totNumSpikes):
spikeTimeTrace = "Times_" + sim + "_" + simConfigName + "_" + str(
spikeIndex)
if not allSpikeTimeDataSets.has_key(spikeTimeTrace):
ds = DataSet(spikeTimeTrace, spikeTimeTrace, "",
"ms", "Number of compartments",
"Spike time")
allSpikeTimeDataSets[spikeTimeTrace] = ds
spikeTrace = allSpikeTimeDataSets[spikeTimeTrace]
print "Adding point to " + spikeTimeTrace
#pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[-1])
##pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[spikeIndex])
morphProp = simData.getSimulationProperties(
).getProperty("Morph summary nRT")
comps = morphProp.split(":")[-1]
pointNum = spikeTrace.addPoint(float(comps),
spikeTimes[spikeIndex])
#spikeTrace.setCommentOnPoint(pointNum, "Point for electrotonic len: "+str(maxElecLen))
spikeTrace.setCommentOnPoint(pointNum, morphProp)
if plotSims:
simConfigName = simData.getSimulationProperties(
).getProperty("Sim Config")
if simConfigName.find('(') >= 0:
simConfigName = simConfigName[0:simConfigName.
find('(')]
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
### Change num in each cell group
simManager.project.cellGroupsInfo.getCellPackingAdapter("lg1").setMaxNumberCells(numCells1)
simManager.project.cellGroupsInfo.getCellPackingAdapter("lg2").setMaxNumberCells(numCells2)
allSims = simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
maxElecLens = multipleRuns,
saveAsHdf5 = saveAsHdf5,
saveOnlySpikes = saveOnlySpikes,
runMode = runMode)
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty("RealSimulationTime")
print "Simulation: %s took %s seconds"%(sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty("Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(paraConfig.find(" host, ")+7, paraConfig.find(" hosts, ")+8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
print times
print procNums
'''
import matplotlib.pyplot as plt
lines = plt.loglog(times, procNums, 'r:')
plt.ylabel('Simulation time')
plt.xlabel('Number of processors')
plt.show()'''
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
plotFrame = PlotManager.getPlotterFrame("Time for simulation run on different numbers of processors", 0, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "Simulation times for: "+str(procNums)
dataSet = DataSet(info, info, "#", "s", "Number of processors", "Simulation time")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for i in range(len(times)):
#dataSet.addPoint(procNums[i],times[i]*procNums[i])
dataSet.addPoint(procNums[i],times[i])
plotFrame.addDataSet(dataSet)
if totNumSpikes <0: totNumSpikes = len(spikeTimes)
for spikeIndex in range(max(totNumSpikes-numSpikes, 0), totNumSpikes):
spikeTimeTrace = "Times_"+sim+"_"+simConfigName+"_"+str(spikeIndex)
if not allSpikeTimeDataSets.has_key(spikeTimeTrace):
ds = DataSet(spikeTimeTrace, spikeTimeTrace, "", "ms", "Number of compartments", "Spike time")
allSpikeTimeDataSets[spikeTimeTrace] = ds
spikeTrace = allSpikeTimeDataSets[spikeTimeTrace]
print "Adding point to "+spikeTimeTrace
#pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[-1])
##pointNum = spikeTrace.addPoint(1/maxElecLen, spikeTimes[spikeIndex])
morphProp = simData.getSimulationProperties().getProperty("Morph summary nRT")
comps = morphProp.split(":")[-1]
pointNum = spikeTrace.addPoint(float(comps), spikeTimes[spikeIndex])
#spikeTrace.setCommentOnPoint(pointNum, "Point for electrotonic len: "+str(maxElecLen))
spikeTrace.setCommentOnPoint(pointNum, morphProp)
if plotSims:
simConfigName = simData.getSimulationProperties().getProperty("Sim Config")
if simConfigName.find('(')>=0:
simConfigName = simConfigName[0:simConfigName.find('(')]
for dataStore in simData.getAllLoadedDataStores():
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
### Change num in each cell group
densityGrC = 1.90e6
densityMF = 6.6e5
densityGoC = 4607
totDens = densityGrC + densityMF + densityGoC
numMF = int(targetNum * densityMF/totDens)
numGoC = int(targetNum * densityGoC/totDens)
numGrC = targetNum - numMF - numGoC
vol = targetNum/(totDens*1e-9)
height = 150
side = math.sqrt(vol/height)
info = "Number in %fx%fx%i box (vol: %f mm^3): GrC: %i, MF: %i, GoC: %i, Total: %i"%(side, side, height, vol*1e-9,numGrC, numMF,numGoC, (numGrC +numMF +numGoC))
print info
SimulationsInfo.addExtraSimProperty("summary", info)
region3D = simManager.project.regionsInfo.getRegionObject("TestGranCellVolume")
region3D.setParameter(region3D.WIDTH_PARAM, side)
region3D.setParameter(region3D.HEIGHT_PARAM, height)
region3D.setParameter(region3D.DEPTH_PARAM, side)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingGrC").setMaxNumberCells(numGrC)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingGoC").setMaxNumberCells(numGoC)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingMF").setMaxNumberCells(numMF)
######simManager.project.cellGroupsInfo.getCellPackingAdapter("lg2").setMaxNumberCells(numCells2)
allSims = simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
maxElecLens = multipleRuns,
saveAsHdf5 = saveAsHdf5,
saveOnlySpikes = saveOnlySpikes,
runMode = runMode)
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty("RealSimulationTime")
print "Simulation: %s took %s seconds"%(sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty("Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(paraConfig.find(" host, ")+7, paraConfig.find(" hosts, ")+8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
print times
print procNums
'''
import matplotlib.pyplot as plt
lines = plt.loglog(times, procNums, 'r:')
plt.ylabel('Simulation time')
plt.xlabel('Number of processors')
plt.show()'''
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
plotFrame = PlotManager.getPlotterFrame("Time for simulation run on different numbers of processors", 0, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "Simulation times for: "+str(procNums)
dataSet = DataSet(info, info, "#", "s", "Number of processors", "Simulation time")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for i in range(len(times)):
dataSet.addPoint(procNums[i],times[i]*procNums[i])
#dataSet.addPoint(procNums[i],times[i])
plotFrame.addDataSet(dataSet)
def reloadSims(waitForSimsToFinish):
print "Trying to reload sims: "+str(allFinishedSims)
plottedSims = []
for simRef in allFinishedSims:
simDir = File(projFile.getParentFile(), "/simulations/"+simRef)
timeFile = File(simDir, "time.dat")
timeFile2 = File(simDir,"time.txt") # for PSICS...
if timeFile.exists() or timeFile2.exists():
if verbose: print "--- Reloading data from simulation in directory: %s"%simDir.getCanonicalPath()
time.sleep(1) # wait a while...
try:
simData = SimulationData(simDir)
simData.initialise()
times = simData.getAllTimes()
if analyseSims:
'''
volts = simData.getVoltageAtAllTimes(cellSegmentRef)
if verbose: print "Got "+str(len(volts))+" data points on cell seg ref: "+cellSegmentRef
analyseStartTime = 0
analyseStopTime = simConfig.getSimDuration()
analyseThreshold = -20 # mV
spikeTimes = SpikeAnalyser.getSpikeTimes(volts, times, analyseThreshold, analyseStartTime, analyseStopTime)
print "Spike times in %s for sim %s: %s"%(cellSegmentRef, simRef, str(spikeTimes))
'''
if plotSims:
simConfigName = simData.getSimulationProperties().getProperty("Sim Config")
if simConfigName.find('(')>=0:
simConfigName = simConfigName[0:simConfigName.find('(')]
for dataStore in simData.getAllLoadedDataStores():
ds = simData.getDataSet(dataStore.getCellSegRef(), dataStore.getVariable(), False)
if not plotVoltageOnly or dataStore.getVariable() == SimPlot.VOLTAGE:
plotFrame = PlotManager.getPlotterFrame("Behaviour of "+dataStore.getVariable() \
+" on: %s for sim config: %s"%(str(simulators), simConfigName))
plotFrame.addDataSet(ds)
plottedSims.append(simRef)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
for simRef in plottedSims:
allFinishedSims.remove(simRef)
if waitForSimsToFinish and len(allRunningSims)>0:
if verbose: print "Waiting for sims: %s to finish..."%str(allRunningSims)
time.sleep(2) # wait a while...
updateSimsRunning()
reloadSims(True)
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
### Change num in each cell group
densityGrC = 1.90e6
densityMF = 6.6e5
densityGoC = 4607
totDens = densityGrC + densityMF + densityGoC
for conf in confs.keys():
numb = conf
mpiConfigs = [confs[conf]]
perProc = 5000
targetNum = perProc*numb
simAllPrefix = "NZ_%i_%i_"%(perProc, numb) # Adds a prefix to simulation reference
print "Simulation pref: "+simAllPrefix
numMF = int(targetNum * densityMF/totDens)
numGoC = int(targetNum * densityGoC/totDens)
numGrC = targetNum - numMF - numGoC
vol = targetNum/(totDens*1e-9)
height = 150
side = math.sqrt(vol/height)
info = "Number in %fx%fx%i box (vol: %f mm^3): GrC: %i, MF: %i, GoC: %i, Total: %i"%(side, side, height, vol*1e-9,numGrC, numMF,numGoC, (numGrC +numMF +numGoC))
print info
SimulationsInfo.addExtraSimProperty("summary", info)
region3D = simManager.project.regionsInfo.getRegionObject("TestGranCellVolume")
region3D.setParameter(region3D.WIDTH_PARAM, side)
region3D.setParameter(region3D.HEIGHT_PARAM, height)
region3D.setParameter(region3D.DEPTH_PARAM, side)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingGrC").setMaxNumberCells(numGrC)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingGoC").setMaxNumberCells(numGoC)
simManager.project.cellGroupsInfo.getCellPackingAdapter("TestScalingMF").setMaxNumberCells(numMF)
######simManager.project.cellGroupsInfo.getCellPackingAdapter("lg2").setMaxNumberCells(numCells2)
allSims = simManager.runMultipleSims(simConfigs = simConfigs,
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
maxElecLens = multipleRuns,
saveAsHdf5 = saveAsHdf5,
saveOnlySpikes = saveOnlySpikes,
runMode = runMode)
if wait:
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(30) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty("RealSimulationTime")
print "Simulation: %s took %s seconds"%(sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty("Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(paraConfig.find(" host, ")+7, paraConfig.find(" hosts, ")+8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
print sys.exc_info()
if totNumSpikes <0: totNumSpikes = len(spikeTimes)
for spikeIndex in range(max(totNumSpikes-numSpikes, 0), totNumSpikes):
spikeTimeTrace = "Times_"+sim+"_"+simConfigName+"_"+str(spikeIndex)
if not allSpikeTimeDataSets.has_key(spikeTimeTrace):
ds = DataSet(spikeTimeTrace, spikeTimeTrace, "", "ms", "Number of compartments", "Spike time")
allSpikeTimeDataSets[spikeTimeTrace] = ds
spikeTrace = allSpikeTimeDataSets[spikeTimeTrace]
print "Adding point to "+spikeTimeTrace
dtUsed = simData.getSimulationProperties().getProperty("dt")
pointNum = spikeTrace.addPoint(float(dtUsed), spikeTimes[spikeIndex])
if plotSims:
simConfigName = simData.getSimulationProperties().getProperty("Sim Config")
if simConfigName.find('(')>=0:
simConfigName = simConfigName[0:simConfigName.find('(')]
for dataStore in simData.getAllLoadedDataStores():
ds = simData.getDataSet(dataStore.getCellSegRef(), dataStore.getVariable(), False)
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from "+ projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims = numConcurrentSims,
verbose = verbose)
### Change num in each cell group
simManager.project.cellGroupsInfo.getCellPackingAdapter("ExcCells").setMaxNumberCells(numExcCells)
simManager.project.cellGroupsInfo.getCellPackingAdapter("INCells").setMaxNumberCells(numINCells)
### Change weights in synapses/gap junctions
simConfig = simManager.project.simConfigInfo.getSimConfig(simConfigName)
for netConnName in simConfig.getNetConns():
print "Changing synaptic delay in %s to %f"%(netConnName, defaultSynapticDelay)
delayGen = NumberGenerator(defaultSynapticDelay)
for synProps in simManager.project.morphNetworkConnectionsInfo.getSynapseList(netConnName):
synProps.setDelayGenerator(delayGen)
# defaultSynapticDelay will be recorded in simulation.props and listed in SimulationBrowser GUI
SimulationsInfo.addExtraSimProperty("defaultSynapticDelay", str(defaultSynapticDelay))
allSims = simManager.runMultipleSims(simConfigs = [simConfigName],
simDt = simDt,
simDuration = simDuration,
simulators = simulators,
runInBackground = runInBackground,
varTimestepNeuron = varTimestepNeuron,
mpiConfigs = mpiConfigs,
suggestedRemoteRunTime = suggestedRemoteRunTime,
simRefGlobalPrefix = simAllPrefix,
runSims = runSims,
neuroConstructSeed = neuroConstructSeed,
simulatorSeed = simulatorSeed)
while (len(simManager.allRunningSims)>0):
print "Waiting for the following sims to finish: "+str(simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/"+sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty("RealSimulationTime")
print "Simulation: %s took %s seconds"%(sim, simTime)
except:
print "Error analysing simulation data from: %s"%simDir.getCanonicalPath()
if mpiConfigs == [MpiSettings.LOCAL_SERIAL] or mpiConfigs == [MpiSettings.MATLEM_1PROC]:
simManager.reloadSims(plotVoltageOnly = True,
plotSims = plotSims,
analyseSims = analyseSims)
def testAll(argv=None):
if argv is None:
argv = sys.argv
print "Loading project from " + projFile.getCanonicalPath()
simManager = nc.SimulationManager(projFile,
numConcurrentSims=numConcurrentSims,
verbose=verbose)
allSims = simManager.runMultipleSims(
simConfigs=simConfigs,
simDt=simDt,
simDuration=simDuration,
simulators=simulators,
runInBackground=runInBackground,
varTimestepNeuron=varTimestepNeuron,
mpiConfigs=mpiConfigs,
suggestedRemoteRunTime=suggestedRemoteRunTime,
simRefGlobalPrefix=simAllPrefix,
runSims=runSims,
maxElecLens=multipleRuns,
saveAsHdf5=saveAsHdf5,
saveOnlySpikes=saveOnlySpikes)
while (len(simManager.allRunningSims) > 0):
print "Waiting for the following sims to finish: " + str(
simManager.allRunningSims)
time.sleep(5) # wait a while...
simManager.updateSimsRunning()
times = []
procNums = []
for sim in allSims:
simDir = File(projFile.getParentFile(), "/simulations/" + sim)
try:
simData = SimulationData(simDir)
simData.initialise()
simTime = simData.getSimulationProperties().getProperty(
"RealSimulationTime")
print "Simulation: %s took %s seconds" % (sim, simTime)
times.append(float(simTime))
paraConfig = simData.getSimulationProperties().getProperty(
"Parallel configuration")
print paraConfig
numProc = int(paraConfig[max(
paraConfig.find(" host, ") + 7,
paraConfig.find(" hosts, ") +
8):paraConfig.find(" processor")])
procNums.append(numProc)
except:
print "Error analysing simulation data from: %s" % simDir.getCanonicalPath(
)
print sys.exc_info()
print times
print procNums
'''
import matplotlib.pyplot as plt
lines = plt.loglog(times, procNums, 'r:')
plt.ylabel('Simulation time')
plt.xlabel('Number of processors')
plt.show()'''
from ucl.physiol.neuroconstruct.gui.plotter import PlotManager
from ucl.physiol.neuroconstruct.gui.plotter import PlotCanvas
from ucl.physiol.neuroconstruct.dataset import DataSet
plotFrame = PlotManager.getPlotterFrame(
"Time for simulation run on different numbers of processors", 0, 1)
plotFrame.setViewMode(PlotCanvas.INCLUDE_ORIGIN_VIEW)
info = "Simulation times for: " + str(procNums)
dataSet = DataSet(info, info, "#", "s", "Number of processors",
"Simulation time")
dataSet.setGraphFormat(PlotCanvas.USE_CIRCLES_FOR_PLOT)
for i in range(len(times)):
dataSet.addPoint(procNums[i], times[i] * procNums[i])
plotFrame.addDataSet(dataSet)
