the keys are the task levels 'model', 'scan', 'sym', 'emit' and 'region'.
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# the keys are the task levels 'model', 'scan', 'domain', 'emit' and 'region'.
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# the values are handlers.TaskHandler objects.
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# the objects can be accessed in attribute or dictionary notation.
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@ -854,12 +859,18 @@ class MscoMaster(MscoProcess):
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the method notifies the handlers of the number of available slave processes (slots).
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some of the tasks handlers adjust their branching according to the number of slots.
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this mechanism may be used to balance the load between the task levels.
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however, the current implementation is very coarse in this respect.
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it advertises all slots to the model handler but a reduced number to the remaining handlers
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depending on the operation mode.
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the region handler receives a maximum of 4 slots except in single calculation mode.
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in single calculation mode, all slots can be used by all handlers.
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this mechanism may be used to adjust the priorities of the task levels,
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i.e., whether one slot handles all calculations of one model
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so that all models of a generation finish around the same time,
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or whether a model is finished completely before the next one is calculated
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so that a result is returned as soon as possible.
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the current algorithm tries to pass as many slots as available
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down to the lowest level (region) in order to minimize wall time.
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the lowest level is restricted to the minimum number of splits
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only if the intermediate levels create a lot of branches,
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in which case splitting scans would not offer a performance benefit.
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"""
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super(MscoMaster, self).setup(project)
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@ -869,7 +880,7 @@ class MscoMaster(MscoProcess):
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self._root_task = CalculationTask()
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self._root_task.file_root = project.output_file
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self._root_task.model = project.create_domain().start
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self._root_task.model = project.create_model_space().start
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for level in self.task_levels:
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self.task_handlers[level] = project.handler_classes[level]()
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@ -877,14 +888,22 @@ class MscoMaster(MscoProcess):
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self.task_handlers.model.datetime_limit = self.datetime_limit
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slaves_adj = max(self._slaves, 1)
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self.task_handlers.model.setup(project, slaves_adj)
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if project.mode != "single":
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slaves_adj = max(slaves_adj / 2, 1)
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self.task_handlers.scan.setup(project, slaves_adj)
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self.task_handlers.sym.setup(project, slaves_adj)
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self.task_handlers.emit.setup(project, slaves_adj)
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if project.mode != "single":
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n_models = self.task_handlers.model.setup(project, slaves_adj)
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if n_models > 1:
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slaves_adj = max(int(slaves_adj / 2), 1)
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n_scans = self.task_handlers.scan.setup(project, slaves_adj)
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if n_scans > 1:
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slaves_adj = max(int(slaves_adj / 2), 1)
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n_doms = self.task_handlers.domain.setup(project, slaves_adj)
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if n_doms > 1:
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slaves_adj = max(int(slaves_adj / 2), 1)
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n_emits = self.task_handlers.emit.setup(project, slaves_adj)
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if n_emits > 1:
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slaves_adj = max(int(slaves_adj / 2), 1)
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n_extra = max(n_scans, n_doms, n_emits)
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if n_extra > slaves_adj * 2:
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slaves_adj = min(slaves_adj, 4)
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logger.debug(BMsg("{regions} slots available for region handler", regions=slaves_adj))
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self.task_handlers.region.setup(project, slaves_adj)
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project.setup(self.task_handlers)
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@ -911,6 +930,7 @@ class MscoMaster(MscoProcess):
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else:
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self._dispatch_tasks()
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self._receive_result()
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self._cleanup_tasks()
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self._check_finish()
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logger.debug("master exiting main loop")
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@ -918,12 +938,32 @@ class MscoMaster(MscoProcess):
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self._save_report()
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def cleanup(self):
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"""
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clean up after all calculations.
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this method must be called after run() has finished.
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in the master process, this calls cleanup() of each task handler and of the project.
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@return: None
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"""
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logger.debug("master entering cleanup")
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for level in reversed(self.task_levels):
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self.task_handlers[level].cleanup()
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self._project.cleanup()
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super(MscoMaster, self).cleanup()
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def _cleanup_tasks(self):
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"""
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periodic clean-up in the main loop.
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once per iteration of the main loop, this method cleans up unnecessary files.
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this is done by the project's cleanup_files() method.
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@return: None
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"""
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self._project.cleanup_files()
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def _dispatch_results(self):
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"""
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pass results through the post-processing modules.
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@ -1122,9 +1162,9 @@ class MscoMaster(MscoProcess):
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scan_tasks = self.task_handlers.scan.create_tasks(task)
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for scan_task in scan_tasks:
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sym_tasks = self.task_handlers.sym.create_tasks(scan_task)
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for sym_task in sym_tasks:
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emitter_tasks = self.task_handlers.emit.create_tasks(sym_task)
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dom_tasks = self.task_handlers.domain.create_tasks(scan_task)
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for dom_task in dom_tasks:
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emitter_tasks = self.task_handlers.emit.create_tasks(dom_task)
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for emitter_task in emitter_tasks:
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region_tasks = self.task_handlers.region.create_tasks(emitter_task)
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for region_task in region_tasks:
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