MantisBT - ParaView
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IDProjectCategoryView StatusDate SubmittedLast Update
0013953ParaView(No Category)public2013-03-21 10:092016-08-12 09:59
Reportermexas@bristol.ac.uk 
Assigned ToKitware Robot 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusclosedResolutionmoved 
PlatformOSOS Version
Product Version3.12 
Target VersionFixed in Version 
ProjectTBD
Topic Name
Typecrash
Summary0013953: MPI error: MPI_Type_create_subarray(124): Argument array_of_starts has value 120 but must be within [0, 116]
DescriptionThe following python script works with pvpython,
but fails with pvbatch.

try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()

z_raw = ImageReader( FilePrefix='z.raw' )

z_raw.DataExtent = [1, 40, 1, 40, 1, 40]
z_raw.DataByteOrder = 'LittleEndian'
z_raw.DataScalarType = 'int'

RenderView1 = GetRenderView()

DataRepresentation1 = Show()
DataRepresentation1.ScalarOpacityUnitDistance = 1.7320508075688776
DataRepresentation1.Representation = 'Outline'
DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5000076295109483]

RenderView1.CenterOfRotation = [19.5, 19.5, 19.5]

a1_ImageFile_PVLookupTable = GetLookupTableForArray( "ImageFile", 1, RGBPoints=[1.0, 0.0, 0.0, 0.0, 26.200000000000003, 0.9019607843137255, 0.0, 0.0, 51.400000000000006, 0.9019607843137255, 0.9019607843137255, 0.0, 64.0, 1.0, 1.0, 1.0], VectorMode='Magnitude', NanColor=[0.0, 0.4980392156862745, 1.0], NumberOfTableValues=64, ColorSpace='RGB', ScalarRangeInitialized=1.0 )

a1_ImageFile_PiecewiseFunction = CreatePiecewiseFunction()

ScalarBarWidgetRepresentation1 = CreateScalarBar( Title='Image', LabelFontSize=12, Enabled=1, LookupTable=a1_ImageFile_PVLookupTable, TitleFontSize=12 )
GetRenderView().Representations.append(ScalarBarWidgetRepresentation1)

RenderView1.CameraViewUp = [-0.8528543278199172, 0.017957183620535777, -0.5218400474046194]
RenderView1.CameraPosition = [-43.07616287436094, 67.5962248918674, 123.42461126225268]
RenderView1.CameraClippingRange = [65.37811338222085, 212.781995926041]
RenderView1.CameraFocalPoint = [19.499999999999975, 19.49999999999995, 19.499999999999993]
RenderView1.CameraParallelScale = 33.77499074759311
RenderView1.Background=[0.3, 0.3, 0.4]
RenderView1.ViewSize=[800,800]

DataRepresentation1.Representation = 'Surface'
DataRepresentation1.ScalarOpacityFunction = a1_ImageFile_PiecewiseFunction
DataRepresentation1.ColorArrayName = 'ImageFile'
DataRepresentation1.LookupTable = a1_ImageFile_PVLookupTable

WriteImage('z.png')

Render()

The computer is www.hector.ac.uk

The MPI used to run pvbatch is:
xt-mpich2 - Cray MPICH2 Message Passing Interface

The data file is in raw binry format.
It is a 40x40x40 array of 4byte integers,
written with fortran 2003 "stream" qualifier.
The file size is 40x40x40x4=256000 bytes.
The compressed file (344 bytes) is at:
 http://seis.bris.ac.uk/~mexas/z.raw.xz [^]

The PBS script:

