bugGNU Octave - Bugs: bug #59476, Octave crash built with...

 
 

bug #59476: Octave crash built with inconsistent set of self-compiled libraries

Submitter:  None
Submitted:  Tue 17 Nov 2020 05:46:14 PM UTC
   
 
Category:  Octave Function Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Segfault, Bus Error, etc.
Status:  Invalid / Not an Octave Bug Assigned to:  None
Originator Name:  David Laxer Originator Email:  -email is unavailable-
Open/Closed:  * Closed Release:  * dev
Operating System:  * GNU/Linux Fixed Release:  None
Planned Release:  None
* Mandatory Fields

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Wed 18 Nov 2020 12:46:14 AM UTC, comment #8: 

New title for the files.

Please have a look at bug #59475 to resolve your issues.

Kai Torben Ohlhus <siko1056>
Group Member
Tue 17 Nov 2020 09:03:40 PM UTC, comment #7: 

Re comment #5: If OpenBLAS is compiled with 64bit indexing and all other numeric libraries are not, you'd have to expect crashes...

Closing as invalid.

Markus Mützel <mmuetzel>
Group administrator
Tue 17 Nov 2020 08:54:15 PM UTC, comment #6: 

./../configure --prefix=$HOME/my_octave CPPFLAGS="-I/usr/include/suitesparse" --with-blas="-lopenblas" -with-lapack=-llapack

david laxer <davidlaxer>
Tue 17 Nov 2020 08:41:00 PM UTC, comment #5: 

I initially compiled OpenBlas with

make BINARY=64

Octave crashed with 64 bit indexes in splneplot.

So, I reverted to 32bit indexes.
But, I never recompiled OpenBlas.
Could this be the source of the segmentation violation?

david laxer <davidlaxer>
Tue 17 Nov 2020 08:16:34 PM UTC, comment #4: 

FYI

This is output of gnuplot "dumb" terminal. One can reproduce it
by setting "graphics_toolkit gnuplot" and GNUTERM=dumb

Dmitri.
--

Dmitri A. Sergatskov <dasergatskov>
Tue 17 Nov 2020 08:15:25 PM UTC, comment #3: 

Yes, it appears to be ascii art.  In octave GUI  it looks like a normal 3d plot.
I can send you a screen snapshot if you like.

david laxer <davidlaxer>
Tue 17 Nov 2020 08:11:40 PM UTC, comment #2: 

Crashing in griddata is usually caused by a mismatch between Octave, BLAS, and possibly SuiteSparse libraries.  It is probably necessary to work out the issue in bug #59475 before this one.

Rik <rik5>
Group administrator
Tue 17 Nov 2020 08:05:15 PM UTC, comment #1: 

Could you include your test/fntests.log file?

Your griddata test code works properly on my install (Octave 7.0.0) except it doesn't print anything like that blob of random symbols in your output? Is that ASCII art for the plot you created?

Anonymous
Tue 17 Nov 2020 05:46:14 PM UTC, original submission:  

I built octave 7.0.0 from source.
$ make check is crashing in grid data.

e 1: 1762676 Segmentation fault      (core dumped) /bin/bash ../run-octave --no-init-file --silent --no-history -p /home/ubuntu/octave/.build/test/mex /home/ubuntu/octave/.build/./../test/fntests.m /home/ubuntu/octave/.build/./../test

However, a simple test of griddata doesn't crash.
e.g.

octave:1> rand ("state", 1);
octave:2> x = 2*rand (1000,1) - 1;
octave:3> y = 2*rand (size (x)) - 1;
octave:4> z = sin (2*(x.^2+y.^2));
octave:5> [xx,yy] = meshgrid (linspace (-1,1,32));
octave:6> zz = griddata (x, y, z, xx, yy);
octave:7> mesh (xx, yy, zz);
                                                                               
                                                                               
                                                                               
