View Issue Details [ Jump to Notes ] [ Print ]
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 
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));
 }

TagsNo tags attached.
ProjectTBD
Topic Name
Typecrash
Attached Files

 Relationships

  Notes
(0030455)
mexas@bristol.ac.uk (reporter)
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 (administrator)
2016-08-12 09:59

 Resolving issue as `moved`.

This issue tracker is no longer used. Further discussion of this issue may take place in the current ParaView Issues page linked in the banner at the top of this page.

 Issue History
Date Modified Username Field Change
2013-03-21 10:09 mexas@bristol.ac.uk New Issue
2013-03-22 08:00 mexas@bristol.ac.uk Note Added: 0030455
2016-08-12 09:59 Kitware Robot Note Added: 0038368
2016-08-12 09:59 Kitware Robot Status backlog => closed
2016-08-12 09:59 Kitware Robot Resolution open => moved
2016-08-12 09:59 Kitware Robot Assigned To => Kitware Robot

Copyright © 2000 - 2018 MantisBT Team