def _os_getpid():
name = ManagementFactory.getRuntimeMXBean().getName()
_id, _at, _name = name.partition('@')
try:
return int(_id)
except ValueError:
return 1
def cause_deadlock():
counter = [0]
lock_one = Lock()
lock_two = Lock()
threads = [
Thread(name="thread #1",
target=acquire_locks,
args=(counter, lock_one, lock_two)),
Thread(name="thread #2 (reversed)",
target=acquire_locks,
args=(counter, lock_two, lock_one))
]
for thread in threads:
thread.setDaemon(True) # make shutdown possible after deadlock
thread.start()
thread_mxbean = ManagementFactory.getThreadMXBean()
while True:
time.sleep(1)
print "monitoring thread", counter[0]
thread_ids = thread_mxbean.findDeadlockedThreads()
if thread_ids:
print "monitoring thread: deadlock detected, shutting down", list(
thread_ids)
break
def getStatistic_common(name):
memoryBean = ManagementFactory.getMemoryMXBean()
if name == "enabler_HEAP_MEMORY_USAGE":
bytes = memoryBean.getHeapMemoryUsage().getUsed()
return bytes / 1024 / 1024 # convert to MiB
elif name == "enabler_NON_HEAP_MEMORY_USAGE":
bytes = memoryBean.getNonHeapMemoryUsage().getUsed()
return bytes / 1024 / 1024 # convert to MiB
elif name == "enabler_DATANODE_DECOMMISION_REQUESTS":
hadoop_home_dir = proxy.getContainer().getRuntimeContext().getVariable('hadoop_enabler_HADOOP_HOME_DIR').getValue()
if ContainerUtils.isWindows():
raise Exception("[hadoop_enabler_common] Windows not yet implemented in by this enabler.")
else:
commandline = "sh " + os.path.join(hadoop_home_dir, "bin", "hadoop") + " fs -count " + decommissionqueue_dir
output = runCommand(commandline, expectedReturnCodes=[0, 255], suppressOutput=True)
if (output[0] == 0):
stdout = str(output[1])
count = int(stdout.split()[1])
return int(count)
elif (output[0] == 255):
# Decommission request directory doesn't exist. Not expected to exist until the some datanode posts the first request
return int(0)
else:
ContainerUtils.getLogger(proxy).warning("[hadoop_enabler_common] Unexpected return code [" + str(output[0]) +
"] while attempting to retrieve statistic enabler_DATANODE_DECOMMISION_REQUESTS statistic. Assuming 0.")
print output
return int(0)
elif name.startswith('enabler_DISK_'):
tmpdir = proxy.getContainer().getRuntimeContext().getVariable('hadoop_enabler_TMP_DIR').getValue()
if name == "enabler_DISK_SPACE_FREE":
blocks = int(getStatistic_disk(tmpdir)[0])
return blocks / 1024 / 1024 # convert 1024-byte blocks to GiB
#return available
elif name == "enabler_DISK_SPACE_USED":
blocks = int(getStatistic_disk(tmpdir)[1])
return blocks / 1024 / 1024 # convert 1024-byte blocks to GiB
#return used
elif name == "enabler_DISK_SPACE_USED_PERCENT":
return getStatistic_disk(tmpdir)[2]
#return int(percent[:-1])
else:
raise Exception("[hadoop_enabler_common] Unsupported statistic type requested [" + str(name) + "]")
else:
raise Exception("[hadoop_enabler_common] Unsupported statistic type requested [" + str(name) + "]")
def __init__(self, chartFun, isTemporal = False):
self.isTemporal = isTemporal
JPanel()
#self.setBackground(Color.LIGHT_GRAY)
self.chartFun = chartFun
self.enableChartFun = False
self.setLayout(GridLayout(6,2))
self.add(JLabel('CPU Cores'))
nprocs = ManagementFactory.getOperatingSystemMXBean().getAvailableProcessors()
procvals = sorted(set([nprocs, 1, 2, 4, 8, 16, 32, 64, 128]))
cores = JComboBox(procvals)
cores.setSelectedIndex(procvals.index(nprocs))
cores.setMaximumSize(cores.getPreferredSize())
self.cores = cores
self.add(self.cores)
self.add(JLabel('# of sims (x1000) '))
numSims = JComboBox(
map(lambda x: str((10+x)*5), range(10)) +
map(lambda x: str(x*100), range(1,11))
)
numSims.setMaximumSize(numSims.getPreferredSize())
self.numSims = numSims
self.add(self.numSims)
if isTemporal:
self.add(JLabel('"Neutral" Ne'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
else:
self.add(JLabel('"Neutral" mean Fst'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
self.add(JLabel('Force mean Fst'))
self.force = JCheckBox()
self.force.addActionListener(self)
self.add(self.force)
self.add(JLabel('Confidence interval '))
ci = JComboBox(['0.95', '0.99', '0.995'])
ci.addItemListener(self)
ci.setMaximumSize(cores.getPreferredSize())
self.ci = ci
self.add(self.ci)
self.add(JLabel('False Disc. Rate'))
