This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.job_metrics.instrumenters.cgroup

"""The module describes the ``cgroup`` job metrics plugin."""
import logging
import numbers
from collections import namedtuple

from galaxy.util import asbool, nice_size
from . import InstrumentPlugin
from .. import formatting

log = logging.getLogger(__name__)

    "memory.memsw.max_usage_in_bytes": "Max memory usage (MEM+SWP)",
    "memory.max_usage_in_bytes": "Max memory usage (MEM)",
    "memory.limit_in_bytes": "Memory limit on cgroup (MEM)",
    "memory.memsw.limit_in_bytes": "Memory limit on cgroup (MEM+SWP)",
    "memory.soft_limit_in_bytes": "Memory softlimit on cgroup",
    "memory.failcnt": "Failed to allocate memory count",
    "memory.oom_control.oom_kill_disable": "OOM Control enabled",
    "memory.oom_control.under_oom": "Was OOM Killer active?",
    "cpuacct.usage": "CPU Time"
    "memory.oom_control.oom_kill_disable": lambda x: "No" if x == 1 else "Yes",
    "memory.oom_control.under_oom": lambda x: "Yes" if x == 1 else "No",
    "cpuacct.usage": lambda x: formatting.seconds_to_str(x / 10**9)  # convert nanoseconds

Metric = namedtuple("Metric", ("key", "subkey", "value"))

class CgroupPluginFormatter(formatting.JobMetricFormatter):

    def format(self, key, value):
        title = TITLES.get(key, key)
        if key in CONVERSION:
            return title, CONVERSION[key](value)
        elif key.endswith("_bytes"):
                return title, nice_size(value)
            except ValueError:
        elif isinstance(value, numbers.Number) and value == int(value):
            value = int(value)
        return title, value

[docs]class CgroupPlugin(InstrumentPlugin): """ Plugin that collects memory and cpu utilization from within a cgroup. """ plugin_type = "cgroup" formatter = CgroupPluginFormatter()
[docs] def __init__(self, **kwargs): self.verbose = asbool(kwargs.get("verbose", False)) params_str = kwargs.get("params", None) if params_str: params = [v.strip() for v in params_str.split(",")] else: params = TITLES.keys() self.params = params
[docs] def post_execute_instrument(self, job_directory): commands = [] commands.append(self.__record_cgroup_cpu_usage(job_directory)) commands.append(self.__record_cgroup_memory_usage(job_directory)) return commands
[docs] def job_properties(self, job_id, job_directory): metrics = self.__read_metrics(self.__cgroup_metrics_file(job_directory)) return metrics
def __record_cgroup_cpu_usage(self, job_directory): return """if [ `command -v cgget` ] && [ -e /proc/$$/cgroup ]; then cat /proc/$$/cgroup | awk -F':' '$2=="cpuacct,cpu"{print $2":"$3}' | xargs -I{} cgget -g {} > %(metrics)s ; else echo "" > %(metrics)s; fi""" % {"metrics": self.__cgroup_metrics_file(job_directory)} def __record_cgroup_memory_usage(self, job_directory): return """if [ `command -v cgget` ] && [ -e /proc/$$/cgroup ]; then cat /proc/$$/cgroup | awk -F':' '$2=="memory"{print $2":"$3}' | xargs -I{} cgget -g {} >> %(metrics)s ; else echo "" > %(metrics)s; fi""" % {"metrics": self.__cgroup_metrics_file(job_directory)} def __cgroup_metrics_file(self, job_directory): return self._instrument_file_path(job_directory, "_metrics") def __read_metrics(self, path): metrics = {} prev_metric = None with open(path, "r") as infile: for line in infile: try: metric, prev_metric = self.__read_key_value(line, prev_metric) except Exception: log.exception("Caught exception attempting to read metric from cgroup line: %s", line) metric = None if not metric: continue self.__add_metric(metrics, prev_metric) prev_metric = metric self.__add_metric(metrics, prev_metric) return metrics def __add_metric(self, metrics, metric): if metric and (metric.subkey in self.params or self.verbose): metrics[metric.subkey] = metric.value def __read_key_value(self, line, prev_metric): if not line.startswith('\t'): # line is a single-line param or the first line of a multi-line param try: subkey, value = line.strip().split(": ", 1) key = subkey except ValueError: # or not a param line at all, ignore return None, prev_metric else: # line is a subsequent line of a multi-line param subkey, value = line.strip().split(" ", 1) key = prev_metric.key subkey = ".".join((key, subkey)) prev_metric = self.__fix_prev_metric(prev_metric) value = self.__type_value(value) return (Metric(key, subkey, value), prev_metric) def __fix_prev_metric(self, metric): # we can't determine whether a param is single-line or multi-line until we read the second line, after which, we # must go back and fix the first param to be subkeyed if metric.key == metric.subkey: try: subkey, value = metric.value.split(" ", 1) subkey = ".".join((metric.key, subkey)) metric = Metric(metric.key, subkey, self.__type_value(value)) except ValueError: pass return metric def __type_value(self, value): try: try: return int(value) except ValueError: return float(value) except ValueError: return value
__all__ = ('CgroupPlugin', )