sierra-research 1.3.11__py3-none-any.whl → 1.5.0__py3-none-any.whl

sierra/core/pipeline/stage2/exp_runner.py

@@ -1,286 +0,0 @@
-# Copyright 2018 London Lowmanstone, John Harwell, All rights reserved.
-#
-#  SPDX-License-Identifier: MIT
-"""Classes for executing experiments via the specified ``--exec-env``.
-
-"""
-
-# Core packages
-import os
-import subprocess
-import time
-import sys
-import datetime
-import logging
-import pathlib
-import typing as tp
-
-# 3rd party packages
-
-# Project packages
-from sierra.core.variables import batch_criteria as bc
-from sierra.core import types, config, platform, utils
-import sierra.core.plugin_manager as pm
-
-
-class ExpShell():
-    """Launch a shell which persists across experimental runs.
-
-    Having a persistent shell is necessary so that running pre- and post-run
-    shell commands have an effect on the actual commands to execute the run. If
-    you set an environment variable before the simulator launches (for example),
-    and then the shell containing that change exits, and the simulator launches
-    in a new shell, then the configuration has no effect. Thus, a persistent
-    shell.
-
-    """
-
-    def __init__(self, exec_strict: bool) -> None:
-        self.env = os.environ.copy()
-        self.logger = logging.getLogger(__name__)
-        self.procs = []  # type: tp.List[subprocess.Popen]
-        self.exec_strict = exec_strict
-
-    def run_from_spec(self, spec: types.ShellCmdSpec) -> bool:
-        self.logger.trace("Cmd: %s", spec.cmd)   # type: ignore
-
-        # We use a special marker at the end of the cmd's output to know when
-        # the environment dump starts.
-        if spec.env:
-            spec.cmd += ' && echo ~~~~ENV_START~~~~ && env'
-
-        proc = subprocess.Popen(spec.cmd,
-                                shell=spec.shell,
-                                stdout=subprocess.PIPE,
-                                stderr=subprocess.PIPE,
-                                env=self.env)
-
-        if not spec.wait:
-            self.procs.append(proc)
-            return True
-
-        # We use communicate(), not wait() to avoid issues with IO buffers
-        # becoming full (i.e., you get deadlocks with wait() regularly).
-        stdout_raw, stderr_raw = proc.communicate()
-
-        # Update the environment for all commands
-        if spec.env:
-            self._update_env(stdout_raw)
-
-        # Only show output if the process failed (i.e., did not return 0)
-        if proc.returncode != 0:
-            self.logger.error("Cmd '%s' failed!", spec.cmd)
-            stdout_str = stdout_raw.decode("ascii")
-            stderr_str = stderr_raw.decode("ascii")
-
-            if spec.env:
-                stdout_str = stdout_str.split("~~~~ENV_START~~~~", maxsplit=1)[0]
-                stderr_str = stderr_str.split("~~~~ENV_START~~~~", maxsplit=1)[0]
-
-            self.logger.error("Cmd stdout (last 10 lines): %s",
-                              '\n + ''\n'.join(stdout_str.split('\n')[-10:]))
-            self.logger.error("Cmd stderr (last 10 lines): %s",
-                              '\n' + '\n'.join(stderr_str.split('\n')[-10:]))
-
-            if self.exec_strict:
-                raise RuntimeError(("Command failed and strict checking was "
-                                    "requested"))
-
-            return False
-        else:
-            return True
-
-    def _update_env(self, stdout) -> None:
-        record = False
-        for e in stdout.decode('ascii').split("\n"):
-            if record:
-                candidate = e.strip().split('=')
-                if len(candidate) != 2:
-                    continue
-
-                key = candidate[0]
-                value = candidate[1]
-
-                if key not in self.env or self.env[key] != value:
-                    self.logger.debug("Update experiment environment: %s=%s",
-                                      key,
-                                      value)
-                    self.env[key] = value
-            elif e.strip() == '~~~~ENV_START~~~~':
-                record = True
-
-
-class BatchExpRunner:
-    """Runs each :term:`Experiment` in :term:`Batch Experiment` in sequence.
