[Paraview] Help with memory crash?
Nikolaos Beratlis
nikos.beratlis at gmail.com
Wed Jan 7 14:55:03 EST 2015
I am trying to run a script on a cluster with Paraview in parallel. The
cluster architecture is 16cores and 64GB per node. The script reads in two
XMF files, one contains a grid of 2002x100x1000 points along with one
variable. There is a loop to perform two iterations:
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
RenderView1 = GetRenderView()
RenderView1.Background = [1.0, 1.0, 1.0]
view = GetActiveView()
view.ViewSize = [ 800, 500 ]
RenderView1.CenterAxesVisibility = 0
#RenderView1.OrientationAxesVisibility = 0
#Define variables
wdir =
'/lustre/groups/balarasgrp/nikosb/Research/Simulations/golfball/stationary/S120/Re200000/gridC1/run_wm'
#wdir =
'/Users/nikosb/colone/Research/Simulations/golfball/stationary/S120/Re200000/gridC1/run_wm'
#wdir = '/Users/nikosb/Research/Simulations/SPHERE/Re100/gridC1/run'
Qval = 0.1
cfmin = -0.001
cfmax = 0.005
index = [None]*9999
m = 0
for i in range(0, 9):
for j in range(0, 9):
for k in range(0, 9):
for l in range(0, 9):
index[m] = chr(i+48)+chr(j+48)+chr(k+48)+chr(l+48)
m = m+1
for i in range(1,3):
cf_VP_xmf = XDMFReader(
FileName=wdir+'/VPfield/XDMF/cf_VP'+index[i]+'.xmf' )
cf_VP_xmf.Sets = []
cf_VP_xmf.Grids = ['STL Grid']
cf_VP_xmf.PointArrays = ['Cf']
RenderView1 = GetRenderView()
RenderView1.CenterOfRotation = [6.2286853790283203e-06,
2.5033950805664062e-06, 7.1227550506591797e-06]
DataRepresentation1 = Show()
DataRepresentation1.EdgeColor = [0.0, 0.0, 0.50000762951094835]
DataRepresentation1.SelectionPointFieldDataArrayName = 'Cf'
DataRepresentation1.ColorArrayName = ('POINT_DATA', 'Cf')
DataRepresentation1.ScalarOpacityUnitDistance = 0.033928799990483226
DataRepresentation1.ScaleFactor = 0.099998557567596444
a1_Cf_PVLookupTable = GetLookupTableForArray( "Cf", 1,
RGBPoints=[-0.0099065126851201057, 0.23000000000000001,
0.29899999999999999, 0.754, 0.0097341262735426426, 0.86499999999999999,
0.86499999999999999, 0.86499999999999999, 0.029374765232205391,
0.70599999999999996, 0.016, 0.14999999999999999], VectorMode='Magnitude',
NanColor=[0.25, 0.0, 0.0], ColorSpace='Diverging',
ScalarRangeInitialized=1.0 )
a1_Cf_PiecewiseFunction = CreatePiecewiseFunction(
Points=[-0.0099065126851201057, 0.0, 0.5, 0.0, 0.029374765232205391, 1.0,
0.5, 0.0] )
DataRepresentation1.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
DataRepresentation1.LookupTable = a1_Cf_PVLookupTable
a1_Cf_PVLookupTable.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
a1_Cf_PVLookupTable.RGBPoints = [cfmin, 0.23000000000000001,
0.29899999999999999, 0.754, -0.002, 0.86499999999999999,
0.86499999999999999, 0.86499999999999999, cfmax, 0.70599999999999996,
0.016, 0.14999999999999999]
a1_Cf_PVLookupTable.ScalarOpacityFunction = a1_Cf_PiecewiseFunction
a1_Cf_PVLookupTable.LockScalarRange = 1
RenderView1.CameraPosition = [6.2286853790283203e-06,
2.5033950805664062e-06, 3.3460035306026636]
