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)
#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
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)