-
-    Attributes:
-
-        batch_exp_root: Absolute path to the root directory for the batch
-                        experiment inputs (i.e. experiment directories are
-                        placed in here).
-
-        batch_stat_root: Absolute path to the root directory for statistics
-                         which are computed in stage {3,4} (i.e. experiment
-                         directories are placed in here).
-
-        batch_stat_exec_root: Absolute path to the root directory for statistics
-                              which are generated as experiments run during
-                              stage 2 (e.g., how long each experiment took).
-
-        cmdopts: Dictionary of parsed cmdline options.
-
-        criteria: Batch criteria for the experiment.
-
-        exec_exp_range: The subset of experiments in the batch to run (can be
-                        None to run all experiments in the batch).
-
-    """
-
-    def __init__(self,
-                 cmdopts: types.Cmdopts,
-                 criteria: bc.BatchCriteria) -> None:
-        self.cmdopts = cmdopts
-        self.criteria = criteria
-
-        self.batch_exp_root = pathlib.Path(self.cmdopts['batch_input_root'])
-        self.batch_stat_root = pathlib.Path(self.cmdopts['batch_stat_root'])
-        self.batch_stat_exec_root = pathlib.Path(self.batch_stat_root / 'exec')
-        self.batch_scratch_root = pathlib.Path(self.cmdopts['batch_scratch_root'])
-        self.exec_exp_range = self.cmdopts['exp_range']
-
-        self.logger = logging.getLogger(__name__)
-
-        utils.dir_create_checked(self.batch_stat_exec_root, exist_ok=True)
-        utils.dir_create_checked(self.batch_scratch_root, exist_ok=True)
-
-    def __call__(self) -> None:
-        """
-        Execute experiments in the batch according to configuration.
-
-        """
-        self.logger.info("Platform='%s' exec_env='%s'",
-                         self.cmdopts['platform'],
-                         self.cmdopts['exec_env'])
-
-        module = pm.pipeline.get_plugin_module(self.cmdopts['platform'])
-
-        # Output some useful information before running
-        if hasattr(module, 'pre_exp_diagnostics'):
-            module.pre_exp_diagnostics(self.cmdopts, self.logger)
-
-        exp_all = [self.batch_exp_root / d
-                   for d in self.criteria.gen_exp_names(self.cmdopts)]
-
-        exp_to_run = utils.exp_range_calc(self.cmdopts,
-                                          self.batch_exp_root,
-                                          self.criteria)
-
-        # Verify environment is OK before running anything
-        if hasattr(platform, 'ExecEnvChecker'):
-            self.logger.debug("Checking execution environment")
-            platform.ExecEnvChecker(self.cmdopts)()
-        else:
-            self.logger.debug("Skip execution environment checking--not needed")
-
-        # Calculate path for to file for logging execution times
-        now = datetime.datetime.now()
-        exec_times_fpath = self.batch_stat_exec_root / now.strftime("%Y-%m-%e-%H:%M")
-
-        # Start a new process for the experiment shell so pre-run commands have
-        # an effect (if they set environment variables, etc.).
-        shell = ExpShell(self.cmdopts['exec_strict'])
-
-        # Run the experiment!
-        for exp in exp_to_run:
-            exp_num = exp_all.index(exp)
-
-            # Run cmds for platform-specific things to setup the experiment
-            # (e.g., start daemons) if needed.
-            generator = platform.ExpShellCmdsGenerator(self.cmdopts,
-                                                       exp_num)
-            for spec in generator.pre_exp_cmds():
-                shell.run_from_spec(spec)
-
-            runner = ExpRunner(self.cmdopts,
-                               exec_times_fpath,
-                               generator,
-                               shell)
-            runner(exp, exp_num)
-
-            # Run cmds to cleanup platform-specific things now that the experiment
-            # is done (if needed).