RenderView1.CameraFocalPoint = [6.2286853790283203e-06,
2.5033950805664062e-06, 7.1227550506591797e-06]
RenderView1.CameraClippingRange = [2.3175641399614015, 4.6486514901655163]
RenderView1.CameraParallelScale = 0.86600759519558368
Contour1 = Contour( PointMergeMethod="Uniform Binning" )
Contour1.PointMergeMethod = "Uniform Binning"
Contour1.ContourBy = ['POINTS', 'Cf']
Contour1.Isosurfaces = [0.0097341262735426426]
DataRepresentation2 = Show()
DataRepresentation2.ColorArrayName = ('POINT_DATA', '')
DataRepresentation2.ScaleFactor = 0.099971860647201538
DataRepresentation2.SelectionPointFieldDataArrayName = 'Cf'
DataRepresentation2.EdgeColor = [0.0, 0.0, 0.50000762951094835]
DataRepresentation2.Representation = 'Wireframe'
DataRepresentation2.AmbientColor = [0.0, 0.0, 0.0]
DataRepresentation1.Visibility = 0
RenderView1.CameraClippingRange = [2.7470738944403328, 4.2397684828477349]
DataRepresentation1.Visibility = 1
RenderView1.CameraClippingRange = [2.3175641399614015, 4.6486514901655163]
Q_VP_xmf = XDMFReader( FileName=wdir+'/VPfield/XDMF/Q_VP'+index[i]+'.xmf'
)
Contour1.Isosurfaces = [0.0]
Q_VP_xmf.Sets = []
Q_VP_xmf.Grids = ['Eulerian Grid']
Q_VP_xmf.PointArrays = ['Q']
DataRepresentation3 = Show()
DataRepresentation3.EdgeColor = [0.0, 0.0, 0.50000762951094835]
DataRepresentation3.SelectionPointFieldDataArrayName = 'Q'
DataRepresentation3.ScalarOpacityUnitDistance = 0.0045778956118952439
DataRepresentation3.Representation = 'Outline'
DataRepresentation3.ScaleFactor = 0.25585924386978148
RenderView1.CameraClippingRange = [0.30866115510384229,
6.1311800002592065]
Contour2 = Contour( PointMergeMethod="Uniform Binning" )
Contour2.PointMergeMethod = "Uniform Binning"
Contour2.ContourBy = ['POINTS', 'Q']
Contour2.Isosurfaces = [-348374.28125]
DataRepresentation4 = Show()
DataRepresentation4.ScaleFactor = 0.1348903000354767
DataRepresentation4.SelectionPointFieldDataArrayName = 'Normals'
DataRepresentation4.EdgeColor = [0.0, 0.0, 0.50000762951094835]
Contour2.Isosurfaces = [0.5]
DataRepresentation3.Visibility = 0
RenderView1.CameraClippingRange = [0.46635874330917981,
5.5760844897764175]
RenderView1.CameraViewUp = [-1.0, 0.0, 0.0]
RenderView1.CameraPosition = [-5.0, 0.0, 5.0]
RenderView1.CameraClippingRange = [3.0180305778980254, 7.5069525367021557]
RenderView1.CameraFocalPoint = [0.0, 0.0, 5.0]
RenderView1.CameraParallelScale = 1.565457167140391
RenderView1.CenterOfRotation = [0.0, 0.0, 0.0]
RenderView1.CameraFocalPoint = [0.0, 0.0, 0.5]
RenderView1.CameraClippingRange = [0.86197012554183883,
4.2263653610655147]
RenderView1.CameraPosition = [0.0, -2.5, 0.0]
WriteImage(wdir+'/POSTPRO/IMAGES/Q_cf_VP'+index[i]+'.jpg')
Delete(DataRepresentation4)
Delete(Contour2)
Delete(DataRepresentation3)
Delete(Q_VP_xmf)
Delete(DataRepresentation2)
Delete(Contour1)
Delete(DataRepresentation1)
Delete(cf_VP_xmf)
The script was created by running an interactive Paraview session and
recording the commands. I then modified it slightly to add the loop and
some variables.