fdr = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
fdr.setValue(0.1)
fdr.addPropertyChangeListener(self)
self.add(fdr)
self.fdr = fdr
def __init__(self, chartFun, isTemporal = False):
self.isTemporal = isTemporal
JPanel()
#self.setBackground(Color.LIGHT_GRAY)
self.chartFun = chartFun
self.enableChartFun = False
self.setLayout(GridLayout(6,2))
self.add(JLabel('CPU Cores'))
cores = JComboBox(['1', '2', '4', '8', '16', '32', '64', '128'])
nprocs = ManagementFactory.getOperatingSystemMXBean().getAvailableProcessors()
pos = min([7, log(ceil(nprocs)) / log(2)])
cores.setSelectedIndex(int(pos))
cores.setMaximumSize(cores.getPreferredSize())
self.cores = cores
self.add(self.cores)
self.add(JLabel('# of sims (x1000) '))
numSims = JComboBox(
map(lambda x: str((10+x)*5), range(10)) +
map(lambda x: str(x*100), range(1,11))
)
numSims.setMaximumSize(numSims.getPreferredSize())
self.numSims = numSims
self.add(self.numSims)
if isTemporal:
self.add(JLabel('"Neutral" Ne'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
else:
self.add(JLabel('"Neutral" mean Fst'))
self.neutral = JCheckBox()
self.neutral.addActionListener(self)
self.add(self.neutral)
self.add(JLabel('Force mean Fst'))
self.force = JCheckBox()
self.force.addActionListener(self)
self.add(self.force)
self.add(JLabel('Confidence interval '))
ci = JComboBox(['0.95', '0.99', '0.995'])
ci.addItemListener(self)
ci.setMaximumSize(cores.getPreferredSize())
self.ci = ci
self.add(self.ci)
self.add(JLabel('False Disc. Rate'))
fdr = JFormattedTextField(
NumberFormat.getNumberInstance(Locale.US))
fdr.setValue(0.1)
fdr.addPropertyChangeListener(self)
self.add(fdr)
self.fdr = fdr
simDt = 0.005
#simDt= 0.01 # for newly added mep tests which will be used for omv tests with jNeuroML_NEURON
neuroConstructSeed = 12345
simulatorSeed = 11111
#simulators = ["NEURON", "GENESIS_PHYS", "MOOSE_PHYS", "MOOSE_SI"] #"GENESIS_SI",
#simulators = ["NEURON", "GENESIS_PHYS"] #"GENESIS_SI",
#simulators = ["GENESIS", "MOOSE"]
simulators = ["NEURON"]
#maxElecLens = [0.01] # 0.01 will give ~700 in FRB & RS
#maxElecLens = [-1] # -1 means don't recompartmentalise use settings in proj
#maxElecLens = [0.025, 0.01,0.005, 0.0025, 0.001,0.0005, 0.00025, 0.0001]
#### Note: the function testAll() below does not recompartmentalise the cells
numConcurrentSims = ManagementFactory.getOperatingSystemMXBean(
).getAvailableProcessors() - 1
if mpiConfig != MpiSettings.LOCAL_SERIAL:
numConcurrentSims = 60
suggestedRemoteRunTime = 80 # mins
varTimestepNeuron = False # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON
varTimestepTolerance = 0.00001
analyseSims = True
plotSims = True
plotVoltageOnly = True
simAllPrefix = "" # Adds a prefix to simulation reference
runInBackground = True #(mpiConf == MpiSettings.LOCAL_SERIAL)
import os
import sys
import shutil
from org.apache.log4j import Logger
from java.lang.management import ManagementFactory
import unittest
#sys.modules['AdminConfig'] = AdminConfig
#sys.modules['AdminControl'] = AdminControl
#sys.modules['AdminApp'] = AdminApp
#sys.modules['AdminTask'] = AdminTask
#sys.modules['Help'] = Help
'''set up the paths, create the tmp working directory and make a props dictionary'''
pidname=ManagementFactory.getRuntimeMXBean().getName()
pidlist=pidname.split('@')
pid=pidlist[0]
currentWorkingDirectory=os.getcwd()
#print currentWorkingDirectory
binPath=currentWorkingDirectory + os.sep + "bin"
confPath=currentWorkingDirectory + os.sep + "conf"
logPath=currentWorkingDirectory + os.sep + "log"
tmpPath=currentWorkingDirectory + os.sep + "tmp" + os.sep + pid
libPath=currentWorkingDirectory + os.sep + "lib"
jythonpath=libPath + os.sep + "jython" + os.sep + "Lib"
srcPath=currentWorkingDirectory + os.sep + "src"
testPath=currentWorkingDirectory + os.sep + "test"
sys.path.append(binPath)
sys.path.append(confPath)
sys.path.append(logPath)
sys.path.append(tmpPath)
