Can't run calculation example

[Skygogogogo]

The cmake .. and build all have finished, and have made the target mpap but it can't run.

[Skygogogogo]

mpap: /usr/include/eigen3/Eigen/src/Core/Block.h:118: Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Index) [with XprType = Eigen::Matrix<double, -1, -1>; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = false; Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Index = long int]: Assertion `(i>=0) && ( ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i<xpr.rows()) ||((BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) && i<xpr.cols()))' failed. [ubuntu:10089] Process received signal [ubuntu:10089] Signal: Aborted (6) [ubuntu:10089] Signal code: (-6) [ubuntu:10089] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f0082786980] [ubuntu:10089] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f007d92fe87] [ubuntu:10089] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f007d9317f1] [ubuntu:10089] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x303fa)[0x7f007d9213fa] [ubuntu:10089] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30472)[0x7f007d921472] [ubuntu:10089] [ 5] ./mpap(_ZN8TreeNodeILi3EE21calcSubdivisionMatrixEv+0xa02)[0x556be6e15732] [ubuntu:10089] [ 6] ./mpap(_ZN12HBSplineBase16prepareInputDataEv+0x88a)[0x556be6d58e4a] [ubuntu:10089] [ 7] ./mpap(_ZN14HBSplineCutFEM16prepareInputDataEv+0x24)[0x556be6d6fc04] [ubuntu:10089] [ 8] ./mpap(_ZN6Domain8readFileERSt14basic_ifstreamIcSt11char_traitsIcEE+0x85)[0x556be6e57ab5] [ubuntu:10089] [ 9] ./mpap(_Z11prgReadFilev+0x654)[0x556be6ea28d4] [ubuntu:10089] [10] ./mpap(main+0x1be)[0x556be6d1599e] [ubuntu:10089] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f007d912c87] [ubuntu:10089] [12] ./mpap(_start+0x2a)[0x556be6d2110a] [ubuntu:10089] End of error message Aborted (core dumped)

[Skygogogogo]

I can't find the root of above problem

[chennachaos]

Hi, Thank you for your interest in my code! Could you please tell me some details about you?

To help you with the issue, please provide more details. Which example you are running and how you are running it?

[Skygogogogo]

Thank you very much.The example in your code all can't run. I have successfully made the target mpap in Ubuntu18. When I run IbeamVertical example. ./mpap ../projece/sampleinputs IbeamVertical. It will project this message :

sky@sky-System-Product-Name:~/Common/mpap/bin$ ./mpap ../project/sampleinputs/ IbeamVertical project directory : ../project/sampleinputs/
input file name : IbeamVertical
output file name : ObeamVertical
time plot file name : TbeamVertical
eps plot file name : PbeamVertical

loading HBSPLINECUTFEM 1 ...

nContX =     0 ...

nContY =     0 ...

nContZ =     0 ...

nElem_Constraint = 0 HBSplineBase::prepareInputData() .... STARTED ... ImmersedFlexibleSolid.... nNode and ndof 341 2 totalDOF = 660 totalDOF 660 Immersed solids preparation DONE ... HBSplineBase : Preparing element data ...... STARTED