                                                                               
                                       $$$$$$$$$                               
                              $$$$$$$$$***$$$$**$$$$$$$$                       
                  $$$$$$$$$$$$**************************$$$$$$$$               
    1     +-+$$$$$$$$$**************************************$$$$$$$$$          
  0.8     +-+$$$$$$$*********************************$$$$******  $$$$          
  0.6     +-+$$$$$$$$$$$$$$$$$*********************$$$$$$$$$$*$$$$$$$          
  0.4     +-+$$$$$$$$$$$$$$$$$$$$$***********$$$$$$$$$$$$ $$$$$$$$$$$          
    0     +-+$$$$$$$$$$$    $$$$$$$ * $$$$*$$$$$$$$$$$$$$$$$$$$$$$$          
 -0.2     +-+    $$$$$$$$$$$$$$$$$$ * $$$$$$$$$$$$$$$$$$$$$$$$$$$$$          
 -0.4  +--+-+$$$$$+$$$$$$$$$$$$$$$$$$* $$$$$$$$$  $$$$$$$$$$$$$$$$$$$-         
        0.5  +-- $$$$$--+$$$$$   $$$$ $$$$$$$$$$$$   $$$$$$$$$$0.5    + 1      
                0  +--.5 +----+$$$$$$*    $$$$$$$$$$$-+0                       
                            -1  +----+$$$$$    -0.5  
./../configure --prefix=$HOME/my_octave CPPFLAGS="-I/usr/include/suitesparse" --with-blas="-lopenblas" -with-lapack=-llapack

...

Octave is now configured for x86_64-pc-linux-gnu

  Source directory:              ./..
  Installation prefix:           /home/ubuntu/my_octave
  C compiler:                    gcc  -pthread -fopenmp  -Wall -W -Wshadow -Wformat -Wpointer-arith -Wmissing-prototypes -Wstrict-prototypes -Wwrite-strings -Wcast-align -Wcast-qual -g -O2
  C++ compiler:                  g++  -pthread -fopenmp  -Wall -W -Wshadow -Woverloaded-virtual -Wold-style-cast -Wformat -Wpointer-arith -Wwrite-strings -Wcast-align -Wcast-qual -g -O2
  Fortran compiler:              gfortran -g -O2 -std=legacy
  Fortran libraries:              -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath
  Lex libraries:                
  LIBS:                          -lutil  -lm
  LDFLAGS:                      
  Extra LDFLAGS:                