#!/bin/bash --login
#PBS -N pvbatch
#PBS -l mppwidth=32
#PBS -l mppnppn=32
#PBS -l walltime=00:10:00
#PBS -j oe

export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
cd $PBS_O_WORKDIR
export XDG_CONFIG_HOME=${HOME}/work/ParaViewIniConfig

module load paraview-servers/3.12.0

if [ -z ${PARAVIEW_SERVER_DIR} ] ; then
  echo "Error: PARAVIEW_SERVER_DIR not set. Exiting"
  exit 4
fi

echo "DEBUG: PBS_O_WORKDIR is" $PBS_O_WORKDIR
echo "DEBUG: PARAVIEW_SERVER_DIR is" ${PARAVIEW_SERVER_DIR}
echo "DEBUG: XDG_CONFIG_HOME is" ${XDG_CONFIG_HOME}

export MPPWIDTH=`qstat -f $PBS_JOBID | awk '/mppwidth/ {print $3}'`
export MPPNPPN=`qstat -f $PBS_JOBID | awk '/mppnppn/ {print $3}'`

aprun -n ${MPPWIDTH} -N ${MPPNPPN} ${PARAVIEW_SERVER_DIR}/bin/pvbatch \
       --use-offscreen-rendering \
       pv2.py


Error:


DEBUG: PBS_O_WORKDIR is /esfs2/e277/e277/mexas/cgca/branches/coarray/tests
DEBUG: PARAVIEW_SERVER_DIR is /work/y07/y07/nag/ParaViewServers-3.12.0-Linux-x86_64
DEBUG: XDG_CONFIG_HOME is /work/e277/e277/mexas/ParaViewIniConfig

Generic Warning: In /work/z03/z03/markr/xe6il/pv_3.12.0/ParaView-3.12.0/VTK/Parallel/vtkMPICommunicator.cxx, line 72
MPI had an error
------------------------------------------------
Invalid argument, error stack:
MPI_Type_create_subarray(340): MPI_Type_create_subarray(ndims=3, array_of_sizes=0x7fffffff9f20, array_of_subsizes=0x7fffffff9f30, array_of_starts=0x7fffffff9f40, order=57, MPI_BYTE, newtype=0x7fffffff9f54) failed
MPI_Type_create_subarray(124): Argument array_of_starts has value 120 but must be within [0,116]
------------------------------------------------

Generic Warning: In /work/z03/z03/markr/xe6il/pv_3.12.0/ParaView-3.12.0/VTK/Parallel/vtkMPICommunicator.cxx, line 72
MPI had an error
------------------------------------------------
Invalid argument, error stack:
MPI_Type_create_subarray(340): MPI_Type_create_subarray(ndims=3, array_of_sizes=0x7fffffff9f20, array_of_subsizes=0x7fffffff9f30, array_of_starts=0x7fffffff9f40, order=57, MPI_BYTE, newtype=0x7fffffff9f54) failed
MPI_Type_create_subarray(124): Argument array_of_starts has value 120 but must be within [0,116]
------------------------------------------------

Generic Warning: In /work/z03/z03/markr/xe6il/pv_3.12.0/ParaView-3.12.0/VTK/Parallel/vtkMPICommunicator.cxx, line 72
MPI had an error
------------------------------------------------
Invalid argument, error stack:
MPI_Type_create_subarray(340): MPI_Type_create_subarray(ndims=3, array_of_sizes=0x7fffffff9f20, array_of_subsizes=0x7fffffff9f30, array_of_starts=0x7fffffff9f40, order=57, MPI_BYTE, newtype=0x7fffffff9f54) failed
MPI_Type_create_subarray(124): Argument array_of_starts has value 30 but must be within [0,29]
------------------------------------------------

and so on, from each MPI process.