mpap: /usr/include/eigen3/Eigen/src/Core/Block.h:122: Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = Eigen::Matrix<double, -1, -1>; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = false; Eigen::Index = long int]: Assertion `(i>=0) && ( ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i<xpr.rows()) ||((BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) && i<xpr.cols()))' failed. [sky-System-Product-Name:06921] Process received signal [sky-System-Product-Name:06921] Signal: Aborted (6) [sky-System-Product-Name:06921] Signal code: (-6) [sky-System-Product-Name:06921] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f275aa50980] [sky-System-Product-Name:06921] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f2754f0ee87] [sky-System-Product-Name:06921] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f2754f107f1] [sky-System-Product-Name:06921] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x303fa)[0x7f2754f003fa] [sky-System-Product-Name:06921] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30472)[0x7f2754f00472] [sky-System-Product-Name:06921] [ 5] ./mpap(_ZN8TreeNodeILi3EE21calcSubdivisionMatrixEv+0x838)[0x5578f3f4b998] [sky-System-Product-Name:06921] [ 6] ./mpap(_ZN12HBSplineBase16prepareInputDataEv+0x87a)[0x5578f3e9211a] [sky-System-Product-Name:06921] [ 7] ./mpap(_ZN14HBSplineCutFEM16prepareInputDataEv+0x24)[0x5578f3eaacc4] [sky-System-Product-Name:06921] [ 8] ./mpap(_ZN6Domain8readFileERSt14basic_ifstreamIcSt11char_traitsIcEE+0x85)[0x5578f3f8a2a5] [sky-System-Product-Name:06921] [ 9] ./mpap(_Z11prgReadFilev+0x654)[0x5578f3fd35a4] [sky-System-Product-Name:06921] [10] ./mpap(main+0x1be)[0x5578f3e544de] [sky-System-Product-Name:06921] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f2754ef1c87] [sky-System-Product-Name:06921] [12] ./mpap(_start+0x2a)[0x5578f3e5ca6a] [sky-System-Product-Name:06921] End of error message

mpirun -n 4 ./mpap ../project/sampleinputs IsquareFixed project directory : ../project/sampleinputs
input file name : IsquareFixed
output file name : OsquareFixed
time plot file name : TsquareFixed
eps plot file name : PsquareFixed

loading HBSPLINECUTFEM 1 ...

HBSplineBase::prepareInputData() .... STARTED ...

Rigid body 0 details

---

Mass matrix

    0.00000000      0.00000000      0.00000000
    0.00000000     20.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

Damping matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.05811950      0.00000000
    0.00000000      0.00000000      0.00000000

Stiffness matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      3.08425000      0.00000000
    0.00000000      0.00000000      0.00000000

totalDOF = 0

 Fixed in X-direction 
 Fixed in Y-direction 
 Fixed in Theta-direction 

Immersed solids preparation DONE ... HBSplineBase : Preparing element data ...... STARTED

