[Paraview] MPI error: MPI_Type_create_subarray(124): Argument array_of_starts has value 120 but must be within [0, 116]
Anton Shterenlikht
mexas at bristol.ac.uk
Tue Mar 19 17:05:36 EDT 2013
I have a python script that I need to run
on Hector (www.hector.ac.uk). It seems
to run fine with pvpython but gives MPI errors with pvbatch.
The MPI used to build and run paraview on hector is (I think):
xt-mpich2 - Cray MPICH2 Message Passing Interface
Hector support staff can reproduce my error,
and suggest that it might indicate a bug in paraview.
They suggested I ask here.
Sorry for a long email.
Below are:
1. python script
2. PBS submission script
3. error message.
4. paraview source snippet that might be relevant,
according to the hector support personnel.
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
Many thanks
Anton
******************************************************************
1. python script, recorded by the trace tool:
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()
******************************************************************
2. 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
******************************************************************
3. error message:
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]
------------------------------------------------
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]
------------------------------------------------
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 80 but must be within [0,76]
------------------------------------------------
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 80 but must be within [0,76]
------------------------------------------------
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]
------------------------------------------------
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 80 but must be within [0,76]
------------------------------------------------
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 80 but must be within [0,76]
------------------------------------------------
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]
------------------------------------------------
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]
------------------------------------------------
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]
------------------------------------------------
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]
------------------------------------------------
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]
------------------------------------------------
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]
------------------------------------------------
Rank 25 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 25
Rank 21 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 21
Rank 29 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 29
Rank 23 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 23
Rank 27 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 27
Rank 30 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 30
Rank 28 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 28
Rank 13 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 13
Rank 19 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 19
Rank 18 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 18
Rank 11 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 11
Rank 10 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 10
Rank 22 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 22
Rank 31 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 31
Rank 6 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 6
Rank 26 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 26
Rank 15 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 15
Rank 14 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 14
Rank 7 [Tue Mar 19 15:18:56 2013] [c11-1c0s0n0] application called MPI_Abort(MPI_COMM_WORLD, 537538828) - process 7
[NID 01760] 2013-03-19 15:18:57 Apid 3924423: initiated application termination
Application 3924423 exit codes: 12
Application 3924423 resources: utime ~14s, stime ~44s
***********************************************************************
4. paraview source snippet that might be relevant
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));
}
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