Source code for galaxy.job_metrics.collectl.processes

""" Modules will run collectl in playback mode and collect various process
statistics for a given pid's process and process ancestors.
import collections
import csv
import logging
import tempfile

from galaxy import util
from ..collectl import stats

log = logging.getLogger(__name__)

# Collectl process information cheat sheet:
# Record process information for current user.
# %  collectl -sZ -f./__instrument_collectl  -i 10:10 --procfilt U$USER
# TSV Replay of processing information in plottable mode...
# % collectl -sZ -P --sep=9 -p __instrument_collectl-jlaptop13-20140322-120919.raw.gz
# Has following columns:
#   Date   Time    PID     User    PR      PPID    THRD    S       VmSize  VmLck   VmRSS   VmData  VmStk   VmExe   VmLib   CPU       SysT    UsrT    PCT     AccumT  RKB     WKB     RKBC    WKBC    RSYS    WSYS    CNCL    MajF    MinF    Command

# Process data dumped one row per process per interval.
    "#Date",  # Date of interval - e.g. 20140322
    "Time",  # Time of interval - 12:18:58
    "PID",  # Process pid.
    "User",  # Process user.
    "PR",  # Priority of process.
    "PPID",  # Parent PID of process.
    "THRD",  # Thread???
    "S",  # Process state - S - Sleeping, D - Uninterruptable Sleep, R - Running, Z - Zombie or T - Stopped/Traced
    # Memory options -
    "CPU",  # CPU number of process
    "SysT",  # Amount of system time consumed during interval
    "UsrT",  # Amount user time consumed during interval
    "PCT",  # Percentage of current interval consumed by task
    "AccumT",  # Total accumulated System and User time since the process began execution
    # kilobytes read/written - requires I/O level monitoring to be enabled in kernel.
    "RKB",  # kilobytes read by process - requires I/O monitoring in kernel
    "RSYS",  # Number of read system calls
    "WSYS",  # Number of write system calls
    "MajF",  # Number of major page faults
    "MinF",  # Number of minor page faults
    "Command",  # Command executed

# Types of statistics this module can summarize
STATISTIC_TYPES = ["max", "min", "sum", "count", "avg"]

COLUMN_INDICES = {col: i for i, col in enumerate(PROCESS_COLUMNS)}

    ("max", "VmSize"),
    ("avg", "VmSize"),
    ("max", "VmRSS"),
    ("avg", "VmRSS"),
    ("sum", "SysT"),
    ("sum", "UsrT"),
    ("max", "PCT"),
    ("avg", "PCT"),
    ("max", "AccumT"),
    ("sum", "RSYS"),
    ("sum", "WSYS"),

def parse_process_statistics(statistics):
    """ Turn string or list of strings into list of tuples in format ( stat,
    resource ) where stat is a value from STATISTIC_TYPES and resource is a
    value from PROCESS_COLUMNS.
    if statistics is None:
        statistics = DEFAULT_STATISTICS

    statistics = util.listify(statistics)
    statistics = [_tuplize_statistic(_) for _ in statistics]
    # Check for validity...
    for statistic in statistics:
        if statistic[0] not in STATISTIC_TYPES:
            raise Exception("Unknown statistic type encountered %s" % statistic[0])
        if statistic[1] not in PROCESS_COLUMNS:
            raise Exception("Unknown process column encountered %s" % statistic[1])
    return statistics

[docs]def generate_process_statistics(collectl_playback_cli, pid, statistics=DEFAULT_STATISTICS): """ Playback collectl file and generate summary statistics. """ with tempfile.NamedTemporaryFile() as tmp_tsv: with open( as tsv_file: return _read_process_statistics(tsv_file, pid, statistics)
def _read_process_statistics(tsv_file, pid, statistics): process_summarizer = CollectlProcessSummarizer(pid, statistics) current_interval = None for row in csv.reader(tsv_file, dialect="excel-tab"): if current_interval is None: for header, expected_header in zip(row, PROCESS_COLUMNS): if header.lower() != expected_header.lower(): raise Exception("Unknown header value encountered while processing collectl playback - %s" % header) # First row, check contains correct header. current_interval = CollectlProcessInterval() continue if current_interval.row_is_in(row): current_interval.add_row(row) else: process_summarizer.handle_interval(current_interval) current_interval = CollectlProcessInterval() # Do we have unsummarized rows... if current_interval and current_interval.rows: process_summarizer.handle_interval(current_interval) return process_summarizer.get_statistics() class CollectlProcessSummarizer: def __init__(self, pid, statistics): = pid self.statistics = statistics self.columns_of_interest = {s[1] for s in statistics} self.tree_statistics = collections.defaultdict(stats.StatisticsTracker) self.process_accum_statistics = collections.defaultdict(stats.StatisticsTracker) self.interval_count = 0 def handle_interval(self, interval): self.interval_count += 1 rows = self.__rows_for_process(interval.rows, for column_name in self.columns_of_interest: column_index = COLUMN_INDICES[column_name] if column_name == "AccumT": # Should not sum this across pids each interval, sum max at end... for r in rows: pid_seconds = self.__time_to_seconds(r[column_index]) self.process_accum_statistics[r[PID_INDEX]].track(pid_seconds) else: # All other stastics should be summed across whole process tree # at each interval I guess. if column_name in ["SysT", "UsrT", "PCT"]: to_num = float else: to_num = int interval_stat = sum(to_num(r[column_index]) for r in rows) self.tree_statistics[column_name].track(interval_stat) def get_statistics(self): if self.interval_count == 0: return [] computed_statistics = [] for statistic in self.statistics: statistic_type, column = statistic if column == "AccumT": # Only thing that makes sense is sum if statistic_type != "max": log.warning("Only statistic max makes sense for AccumT") continue value = sum(v.max for v in self.process_accum_statistics.values()) else: statistics_tracker = self.tree_statistics[column] value = getattr(statistics_tracker, statistic_type) computed_statistic = (statistic, value) computed_statistics.append(computed_statistic) return computed_statistics def __rows_for_process(self, rows, pid): process_rows = [] pids = self.__all_child_pids(rows, pid) for row in rows: if row[PID_INDEX] in pids: process_rows.append(row) return process_rows def __all_child_pids(self, rows, pid): pids_in_process_tree = {str(} added = True while added: added = False for row in rows: pid = row[PID_INDEX] parent_pid = row[PARENT_PID_INDEX] if parent_pid in pids_in_process_tree and pid not in pids_in_process_tree: pids_in_process_tree.add(pid) added = True return pids_in_process_tree def __time_to_seconds(self, minutes_str): parts = minutes_str.split(":") seconds = 0.0 for i, val in enumerate(parts): seconds += float(val) * (60 ** (len(parts) - (i + 1))) return seconds class CollectlProcessInterval: """ Represent all rows in collectl playback file for given time slice with ability to filter out just rows corresponding to the process tree corresponding to a given pid. """ def __init__(self): self.rows = [] def row_is_in(self, row): if not self.rows: # No rows, this row defines interval. return True first_row = self.rows[0] return first_row[0] == row[0] and first_row[1] == row[1] def add_row(self, row): self.rows.append(row) def _tuplize_statistic(statistic): if not isinstance(statistic, tuple): statistic_split = statistic.split("_", 1) statistic = (statistic_split[0].lower(), statistic_split[1]) return statistic __all__ = ('generate_process_statistics', )