mpap: /usr/include/eigen3/Eigen/src/Core/Block.h:122: Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = Eigen::Matrix<double, -1, -1>; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = false; Eigen::Index = long int]: Assertion (i>=0) && ( ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i<xpr.rows()) ||((BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) && i<xpr.cols()))' failed. [sky-System-Product-Name:05535] *** Process received signal *** [sky-System-Product-Name:05535] Signal: Aborted (6) [sky-System-Product-Name:05535] Signal code: (-6) mpap: /usr/include/eigen3/Eigen/src/Core/Block.h:122: Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = Eigen::Matrix<double, -1, -1>; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = false; Eigen::Index = long int]: Assertion(i>=0) && ( ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i<xpr.rows()) ||((BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) && i<xpr.cols()))' failed. [sky-System-Product-Name:05535] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f855ae34980] [sky-System-Product-Name:05535] [ 1] [sky-System-Product-Name:05534] Process received signal [sky-System-Product-Name:05534] Signal: Aborted (6) [sky-System-Product-Name:05534] Signal code: (-6) /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f85552f2e87] [sky-System-Product-Name:05535] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f85552f47f1] [sky-System-Product-Name:05535] [ 3] [sky-System-Product-Name:05534] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(/lib/x86_64-linux-gnu/libc.so.6(+0x303fa)[0x7f85552e43fa] [sky-System-Product-Name:05535] [ 4] +0x12980)[0x7f62295a2980] [sky-System-Product-Name:05534] [ 1] mpap: /usr/include/eigen3/Eigen/src/Core/Block.h:122: Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = Eigen::Matrix<double, -1, -1>; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = false; Eigen::Index = long int]: Assertion (i>=0) && ( ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i<xpr.rows()) ||((BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) && i<xpr.cols()))' failed. /lib/x86_64-linux-gnu/libc.so.6(+0x30472)[0x7f85552e4472] [sky-System-Product-Name:05535] [ 5] [sky-System-Product-Name:05536] *** Process received signal *** /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f6223a60e87] [sky-System-Product-Name:05534] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[sky-System-Product-Name:05536] Signal: Aborted (6) [sky-System-Product-Name:05536] Signal code: (-6) ./mpap(_ZN8TreeNodeILi3EE21calcSubdivisionMatrixEv+0x838)[0x560edc991998] [sky-System-Product-Name:05535] [ 6] [0x7f6223a627f1] [sky-System-Product-Name:05534] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x303fa)[0x7f6223a523fa] [sky-System-Product-Name:05534] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30472)[0x7f6223a52472] [sky-System-Product-Name:05534] [ 5] [sky-System-Product-Name:05536] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f91c3364980] [sky-System-Product-Name:05536] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f91bd822e87] [sky-System-Product-Name:05536] [ 2] ./mpap(_ZN12HBSplineBase16prepareInputDataEv+0x87a)[0x560edc8d811a] [sky-System-Product-Name:05535] [ 7] ./mpap(_ZN14HBSplineCutFEM16prepareInputDataEv+0x24)[0x560edc8f0cc4] [sky-System-Product-Name:05535] [ 8] ./mpap(_ZN8TreeNodeILi3EE21calcSubdivisionMatrixEv+0x838)[0x560690b83998] [sky-System-Product-Name:05534] [ 6] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f91bd8247f1] [sky-System-Product-Name:05536] [ 3] ./mpap(_ZN12HBSplineBase16prepareInputDataEv+0x87a)[0x560690aca11a] [sky-System-Product-Name:05534] [ 7] ./mpap(_ZN6Domain8readFileERSt14basic_ifstreamIcSt11char_traitsIcEE+0x85)[0x560edc9d02a5] ./mpap(_ZN14HBSplineCutFEM16prepareInputDataEv+0x24)[0x560690ae2cc4] [sky-System-Product-Name:05534] /lib/x86_64-linux-gnu/libc.so.6(+0x303fa)[0x7f91bd8143fa] [sky-System-Product-Name:05536] [ 4] [sky-System-Product-Name:05535] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x30472)[0x7f91bd814472] [sky-System-Product-Name:05536] [ 5] [ 8] ./mpap(_Z11prgReadFilev+0x654)[0x560edca195a4] [sky-System-Product-Name:05535] [10] ./mpap(_ZN6Domain8readFileERSt14basic_ifstreamIcSt11char_traitsIcEE+0x85)[0x560690bc22a5] [sky-System-Product-Name:05534] [ 9] ./mpap(main+0x1be)[0x560edc89a4de] [sky-System-Product-Name:05535] [11] ./mpap(_ZN8TreeNodeILi3EE21calcSubdivisionMatrixEv+0x838)[0x55c9d5bc2998] [sky-System-Product-Name:05536] [ 6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)./mpap(_Z11prgReadFilev+0x654)[0x560690c0b5a4] [sky-System-Product-Name:05534] [10] [0x7f85552d5c87] [sky-System-Product-Name:05535] [12] ./mpap(_ZN12HBSplineBase16prepareInputDataEv+0x87a)[0x55c9d5b0911a] [sky-System-Product-Name:05536] [ 7] ./mpap(main+0x1be)[0x560690a8c4de] [sky-System-Product-Name:05534] [11] ./mpap(_start+0x2a)[0x560edc8a2a6a] mpap: /usr/include/eigen3/Eigen/src/Core/Block.h:122: Eigen::Block<XprType, BlockRows, BlockCols, InnerPanel>::Block(XprType&, Eigen::Index) [with XprType = Eigen::Matrix<double, -1, -1>; int BlockRows = 1; int BlockCols = -1; bool InnerPanel = false; Eigen::Index = long int]: Assertion(i>=0) && ( ((BlockRows==1) && (BlockCols==XprType::ColsAtCompileTime) && i<xpr.rows()) ||((BlockRows==XprType::RowsAtCompileTime) && (BlockCols==1) && i<xpr.cols()))' failed. /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xe7)[0x7f6223a43c87[sky-System-Product-Name:05537] Process received signal [sky-System-Product-Name:05535] End of error message ./mpap(_ZN14HBSplineCutFEM16prepareInputDataEv+0x24)[0x55c9d5b21cc4] [sky-System-Product-Name:05536] ] [sky-System-Product-Name:05534] [12] [sky-System-Product-Name:05537] Signal: Aborted (6) [sky-System-Product-Name:05537] Signal code: (-6) [ 8] ./mpap(_start+0x2a)[0x560690a94a6a] [sky-System-Product-Name:05534] End of error message [sky-System-Product-Name:05537] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(./mpap(_ZN6Domain8readFileERSt14basic_ifstreamIcSt11char_traitsIcEE+0x85)[0x55c9d5c012a5] [sky-System-Product-Name:05536] +0x12980)[0x7fd0ae012980] [sky-System-Product-Name:05537] [ 1] [ 9] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7fd0a84d0e87] [sky-System-Product-Name:05537] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7fd0a84d27f1] [sky-System-Product-Name:05537] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x303fa./mpap(_Z11prgReadFilev+0x654)[0x55c9d5c4a5a4] [sky-System-Product-Name:05536] [10] )[0x7fd0a84c23fa] [sky-System-Product-Name:05537] [ 4] ./mpap(main+0x1be)[0x55c9d5acb4de] [sky-System-Product-Name:05536] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x30472)[0x7fd0a84c2472] [sky-System-Product-Name:05537] [ 5] /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0xe7)[0x7f91bd805c87] [sky-System-Product-Name:05536] [12] ./mpap(_ZN8TreeNodeILi3EE21calcSubdivisionMatrixEv+0x838)[0x55bd5160f998] [sky-System-Product-Name:05537] [ 6] ./mpap(_start+0x2a)[0x55c9d5ad3a6a] [sky-System-Product-Name:05536] End of error message ./mpap(_ZN12HBSplineBase16prepareInputDataEv+0x87a)[0x55bd5155611a] [sky-System-Product-Name:05537] [ 7] ./mpap(_ZN14HBSplineCutFEM16prepareInputDataEv+0x24)[0x55bd5156ecc4] [sky-System-Product-Name:05537] [ 8] ./mpap(_ZN6Domain8readFileERSt14basic_ifstreamIcSt11char_traitsIcEE+0x85)[0x55bd5164e2a5] [sky-System-Product-Name:05537] [ 9] ./mpap(_Z11prgReadFilev+0x654)[0x55bd516975a4] [sky-System-Product-Name:05537] [10] ./mpap(main+0x1be)[0x55bd515184de] [sky-System-Product-Name:05537] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fd0a84b3c87] [sky-System-Product-Name:05537] [12] ./mpap(_start+0x2a)[0x55bd51520a6a] [sky-System-Product-Name:05537] End of error message

mpirun noticed that process rank 2 with PID 0 on node sky-System-Product-Name exited on signal 6 (Aborted).

when run Itest2bodies they will project message:

sky@sky-System-Product-Name:~/Common/mpap/bin$ ./mpap ../project/sampleinputs/ Itest2bodies project directory : ../project/sampleinputs/
input file name : Itest2bodies
output file name : Otest2bodies
time plot file name : Ttest2bodies
eps plot file name : Ptest2bodies

loading HBSPLINECUTFEM 1 ...

HBSplineBase::prepareInputData() .... STARTED ...

Rigid body 0 details

---

Mass matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

Damping matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

Stiffness matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

totalDOF = 0

 Fixed in X-direction 
 Fixed in Y-direction 
 Fixed in Theta-direction 

Rigid body 1 details

---

Mass matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

Damping matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

Stiffness matrix

    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000
    0.00000000      0.00000000      0.00000000

totalDOF = 0

 Fixed in X-direction 
 Fixed in Y-direction 
 Fixed in Theta-direction 

Immersed solids preparation DONE ... HBSplineBase : Preparing element data ...... STARTED

Number of basis functions in the background grid  =   1364

 HBSplineBase::prepareInputData()  .... FINISHED ...

 HBSplineCutFEM::prepareInputData()  .... FINISHED ...

loading TIME_FUNCTIONS ...

loading RUN_CONTROL ...

preparing interactions for HBSPLINECUTFEM 1 ...

The file Itest2bodies has been read successfully.

preparing cut elements TreeNode<3>::prepareCutCell() ... Subtriangulation is not implemented for 3D problems ... Error in prepareCutCell() for TreeNode<>::prepareCutCell() 0

[Skygogogogo]

[Skygogogogo]

[Skygogogogo]

[Skygogogogo]

This is my CmakeLists: cmake_minimum_required(VERSION 2.6) project(igampap)

enable_language(CXX Fortran)

##################################

project directories

##################################

PROJECT_BINARY_DIR

PROJECT_SOURCE_DIR

##################################

compiler options

##################################

C++ compiler

set(CMAKE_CXX_COMPILER "/usr/bin/gcc")

-DPARDISO_SOLVER

set(COPT "-std=c++14 -O3 -D BIT64 -Wno-uninitialized -Wno-sign-compare -Wno-write-strings -Wno-deprecated -Wno-unused -Wno-format -Wno-narrowing -Wno-ignored-attributes -Wno-reorder -Wreturn-type -D_DOMAIN3D -fopenmp -fpermissive -frounding-math")

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COPT}")

##################################

include directories

################################## include_directories( src/HBsplines src/lib src/myGeom src/mySolvers src/standardFEM src/utilities /usr/include/eigen3 /usr/include/eigen3/unsupported /usr/include/vtk-7.1 /usr/lib/x86_64-linux-gnu/openmpi/include /usr/petsc/arch-linux-c-debug/include /usr/petsc/include /usr/include/

/usr/include/boost

)

##################################

lib directories

################################## link_directories( /usr/lib/gcc/x86_64-linux-gnu/7 /usr/lib/x86_64-linux-gnu /usr/petsc/arch-linux-c-debug/lib /usr/lib /home/sky/Common/mpap/lib
/usr/lib/x86_64-linux-gnu
/usr/x86_64-linux-gnu/lib )

##################################

source files

##################################

file(GLOB sources1 src//h) file(GLOB sources2 src//cpp) file(GLOB sources3 src//for)

################################## ##################################

add_executable(mpap src/program/main.cpp ${sources1} ${sources2} ${sources3})

pardiso600-GNU720-X86-64

target_link_libraries(mpap stdc++ gmp mpfr stdc++ gfortran gomp pthread m blas lapack metis parmetis petsc mpi mpi_cxx superlu CGAL CGAL_Core CGAL_ImageIO vtkCommonCore-7.1 vtkIOCore-7.1 vtkIOGeometry-7.1 vtkIOXML-7.1 vtkIOExport-7.1 vtkFiltersCore-7.1 vtkFiltersGeneral-7.1 vtkFiltersModeling-7.1 vtkFiltersSources-7.1 vtkCommonExecutionModel-7.1 vtkCommonDataModel-7.1 vtkIOParallel-7.1 vtkIOParallelXML-7.1)

install(TARGETS mpap RUNTIME DESTINATION /home/sky/Common/mpap/bin)

[Skygogogogo]

I can't find where is the root of above problems.

[Skygogogogo]

I try to change the versions of libraries, but it has no effect, shows same problem.

[chennachaos]

Thank you for providing the details!

The issue is in the CMake file. The default option at the moment is for 3D problems. For the 2D problem, -D_DOMAIN3D needs to be changed to -D_DOMAIN2D. Make this change in the CMake file and recompile from scratch. After successful compilation and building of the executable, you should be able to run the 2D examples.