I have been able to run the script successfully on 1,2,16 and 32 cores
successfully and it loops twice. However when I try to run on 64 cores I
get the following error message:
[node116:58372] 63 more processes have sent help message
help-mpi-common-cuda.txt / dlopen failed
[node116:58372] Set MCA parameter "orte_base_help_aggregate" to 0 to see
all help / error messages
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
[node125:37180] *** Process received signal ***
[node125:37180] Signal: Aborted (6)
[node125:37180] Signal code: (-6)
[node125:37180] [ 0] /lib64/libpthread.so.0(+0xf710) [0x2aaab28f3710]
[node125:37180] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x2aaab479f625]
[node125:37180] [ 2] /lib64/libc.so.6(abort+0x175) [0x2aaab47a0e05]
[node125:37180] [ 3]
/usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d)
[0x2aaab408aa7d]
[node125:37180] [ 4] /usr/lib64/libstdc++.so.6(+0xbcbd6) [0x2aaab4088bd6]
[node125:37180] [ 5] /usr/lib64/libstdc++.so.6(+0xbcc03) [0x2aaab4088c03]
[node125:37180] [ 6] /usr/lib64/libstdc++.so.6(+0xbcd22) [0x2aaab4088d22]
[node125:37180] [ 7] /usr/lib64/libstdc++.so.6(_Znwm+0x7d) [0x2aaab408911d]
[node125:37180] [ 8] /usr/lib64/libstdc++.so.6(_Znam+0x9) [0x2aaab40891d9]
[node125:37180] [ 9]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN16vtkXdmfHeavyData10ReadPointsEP12XdmfGeometryPiS2_+0x3a6)
[0x2aaab716310c]
[node125:37180] [10]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN16vtkXdmfHeavyData21RequestStructuredGridEP8XdmfGrid+0xfb)
[0x2aaab716292f]
[node125:37180] [11]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN16vtkXdmfHeavyData15ReadUniformDataEP8XdmfGrid+0x14c)
[0x2aaab71614ce]
[node125:37180] [12]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN16vtkXdmfHeavyData8ReadDataEP8XdmfGrid+0xd1)
[0x2aaab7160c91]
[node125:37180] [13]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN16vtkXdmfHeavyData8ReadDataEv+0x4f)
[0x2aaab7160a0f]
[node125:37180] [14]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN13vtkXdmfReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x31c)
[0x2aaab716daf0]
[node125:37180] [15]
/c1/apps/paraview/4.1.0/lib/libvtkIOLegacy-pv4.1.so.1(_ZN13vtkDataReader14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x62)
[0x2aaab0b3b9be]
[node125:37180] [16]
/c1/apps/paraview/4.1.0/lib/libvtkIOXdmf2-pv4.1.so.1(_ZN13vtkXdmfReader14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x76)
[0x2aaab716c702]
[node125:37180] [17]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3_+0x8d)
[0x2aaab10c63d1]
[node125:37180] [18]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x76)
[0x2aaab10c0b1c]
[node125:37180] [19]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN24vtkCompositeDataPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x468)
[0x2aaab10b9950]
[node125:37180] [20]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x522)
[0x2aaab10c0248]
[node125:37180] [21]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0xa6c)
[0x2aaab10e5ace]
[node125:37180] [22]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN24vtkCompositeDataPipeline15ForwardUpstreamEP14vtkInformation+0x2d6)
[0x2aaab10bbb6e]
[node125:37180] [23]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x48a)
[0x2aaab10c01b0]
[node125:37180] [24]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0xa6c)
[0x2aaab10e5ace]
[node125:37180] [25]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0x2fb)
[0x2aaab10c0965]
[node125:37180] [26]
/c1/apps/paraview/4.1.0/lib/libvtkCommonExecutionModel-pv4.1.so.1(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEi+0xf8)
[0x2aaab10e5d3e]
[node125:37180] [27]
/c1/apps/paraview/4.1.0/lib/libvtkPVServerImplementationCore-pv4.1.so.1(_ZN16vtkSISourceProxy14UpdatePipelineEidb+0x196)
[0x2aaaac77ef72]
[node125:37180] [28]
/c1/apps/paraview/4.1.0/lib/libvtkPVServerManagerApplication-pv4.1.so.1(_Z23vtkSISourceProxyCommandP26vtkClientServerInterpreterP13vtkObjectBasePKcRK21vtkClientServerStreamRS5_Pv+0x6ee)
[0x2aaaab7f27bd]
[node125:37180] [29]
/c1/apps/paraview/4.1.0/lib/libvtkClientServer-pv4.1.so.1(_ZN26vtkClientServerInterpreter19CallCommandFunctionEPKcP13vtkObjectBaseS1_RK21vtkClientServerStreamRS4_+0x343)
[0x2aaaafb57aa5]
[node125:37180] *** End of error message ***
I am afraid there is an issue with memory leakage or improper memory
allocation and deallocation. At this point I do not know how to proceed to
debug it. Is there an obvious problem in in the script and the way datasets
are deallocated at the end of each iteration?
Regards,
Nikos
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