#simDt= 0.01 # for newly added mep tests which will be used for omv tests with jNeuroML_NEURON neuroConstructSeed = 12345 simulatorSeed = 11111 #simulators = ["NEURON", "GENESIS_PHYS", "MOOSE_PHYS", "MOOSE_SI"] #"GENESIS_SI", #simulators = ["NEURON", "GENESIS_PHYS"] #"GENESIS_SI", #simulators = ["GENESIS", "MOOSE"] simulators = ["NEURON"] #maxElecLens = [0.01] # 0.01 will give ~700 in FRB & RS #maxElecLens = [-1] # -1 means don't recompartmentalise use settings in proj #maxElecLens = [0.025, 0.01,0.005, 0.0025, 0.001,0.0005, 0.00025, 0.0001] #### Note: the function testAll() below does not recompartmentalise the cells numConcurrentSims = ManagementFactory.getOperatingSystemMXBean().getAvailableProcessors() -1 if mpiConfig != MpiSettings.LOCAL_SERIAL: numConcurrentSims = 60 suggestedRemoteRunTime = 80 # mins varTimestepNeuron = False # could be more accurate with var time step in nrn, but need to compare these to jNeuroML_NEURON varTimestepTolerance = 0.00001 analyseSims = True plotSims = True plotVoltageOnly = True simAllPrefix = "" # Adds a prefix to simulation reference
import openhab
from java.lang.management import ManagementFactory
from com.sun.management import HotSpotDiagnosticMXBean
hotSpotDiagnosticMXBean = ManagementFactory.getPlatformMXBean(HotSpotDiagnosticMXBean)
@openhab.rule
class HeapDumpRule(object):
"""Dump the Java heap when thread count exceeds a specified threshold"""
def __init__(self, maxThreads, outpath, notify=False):
self._maxThreads = maxThreads
self._outpath = outpath
self._notify = notify
self._dumped = False
def getEventTrigger(self):
return [ ChangedEventTrigger("JmxThreadCount") ]
def execute(self, event):
if not self._dumped and event.item.state.intValue() > self._maxThreads:
self._dumped = True
message = "EXCESSIVE THREADS: count={}, dumping heap".format(event.item.state)
self.log.error(message)
if self._notify:
self.sendNotification(message)
hotSpotDiagnosticMXBean.dumpHeap(self._outpath, True)
def getRules():
return RuleSet([ HeapDumpRule(400, "/opt/openhab-1.7.1/memory_dump.hprof", True) ])
backend_pid = inv.getLong("backend_pid")
con = Hiber.session().connection()
stmt = con.createStatement()
stmt.execute("select pg_terminate_backend(" + str(backend_pid) + ")")
stmt.close()
Hiber.commit()
source.appendChild(MonadMessage("Cancelled backend.").toXml(doc))
df = DecimalFormat("###,###,###,###,##0")
runtime = Runtime.getRuntime()
source.setAttribute("free-memory", df.format(runtime.freeMemory()))
source.setAttribute("max-memory", df.format(runtime.maxMemory()))
source.setAttribute("total-memory", df.format(runtime.totalMemory()))
source.setAttribute("available-processors", str(runtime.availableProcessors()))
source.setAttribute("system-load-average", str(ManagementFactory.getOperatingSystemMXBean().getSystemLoadAverage()))
mon = JavaSysMon()
source.setAttribute("cpu-frequency-in-hz", df.format(mon.cpuFrequencyInHz()))
source.setAttribute("current-pid", df.format(mon.currentPid()))
source.setAttribute("num-cpus", df.format(mon.numCpus()))
source.setAttribute("os-name", mon.osName())
source.setAttribute("uptime-in-seconds", df.format(mon.uptimeInSeconds()))
cpu = mon.cpuTimes()
source.setAttribute("idle-millis", df.format(cpu.getIdleMillis()))
source.setAttribute("system-millis", df.format(cpu.getSystemMillis()))
source.setAttribute("total-millis", df.format(cpu.getTotalMillis()))
source.setAttribute("user-millis", df.format(cpu.getUserMillis()))
props = doc.createElement("properties")
source.appendChild(props)
def getThreadInfo(thread):
"""Get the thread info object from the Java ThreadMXBean. Thing."""
from java.lang.management import ManagementFactory
TMXB = ManagementFactory.getThreadMXBean()
return TMXB.getThreadInfo(thread.id)
def _os_getpid():
return ManagementFactory.getRuntimeMXBean().getName()
import openhab
from java.lang.management import ManagementFactory
jmx_beans = {
'Threads' : ManagementFactory.getThreadMXBean(),
'Memory' : ManagementFactory.getMemoryMXBean(),
}
for bean in ManagementFactory.getMemoryPoolMXBeans():
jmx_beans[bean.name] = bean
@openhab.rule
class JmxBinding(object):
# Binding all items in one rule to avoid numerous timers. If some items
# should be updated at a different frequencies, then multiple rules can be
# instantiated.
def __init__(self, item_specs, cronspec="0 * * * * ?"):
self._item_specs = item_specs
self._cronspec = cronspec
def getEventTrigger(self):
return [
StartupTrigger(),
TimerTrigger(self._cronspec)
]
def execute(self, event):
for item_name, bean_name, attr_path, transform in self._item_specs:
try:
bean = jmx_beans.get(bean_name)