  AMD CPPFLAGS:                 
  AMD LDFLAGS:                  
  AMD libraries:                 -lamd
  ARPACK CPPFLAGS:               -I/usr/include/arpack
  ARPACK LDFLAGS:               
  ARPACK libraries:              -larpack
  BLAS libraries:                -lopenblas
  BZ2 CPPFLAGS:                 
  BZ2 LDFLAGS:                  
  BZ2 libraries:                 -lbz2
  CAMD CPPFLAGS:                
  CAMD LDFLAGS:                 
  CAMD libraries:                -lcamd
  CARBON libraries:             
  CCOLAMD CPPFLAGS:             
  CCOLAMD LDFLAGS:              
  CCOLAMD libraries:             -lccolamd
  CHOLMOD CPPFLAGS:             
  CHOLMOD LDFLAGS:              
  CHOLMOD libraries:             -lcholmod
  COLAMD CPPFLAGS:              
  COLAMD LDFLAGS:               
  COLAMD libraries:              -lcolamd
  CURL CPPFLAGS:                
  CURL LDFLAGS:                 
  CURL libraries:                -lcurl
  CXSPARSE CPPFLAGS:            
  CXSPARSE LDFLAGS:             
  CXSPARSE libraries:            -lcxsparse
  DL libraries:                  -ldl
  FFTW3 CPPFLAGS:               
  FFTW3 LDFLAGS:                
  FFTW3 libraries:               -lfftw3_threads -lfftw3
  FFTW3F CPPFLAGS:              
  FFTW3F LDFLAGS:               
  FFTW3F libraries:              -lfftw3f_threads -lfftw3f
  FLTK CPPFLAGS:                 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/freetype2 -I/usr/include/libpng16
  FLTK LDFLAGS:                 
  FLTK libraries:                -lfltk_gl -lfltk -lX11
  fontconfig CPPFLAGS:           -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
  fontconfig libraries:          -lfontconfig -lfreetype
  FreeType2 CPPFLAGS:            -I/usr/include/freetype2 -I/usr/include/libpng16
  FreeType2 libraries:           -lfreetype
  GLPK CPPFLAGS:                
  GLPK LDFLAGS:                 
  GLPK libraries:                -lglpk
  HDF5 CPPFLAGS:                 -I/usr/include/hdf5/serial
  HDF5 LDFLAGS:                  -L/usr/lib/x86_64-linux-gnu/hdf5/serial
  HDF5 libraries:                -lhdf5
  Java home:                     /usr/lib/jvm/java-8-oracle
  Java JVM path:                 /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server
  Java CPPFLAGS:                 -I/usr/lib/jvm/java-8-oracle/include -I/usr/lib/jvm/java-8-oracle/include/linux
  Java libraries:               
  KLU CPPFLAGS:                 
  KLU LDFLAGS:                  
  KLU libraries:                 -lklu
  LAPACK libraries:              -llapack
  LLVM CPPFLAGS:                
  LLVM LDFLAGS:                 
  LLVM libraries:               
  Magick++ CPPFLAGS:             -I/usr/include/GraphicsMagick
  Magick++ LDFLAGS:             
  Magick++ libraries:            -lGraphicsMagick++ -lGraphicsMagick
  OpenGL libraries:              -lGL -lGLU
  PCRE CPPFLAGS:                
  PCRE LDFLAGS:                 
  PCRE libraries:                -lpcre
  PortAudio CPPFLAGS:           
  PortAudio LDFLAGS:            
  PortAudio libraries:           -lportaudio -lasound -lm -lpthread
  PTHREAD flags:                 -pthread
  PTHREAD libraries:            
  QHULL CPPFLAGS:               
  QHULL LDFLAGS:                
  QHULL libraries:               -lqhull
  QRUPDATE CPPFLAGS:            
  QRUPDATE LDFLAGS:             
  QRUPDATE libraries:            -lqrupdate
  Qt CPPFLAGS:                   -I/usr/include/x86_64-linux-gnu/qt5/QtNetwork -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtPrintSupport -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtHelp -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtWidgets -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtGui -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtSql -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtXml -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I/usr/include/x86_64-linux-gnu/qt5
  Qt LDFLAGS:                   
  Qt GUI libraries:              -lQt5Network -lQt5PrintSupport -lQt5Help -lQt5Widgets -lQt5Gui -lQt5Sql -lQt5Xml -lQt5Core -lqscintilla2_qt5
  Qt OpenGL libraries:           -lQt5OpenGL -lQt5Widgets -lQt5Gui -lQt5Core
  Qt moc:                        moc -qt5
  Qt uic:                        uic -qt5
  Qt rcc:                        rcc -qt5
  Qt lrelease:                   lrelease -qt5
  Qt qcollectiongenerator:       qcollectiongenerator -qt5
  Qt qhelpgenerator:             qhelpgenerator -qt5
  READLINE libraries:            -lreadline
  Sndfile CPPFLAGS:             
  Sndfile LDFLAGS:              
  Sndfile libraries:             -lsndfile
  SuiteSparse config libraries:  -lsuitesparseconfig
  SUNDIALS IDA CPPFLAGS:        
  SUNDIALS IDA LDFLAGS:         
  SUNDIALS IDA libraries:        -lsundials_ida
  SUNDIALS NVECTOR CPPFLAGS:    
  SUNDIALS NVECTOR LDFLAGS:     
  SUNDIALS NVECTOR libraries:    -lsundials_nvecserial
  SUNLINSOL KLU CPPFLAGS:       
  SUNLINSOL KLU LDFLAGS:        
  SUNLINSOL KLU libraries:       -lsundials_sunlinsolklu
  TERM libraries:                -lncurses
  UMFPACK CPPFLAGS:             
  UMFPACK LDFLAGS:              
  UMFPACK libraries:             -lumfpack
  X11 include flags:            
  X11 libraries:                 -lX11
  Z CPPFLAGS:                   
  Z LDFLAGS:                    
  Z libraries:                   -lz

  Default pager:                 less
  gnuplot:                       gnuplot

  Build Octave Qt GUI:                  yes (version: 5)
  JIT compiler for loops:               no
  Build Java interface:                 yes
  Build static libraries:               no
  Build shared libraries:               yes
  Dynamic Linking API:                  dlopen
  Include support for GNU readline:     yes
  Use push parser in command line REPL: yes
  64-bit array dims and indexing:       yes
  64-bit BLAS array dims and indexing:  no
  OpenMP SMP multithreading:            yes
  Truncate intermediate FP results:     yes
  Build cross tools:                    no
  Build docs:                           yes

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Attached Files
file #50289:  griddata.ofig added by davidlaxer (71KiB - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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    Follow 4 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2020-11-18 siko1056 Summarye 1: 1762676 Segmentation fault (core dumped) /bin/bash ../run-octave --no-init-file --silent --no-history -p /home Octave crash built with inconsistent set of self-compiled libraries
    2020-11-17 mmuetzel StatusNone Invalid / Not an Octave Bug
        Open/ClosedOpen Closed
    2020-11-17 davidlaxer Attached File- Added griddata.ofig, #50289

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