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Merge pull request #5016 from natefoo/memory-mb-metric

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Add metric to the core plugin to collect $GALAXY_MEMORY_MB
This commit is contained in:
Björn Grüning
2017-11-17 08:50:53 +01:00
committed by GitHub
parent b5864ad4f7 d5aa2595aa
commit 83e9e07bd5
1 changed files with 13 additions and 0 deletions
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lib/galaxy/jobs/metrics/instrumenters/core.py
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@@ -8,6 +8,7 @@ from ...metrics import formatting
log = logging.getLogger(__name__)
GALAXY_SLOTS_KEY = "galaxy_slots"
GALAXY_MEMORY_MB_KEY = "galaxy_memory_mb"
START_EPOCH_KEY = "start_epoch"
END_EPOCH_KEY = "end_epoch"
RUNTIME_SECONDS_KEY = "runtime_seconds"
@@ -19,6 +20,8 @@ class CorePluginFormatter(formatting.JobMetricFormatter):
value = int(value)
if key == GALAXY_SLOTS_KEY:
return ("Cores Allocated", "%d" % value)
elif key == GALAXY_MEMORY_MB_KEY:
return ("Memory Allocated (MB)", "%d" % value)
elif key == RUNTIME_SECONDS_KEY:
return ("Job Runtime (Wall Clock)", formatting.seconds_to_str(value))
else:
@@ -40,6 +43,7 @@ class CorePlugin(InstrumentPlugin):
def pre_execute_instrument(self, job_directory):
commands = []
commands.append(self.__record_galaxy_slots_command(job_directory))
commands.append(self.__record_galaxy_memory_mb_command(job_directory))
commands.append(self.__record_seconds_since_epoch_to_file(job_directory, "start"))
return commands
@@ -50,9 +54,11 @@ class CorePlugin(InstrumentPlugin):
def job_properties(self, job_id, job_directory):
galaxy_slots_file = self.__galaxy_slots_file(job_directory)
galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
properties = {}
properties[GALAXY_SLOTS_KEY] = self.__read_integer(galaxy_slots_file)
properties[GALAXY_MEMORY_MB_KEY] = self.__read_integer(galaxy_memory_mb_file)
start = self.__read_seconds_since_epoch(job_directory, "start")
end = self.__read_seconds_since_epoch(job_directory, "end")
if start is not None and end is not None:
@@ -65,6 +71,10 @@ class CorePlugin(InstrumentPlugin):
galaxy_slots_file = self.__galaxy_slots_file(job_directory)
return '''echo "$GALAXY_SLOTS" > '%s' ''' % galaxy_slots_file
def __record_galaxy_memory_mb_command(self, job_directory):
galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
return '''echo "$GALAXY_MEMORY_MB" > '%s' ''' % galaxy_memory_mb_file
def __record_seconds_since_epoch_to_file(self, job_directory, name):
path = self._instrument_file_path(job_directory, "epoch_%s" % name)
return 'date +"%s" > ' + path
@@ -76,6 +86,9 @@ class CorePlugin(InstrumentPlugin):
def __galaxy_slots_file(self, job_directory):
return self._instrument_file_path(job_directory, "galaxy_slots")
def __galaxy_memory_mb_file(self, job_directory):
return self._instrument_file_path(job_directory, "galaxy_memory_mb")
def __read_integer(self, path):
value = None
try: