Segmentation violation when compiling stand alone

youngrootuser · March 24, 2020, 1:48pm

I try to compile a standalone with a GUI using gcc in the codeblocks IDE. When running the code with root using root complex_testgui.cpp, everything works without an issue. Also compilation works without any problems. But when I try to run the executable, I get the error:

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007fb8c34a5687 in __GI___waitpid (pid=16257, stat_loc=stat_loc
entry=0x7ffca816c7a8, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007fb8c3410067 in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149
#2  0x00007fb8c43e7ef3 in TUnixSystem::StackTrace() () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#3  0x00007fb8c43ea8e4 in TUnixSystem::DispatchSignals(ESignals) () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#4  <signal handler called>
#5  0x00007fb8bcf84783 in TClingCallFunc::SetArg(long) () from /home/timo/root-6.20.00/mybuild/lib/libCling.so
#6  0x00007fb8c428b60f in TApplication::LoadGraphicsLibs() () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#7  0x00007fb8c428a9fc in TApplication::InitializeGraphics() () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#8  0x00007fb8c428fd93 in TApplication::TApplication(char const*, int*, char**, void*, int) () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#9  0x000055a318a113e8 in main (argc=1, argv=0x7ffca816f5b8) at /home/timo/Schreibtisch/tiffanalysis/Tiff_analysis/complex_testgui.cpp:1022
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum http://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at http://root.cern.ch/bugs Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x00007fb8bcf84783 in TClingCallFunc::SetArg(long) () from /home/timo/root-6.20.00/mybuild/lib/libCling.so
#6  0x00007fb8c428b60f in TApplication::LoadGraphicsLibs() () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#7  0x00007fb8c428a9fc in TApplication::InitializeGraphics() () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#8  0x00007fb8c428fd93 in TApplication::TApplication(char const*, int*, char**, void*, int) () from /home/timo/root-6.20.00/mybuild/lib/libCore.so
#9  0x000055a318a113e8 in main (argc=1, argv=0x7ffca816f5b8) at /home/timo/Schreibtisch/tiffanalysis/Tiff_analysis/complex_testgui.cpp:1022
===========================================================

The line /tiffanalysis/Tiff_analysis/complex_testgui.cpp:1022 is simply

TApplication theApp("App", &argc, argv);

I did build the root version 6.20/00 myself. Probably something went wrong there. When I navigate to the directory /home/timo/root-6.20.00/mybuild/ and type cmake …, I get the following output with a lot of warnings:

-- ROOT default compression algorithm: zlib
-- Found GCC. Major version 7, minor version 5
-- Found a 64bit system
-- Found GNU compiler collection
-- ROOT Platform: linux
-- ROOT Architecture: linuxx8664gcc
-- Build Type: Release (flags = '-O3 -DNDEBUG')
-- Compiler Flags: -O3 -DNDEBUG  -std=c++11 -Wno-implicit-fallthrough -Wno-noexcept-type -pipe  -Wshadow -Wall -W -Woverloaded-virtual -fsigned-char -pthread
-- Looking for ZLib
-- Looking for Freetype
-- Looking for PCRE
-- Building LZMA version 5.2.4 included in ROOT itself
-- Looking for X11
-- Could NOT find GIF (missing: GIF_LIBRARY GIF_INCLUDE_DIR) 
-- Building AfterImage library included in ROOT itself
-- Looking for GSL
-- Downloading and building GSL version 2.5
-- Looking for python
-- Looking for OpenGL
-- Looking for GLEW
-- Looking for LibXml2
-- Looking for MySQL
-- Looking for FFTW3
-- Looking for CFITSIO
-- Looking for TBB
-- Looking for VDT
-- Looking for BLAS for optional parts of TMVA
-- A library with BLAS API not found. Please specify library location.
-- Using GSL CBLAS for optional parts of TMVA
-- Building LLVM in 'Release' mode.
-- Native target architecture is X86
-- Threads disabled.
-- Doxygen disabled.
-- Go bindings disabled.
-- LLVM host triple: x86_64-unknown-linux-gnu
-- LLVM default target triple: x86_64-unknown-linux-gnu
-- Building with -fPIC
-- Constructing LLVMBuild project information
-- Linker detection: GNU ld
-- SysLibs: rt;dl;tinfo;-lpthread;/usr/lib/x86_64-linux-gnu/libz.so
-- Targeting X86
-- Targeting NVPTX
-- Clang version: 5.0.0
-- Cling version (from VERSION file): ROOT_0.7~dev
-- Cling will look for C++ headers in '/usr/include/c++/7:/usr/include/x86_64-linux-gnu/c++/7:/usr/include/c++/7/backward' at runtime.
-- And then fallback to: 'x86_64-linux-gnu-g++-7'
-- Performing Test found_stdstringview
-- Performing Test found_stdstringview - Failed
-- Performing Test found_stdexpstringview
-- Performing Test found_stdexpstringview - Failed
-- Performing Test found_stdapply
-- Performing Test found_stdapply - Failed
-- Performing Test found_stdinvoke
-- Performing Test found_stdinvoke - Failed
-- Performing Test found_stdindexsequence
-- Performing Test found_stdindexsequence - Failed
-- Enabled support for:  asimage builtin_afterimage builtin_clang builtin_gl2ps builtin_gsl builtin_llvm builtin_lz4 builtin_lzma builtin_xxhash builtin_zstd clad dataframe exceptions fftw3 fitsio gdml gsl_shared http imt mathmore mlp minuit2 mysql opengl python roofit runtime_cxxmodules shared ssl tmva tmva-cpu spectrum vdt x11 xml
-- Configuring done
CMake Error in math/vecops/CMakeLists.txt:
  Target "ROOTVecOps" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/timo/root-6.20.00/mybuild/include"

  which is prefixed in the build directory.


CMake Error in math/vecops/CMakeLists.txt:
  Target "ROOTVecOps" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/timo/root-6.20.00/mybuild/include"

  which is prefixed in the build directory.Target "ROOTVecOps"
  INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/timo/root-6.20.00/mybuild/include"

  which is prefixed in the source directory.


CMake Error in tmva/tmva/CMakeLists.txt:
  Target "TMVA" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/timo/root-6.20.00/mybuild/include"

  which is prefixed in the build directory.


CMake Error in tmva/tmva/CMakeLists.txt:
  Target "TMVA" INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/timo/root-6.20.00/mybuild/include"

  which is prefixed in the build directory.Target "TMVA"
  INTERFACE_INCLUDE_DIRECTORIES property contains path:

    "/home/timo/root-6.20.00/mybuild/include"

  which is prefixed in the source directory.


CMake Warning at cmake/modules/RootMacros.cmake:760 (add_library):
  Cannot generate a safe runtime search path for target Genetic because there
  is a cycle in the constraint graph:

    dir 0 is [/home/timo/root-6.20.00/mybuild/lib]
      dir 1 must precede it due to runtime library [libvdt.so]
    dir 1 is [/usr/local/lib]
      dir 0 must precede it due to runtime library [libTMVA.so]

  Some of these libraries may not be found correctly.
Call Stack (most recent call first):
  cmake/modules/RootMacros.cmake:1145 (ROOT_LINKER_LIBRARY)
  math/genetic/CMakeLists.txt:12 (ROOT_STANDARD_LIBRARY_PACKAGE)


CMake Warning at cmake/modules/RootMacros.cmake:760 (add_library):
  Cannot generate a safe runtime search path for target ROOTVecOps because
  there is a cycle in the constraint graph:

    dir 0 is [/home/timo/root-6.20.00/mybuild/lib]
      dir 1 must precede it due to runtime library [libvdt.so]
    dir 1 is [/usr/local/lib]
      dir 0 must precede it due to runtime library [libCore.so]

  Some of these libraries may not be found correctly.
Call Stack (most recent call first):
  cmake/modules/RootMacros.cmake:1145 (ROOT_LINKER_LIBRARY)
  math/vecops/CMakeLists.txt:16 (ROOT_STANDARD_LIBRARY_PACKAGE)


CMake Warning at cmake/modules/RootMacros.cmake:760 (add_library):
  Cannot generate a safe runtime search path for target ROOTDataFrame because
  there is a cycle in the constraint graph:

    dir 0 is [/home/timo/root-6.20.00/mybuild/lib]
      dir 1 must precede it due to runtime library [libvdt.so]
    dir 1 is [/usr/local/lib]
      dir 0 must precede it due to runtime library [libTreePlayer.so]

  Some of these libraries may not be found correctly.
Call Stack (most recent call first):
  cmake/modules/RootMacros.cmake:1145 (ROOT_LINKER_LIBRARY)
  tree/dataframe/CMakeLists.txt:30 (ROOT_STANDARD_LIBRARY_PACKAGE)


CMake Warning at cmake/modules/RootMacros.cmake:760 (add_library):
  Cannot generate a safe runtime search path for target PyROOT because there
  is a cycle in the constraint graph:

    dir 0 is [/home/timo/root-6.20.00/mybuild/lib]
      dir 1 must precede it due to runtime library [libvdt.so]
    dir 1 is [/usr/local/lib]
      dir 0 must precede it due to runtime library [libMathCore.so]

  Some of these libraries may not be found correctly.
Call Stack (most recent call first):
  cmake/modules/RootMacros.cmake:1145 (ROOT_LINKER_LIBRARY)
  bindings/pyroot/CMakeLists.txt:11 (ROOT_STANDARD_LIBRARY_PACKAGE)


CMake Warning at cmake/modules/RootMacros.cmake:760 (add_library):
  Cannot generate a safe runtime search path for target TMVA because there is
  a cycle in the constraint graph:

    dir 0 is [/home/timo/root-6.20.00/mybuild/lib]
      dir 1 must precede it due to runtime library [libvdt.so]
    dir 1 is [/usr/local/lib]
      dir 0 must precede it due to runtime library [libMinuit.so]

  Some of these libraries may not be found correctly.
Call Stack (most recent call first):
  cmake/modules/RootMacros.cmake:1145 (ROOT_LINKER_LIBRARY)
  tmva/tmva/CMakeLists.txt:50 (ROOT_STANDARD_LIBRARY_PACKAGE)


CMake Warning at cmake/modules/RootMacros.cmake:760 (add_library):
  Cannot generate a safe runtime search path for target TMVAGui because there
  is a cycle in the constraint graph:

    dir 0 is [/home/timo/root-6.20.00/mybuild/lib]
      dir 1 must precede it due to runtime library [libvdt.so]
    dir 1 is [/usr/local/lib]
      dir 0 must precede it due to runtime library [libTreeViewer.so]

  Some of these libraries may not be found correctly.
Call Stack (most recent call first):
  cmake/modules/RootMacros.cmake:1145 (ROOT_LINKER_LIBRARY)
  tmva/tmvagui/CMakeLists.txt:12 (ROOT_STANDARD_LIBRARY_PACKAGE)


-- Generating done
-- Build files have been written to: /home/timo/root-6.20.00/mybuild

Any ideas, what the problem is?

_ROOT Version: 6.20/00
_Platform: ubuntu18.04.4
_Compiler:linuxx8664gcc

bellenot · March 24, 2020, 2:00pm

How did you compile your stand-alone app? Did you use root-config --cflags as compiler flags and root-config --glibs for the libraries? Did you try to run it with gdb?

youngrootuser · March 24, 2020, 4:58pm

Thanks a lot bellenot!
I had added all libraries in my root build directory /home/timo/root-6.20.00/mybuild/lib to the list of linked libraries. I now replaced this by the output of root-config --glibs,
and added the compiler options from root-config --cflags . This solved the first problem, thank you very much.
Now, only the problem with the not working buttons remains. I still get the output, that the slots would not exist even though I created the class MyMainFrame in a separate MyMainFrame.h as follows:

#include "Riostream.h"
#include "TH1.h"
#include "TH2.h"
#include "TCanvas.h"
#include <TApplication.h>
#include "TGClient.h"
#include "TGraph.h"
#include "TGraphErrors.h"
#include "TF1.h"
#include "TCollection.h"
#include "TObjArray.h"
class TGTextEntry;
class TGTextButton;
class TGListBox;
class TGNumberEntry;
class TCanvas;
class TH2I;
class TH2D;
class TF1;
class TGraph;
class TGraphErrors;
class TObjArray;

class MyMainFrame : public TGMainFrame {
   RQ_OBJECT("MyMainFrame")
private:
    TGMainFrame *fMainFrame;
//   TGCompositeFrame *fCompositeFrame;
//   TGTextEntry *fTextEntryCalibrationFilm;
    TGTextEntry *fTextEntryCalibrationFilm;
    TGTextButton *fTextButtonQUIT;
    TGTextButton *fTextButtonSelectBackground;
    TGTextButton *fTextButtonSelectRegion;
    TGTextButton *fTextButtonCorrectPixels;
    TGTextButton *fTextButtonSaveCalib;
    TGTextButton *fTextButtonFitHistogram;
    TGTextButton *fTextButtonLoadFilm;
    TGTextButton *fTextButtonFitCalibrationCurveGray;
    TGTextButton *fTextButtonFitCalibrationCurveNetOD;
    TGListBox *fListBoxFluences;
    TGNumberEntry *fTGNumberEntryRebin;
    TGTextButton *fTextButtonRebin;
    TCanvas *coriginal;
    TCanvas *chistogram;
    TCanvas *cCalibGrayvalues;
    TCanvas *cCalibNetOD;
    TH2I *horiginal;
    TH2D *hcorrected;
    TH1I *hhistogram;
    TH1D *hpixelcorrection;
    TH1D *hbackgroundhist;
    Double_t *unidentifiedgrayvalues;
    TGraph *gidentifiedgrayvalues;
    TGraph *gidentifiednetODs;
    TGraphErrors *gCalibrationPointsGray;
    TGraphErrors *gCalibrationPointsNetOD;
    TGraphErrors *gCalibrationUncertainties;
    TF1 *CalibrationCurveNetOD;
    TF1 *CalibrationCurveGray;
    TObjArray *grayvaluecollection = new TObjArray(100);
    TObjArray *netODcollection= new TObjArray(100);
    double gray_empty=58240;
    double gray_empty_error=0;
    int backgroundlines=0;


public:
    MyMainFrame(const TGWindow *p,UInt_t w,UInt_t h);
    //MyMainFrame();
    virtual ~MyMainFrame();
    int LoadFilm();
    int SelectRange();
    int FitHistogram();
    int FitCalibrationCurveNetOD();
    int FitCalibrationCurveGrayValues();
    int SelectBackground();
    int CorrectPixels();
    virtual void CloseWindow();
    int Rebin();

};

Any ideas what the problem is? As I said, it works inside ROOT

bellenot · March 24, 2020, 5:03pm

You have to generate a dictionary for your MyMainFrame class with rootcling, and add the generated source file to your project
And see also tips for efficient and successful posting

youngrootuser · March 24, 2020, 6:57pm

Thanks for your help. This did solve my problem. And sorry for coming up with a second issue, that was not linked to the title problem anymore.

bellenot · March 24, 2020, 8:17pm

You’re welcome. And no problem, don’t worry

system · April 7, 2020, 8:17pm

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