-            for spec in generator.post_exp_cmds():
-                shell.run_from_spec(spec)
-
-
-class ExpRunner:
-    """
-    Execute each :term:`Experimental Run` in an :term:`Experiment`.
-
-    In parallel if the selected execution environment supports it, otherwise
-    sequentially.
-
-    """
-
-    def __init__(self,
-                 cmdopts: types.Cmdopts,
-                 exec_times_fpath: pathlib.Path,
-                 generator: platform.ExpShellCmdsGenerator,
-                 shell: ExpShell) -> None:
-
-        self.exec_times_fpath = exec_times_fpath
-        self.shell = shell
-        self.generator = generator
-        self.cmdopts = cmdopts
-        self.logger = logging.getLogger(__name__)
-
-    def __call__(self,
-                 exp_input_root: pathlib.Path,
-                 exp_num: int) -> None:
-        """Execute experimental runs for a single experiment.
-        """
-
-        self.logger.info("Running exp%s in '%s'",
-                         exp_num,
-                         exp_input_root)
-        sys.stdout.flush()
-
-        wd = exp_input_root.relative_to(pathlib.Path().home())
-        start = time.time()
-
-        scratch_root = self.cmdopts['batch_scratch_root'] / exp_input_root.name
-        utils.dir_create_checked(scratch_root, exist_ok=True)
-
-        assert self.cmdopts['exec_jobs_per_node'] is not None, \
-            "# parallel jobs can't be None"
-
-        exec_opts = {
-            'exp_input_root': str(exp_input_root),
-            'work_dir': str(wd),
-            'scratch_dir': str(scratch_root),
-            'cmdfile_stem_path': str(exp_input_root / config.kGNUParallel['cmdfile_stem']),
-            'cmdfile_ext': config.kGNUParallel['cmdfile_ext'],
-            'exec_resume': self.cmdopts['exec_resume'],
-            'n_jobs': self.cmdopts['exec_jobs_per_node'],
-            'nodefile': self.cmdopts['nodefile']
-        }
-        for spec in self.generator.exec_exp_cmds(exec_opts):
-            if not self.shell.run_from_spec(spec):
-                self.logger.error("Check outputs in %s for full details",
-                                  exec_opts['scratch_dir'])
-
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-        self.logger.info('Exp%s elapsed time: %s', exp_num, sec)
-
-        with utils.utf8open(self.exec_times_fpath, 'a') as f:
-            f.write('exp' + str(exp_num) + ': ' + str(sec) + '\n')
-
-
-__api__ = [
-    'BatchExpRunner',
-    'ExpRunner',
-    'ExpShell'
-
-
-]

sierra/core/pipeline/stage3/imagizer.py

@@ -1,149 +0,0 @@
-# Copyright 2019 John Harwell, All rights reserved.
-#
-#  SPDX-License-Identifier: MIT
-
-"""Classes for creating image files from ``.mean`` files for experiments.
-
-See :ref:`ln-sierra-usage-rendering` for usage documentation.
-
-"""
-
-# Core packages
-import multiprocessing as mp
-import queue
-import logging
-import pathlib
-
-# 3rd party packages
-import psutil
-
-# Project packages
-from sierra.core.graphs.heatmap import Heatmap
-import sierra.core.variables.batch_criteria as bc
-from sierra.core import types, config, utils
-
-
-class BatchExpParallelImagizer:
-    """Generate images for each :term:`Experiment` in the :term:`Batch Experiment`.
-
-    Ideally this is done in parallel across experiments, but this can be changed
-    to serial if memory on the SIERRA host machine is limited via
-    ``--processing-serial``.