I was told by the Hector support stuff
that the problem might be in this snippet:



 void vtkMPIImageReader::SetupFileView(vtkMPIOpaqueFileHandle &file,
                                       const int extent[6])
 {
   int arrayOfSizes[3];
   int arrayOfSubSizes[3];
   int arrayOfStarts[3];

   for (int i = 0; i < this->GetFileDimensionality(); i++)
     {
     arrayOfSizes[i] = this->DataExtent[i*2+1] - this->DataExtent[i*2] + 1;
     arrayOfSubSizes[i] = extent[i*2+1] - extent[i*2] + 1;
     arrayOfStarts[i] = extent[i*2];
     }
   // Adjust for base size of data type and tuple size.
   int baseSize = this->GetDataScalarTypeSize() * this->NumberOfScalarComponents;
   arrayOfSizes[0] *= baseSize;
   arrayOfSubSizes[0] *= baseSize;
   arrayOfStarts[0] *= baseSize;

   // Create a view in MPIIO.
   MPI_Datatype view;
   MPICall(MPI_Type_create_subarray(this->GetFileDimensionality(),
                                    arrayOfSizes, arrayOfSubSizes, arrayOfStarts,
                                    MPI_ORDER_FORTRAN, MPI_BYTE, &view));
   MPICall(MPI_Type_commit(&view));
   MPICall(MPI_File_set_view(file.Handle, this->GetHeaderSize(file), MPI_BYTE,
                             view, const_cast<char *>("native"), MPI_INFO_NULL));
   MPICall(MPI_Type_free(&view));
 }

Steps To Reproduce
Additional Information
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Issue History
Date ModifiedUsernameFieldChange
2013-03-21 10:09mexas@bristol.ac.ukNew Issue
2013-03-22 08:00mexas@bristol.ac.ukNote Added: 0030455
2016-08-12 09:59Kitware RobotNote Added: 0038368
2016-08-12 09:59Kitware RobotStatusbacklog => closed
2016-08-12 09:59Kitware RobotResolutionopen => moved
2016-08-12 09:59Kitware RobotAssigned To => Kitware Robot

Notes
(0030455)
mexas@bristol.ac.uk   
2013-03-22 08:00   
I get a similar error with 3.98 on another
linux box with an even simpler script:

from paraview.simple import *
#Connect()

#parameters
ext1=80
ext2=ext1
ext3=640
minval=1
maxval=40

# files
infile="z9end.raw"
outfile="z.png"

reader=ImageReader(FilePrefix= infile )
reader.DataByteOrder=1
reader.DataExtent=[1,ext1,1,ext2,1,ext3 ]
reader.DataScalarType=6

view = GetActiveView()
if not view:
 view = CreateRenderView()
view.ViewSize=[800,800]
view.Background=[0.3249412, 0.34902, 0.427451]

Show()

dp = GetDisplayProperties(reader)
dp.LookupTable = MakeBlueToRedLT(minval,maxval)
dp.ColorAttributeType = 'POINT_DATA'
dp.ColorArrayName = 'ImageFile'
dp.Representation = "Surface"

bar = CreateScalarBar(LookupTable=dp.LookupTable, Title="grain")
#bar.Position=[0.80,0.15]

GetRenderView().Representations.append(bar)

camera = GetActiveCamera()
camera.SetViewUp(-1,0,0)
camera.Azimuth(30)
camera.Elevation(30)

#camera.SetPosition(0,0,100)
#camera.Roll(-90)

Render()

WriteImage( outfile )


Error:



bigblue2> pvbatch --use-offscreen-rendering pv1.py
Generic Warning: In /home/utkarsh/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Parallel/MPI/vtkMPICommunicator.cxx, line 72
MPI had an error
------------------------------------------------
Invalid argument, error stack:
MPI_Type_create_subarray(334): MPI_Type_create_subarray(ndims=3, array_of_sizes=0x7fff1acb1ad0, array_of_subsizes=0x7fff1acb1ac0, array_of_starts=0x7fff1acb1ab0, order=57, MPI_BYTE, newtype=0x7fff1acb1ae8) failed
MPI_Type_create_subarray(124): Argument array_of_starts has value 4 but must be within [0,0]
------------------------------------------------

application called MPI_Abort(MPI_COMM_WORLD, 269077004) - process 0
bigblue2>


Again, it works fine with pvpython, but fails with pvbatch
(0038368)
Kitware Robot   
2016-08-12 09:59   
Resolving issue as `moved`.

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