-
-    """
-
-    def __init__(self,
-                 main_config: types.YAMLDict,
-                 cmdopts: types.Cmdopts) -> None:
-        self.main_config = main_config
-        self.cmdopts = cmdopts
-
-    def __call__(self,
-                 HM_config: types.YAMLDict,
-                 criteria: bc.IConcreteBatchCriteria) -> None:
-        exp_to_imagize = utils.exp_range_calc(self.cmdopts,
-                                              self.cmdopts['batch_output_root'],
-                                              criteria)
-
-        q = mp.JoinableQueue()  # type: mp.JoinableQueue
-
-        for exp in exp_to_imagize:
-            leaf = exp.name
-            exp_stat_root = pathlib.Path(self.cmdopts['batch_stat_root']) / leaf
-            exp_imagize_root = pathlib.Path(
-                self.cmdopts['batch_imagize_root']) / leaf
-            self._enqueue_for_exp(exp_stat_root, exp_imagize_root, q)
-
-        if self.cmdopts['processing_serial']:
-            parallelism = 1
-        else:
-            parallelism = psutil.cpu_count()
-
-        for _ in range(0, parallelism):
-            p = mp.Process(target=BatchExpParallelImagizer._thread_worker,
-                           args=(q, HM_config))
-            p.start()
-
-        q.join()
-
-    def _enqueue_for_exp(self,
-                         exp_stat_root: pathlib.Path,
-                         exp_imagize_root: pathlib.Path,
-                         q: mp.JoinableQueue) -> None:
-        for candidate in exp_stat_root.iterdir():
-            if candidate.is_dir():
-                imagize_output_root = exp_imagize_root / candidate.name
-                imagize_opts = {
-                    'input_root': exp_stat_root,
-                    'graph_stem': candidate.name,
-                    'output_root': imagize_output_root
-                }
-
-                utils.dir_create_checked(imagize_output_root, exist_ok=True)
-                q.put(imagize_opts)
-
-    @staticmethod
-    def _thread_worker(q: mp.Queue, HM_config: types.YAMLDict) -> None:
-        while True:
-            # Wait for 3 seconds after the queue is empty before bailing
-            try:
-                imagize_opts = q.get(True, 3)
-                ExpImagizer()(HM_config, imagize_opts)
-                q.task_done()
-            except queue.Empty:
-                break
-
-
-class ExpImagizer:
-    """Create images from the averaged ``.mean`` files from an experiment.
-
-    If no ``.mean`` files suitable for averaging are found, nothing is done. See
-    :ref:`ln-sierra-usage-rendering` for per-platform descriptions of what
-    "suitable" means.
-
-    Arguments:
-
-        HM_config: Parsed YAML configuration for heatmaps.
-
-        imagize_opts: Dictionary of imagizing options.
-
-    """
-
-    def __init__(self) -> None:
-        self.logger = logging.getLogger(__name__)
-
-    def __call__(self,
-                 HM_config: types.YAMLDict,
-                 imagize_opts: dict) -> None:
-        path = imagize_opts['input_root'] / imagize_opts['graph_stem']
-
-        self.logger.info("Imagizing CSVs in %s...", str(path))
-
-        for csv in path.iterdir():
-            # For each category of heatmaps we are generating
-            match = None
-            for category in HM_config:
-                # For each graph in each category
-                for graph in HM_config[category]['graphs']:
-                    if graph['src_stem'] == imagize_opts['graph_stem']:
-                        match = graph
-
-            if match is not None:
-                ipath = csv.with_suffix(config.kStats['mean'].exts['mean'])
-                opath = imagize_opts['output_root'] / (csv.name + config.kImageExt)
-                Heatmap(input_fpath=ipath,
-                        output_fpath=opath,
-                        title=match['title'],
-                        xlabel='X',
-                        ylabel='Y').generate()
-
-            else:
-                self.logger.warning(("No match for graph with src_stem='%s' "
-                                     "found in configuration"),
-                                    imagize_opts['graph_stem'])
-
-
-__api__ = [
-    'BatchExpParallelImagizer',
-    'ExpImagizer'
-]