Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

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Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

sanja

Hi All,

I am experiencing the problem that I always get Segmentation fault (core dumped) and my program does not finish when running


    state = minimize_blockmodel_dl(g, overlap=True)


When overlap=False, there is no problem.

I have the 2.24 graph-tool version installed from Ubuntu repo. I tried this with both python2.7 and python3 -- in both cases, I get the segmentation fault error.

Also, this is not due to the size of my graph, I tried with a toy example with only 10 nodes, it still happens.

Any ideas what I could do are very much appreciated.

Thanks,
Sanja


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Re: Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

Tiago Peixoto
Administrator
On 30.10.2017 13:49, Sanja Šćepanović wrote:
> I have the 2.24 graph-tool version installed from Ubuntu repo. I tried this
> with both python2.7 and python3 -- in both cases, I get the segmentation
> fault error.

Could you please try with the newest version, 2.25?

If you encounter the same problem, please open an issue at the website:

   https://graph-tool.skewed.de/issues

When opening the issue, please provide a _minimal_ and _self-contained_
script that reproduces the problem.

Best,
Tiago

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Re: Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

sanja
Hi,

I am unable to install the version 2.25.

After configuring I receive a make error as below:

In file included from graph_motifs.cc:26:0:
../../../src/graph/graph_python_interface.hh: In constructor
‘graph_tool::CoroGenerator::CoroGenerator(Dispatch&)’:
../../../src/graph/graph_python_interface.hh:94:18: error: ‘fixedsize_stack’
is not a member of ‘graph_tool::coroutines’
                 (coroutines::fixedsize_stack(BOOST_COROUTINE_STACK_SIZE),


That I am unable to resolve, so unfortunately I cannot test this version.

Thanks,
Sanja



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Re: Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

Tiago Peixoto
Administrator
On 31.10.2017 18:22, sanja wrote:

> Hi,
>
> I am unable to install the version 2.25.
>
> After configuring I receive a make error as below:
>
> In file included from graph_motifs.cc:26:0:
> ../../../src/graph/graph_python_interface.hh: In constructor
> ‘graph_tool::CoroGenerator::CoroGenerator(Dispatch&)’:
> ../../../src/graph/graph_python_interface.hh:94:18: error: ‘fixedsize_stack’
> is not a member of ‘graph_tool::coroutines’
>                  (coroutines::fixedsize_stack(BOOST_COROUTINE_STACK_SIZE),
>
Please provide information regarding the operating system you are using, and
the boost version you have installed. Also, please include the entire output
of the configure and make commands (not only excerpts), as well as the
entire contents of the config.log file.

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Re: Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

Alexandre Bovet
Hi,

Sorry for hijacking this thread, but I have the same problem when trying to compile graph-tool under Linux Mint 18.1 Serena with python3.5. I don't use the graph-tool ubuntu package because I want to install it in a virtual env.

I have boost 1.58 installed with `sudo apt-get install libboost-all-dev'.

below are the entire outputs of configure and make. I also attached the config.log file.

$ ./configure --prefix=/home/abovet/graphtoolenv
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a pax tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gcc option to accept ISO C99... unsupported
checking for gcc option to accept ISO C89... (cached) none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking whether g++ supports C++14 features by default... no
checking whether g++ supports C++14 features with -std=gnu++14... yes
checking whether to enable debug info... no
checking whether to enable parallel algorithms with openmp... checking for OpenMP flag of C++ compiler... -fopenmp
checking whether to enable cairo drawing... yes
checking for Expat XML Parser headers in /usr/include... found
checking for Expat XML Parser libraries... found
checking for Expat XML Parser... yes
checking for a Python interpreter with version >= 2.7... python
checking for python... /home/abovet/graphtoolenv/bin/python
checking for python version... 3.5
checking for python platform... linux
checking for python script directory... ${prefix}/lib/python3.5/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python3.5/site-packages
checking for python3.5... (cached) /home/abovet/graphtoolenv/bin/python
checking for a version of Python >= '2.1.0'... yes
checking for a version of Python == '3.5.2'... yes
checking for the distutils Python package... yes
checking for Python include path... -I/usr/include/python3.5m
checking for Python library path... -L/usr/lib -lpython3.5m
checking for Python site-packages path... /home/abovet/graphtoolenv/lib/python3.5/site-packages
checking python extra libraries... -lpthread -ldl  -lutil -lm
checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
checking consistency of all components of python development environment... yes
checking for boostlib >= 1.55.0 (105500)... yes
checking whether the Boost::Python library is available... yes
checking whether boost_python is the correct library... no
checking whether boost_python-py27 is the correct library... no
checking whether boost_python-py27 is the correct library... (cached) no
checking whether boost_python-py27 is the correct library... (cached) no
checking whether boost_python-py35 is the correct library... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex... yes
checking whether the Boost::Context library is available... yes
checking for exit in -lboost_context... yes
checking whether the Boost::Coroutine library is available... yes
checking for exit in -lboost_coroutine... yes
checking whether the Boost::Graph library is available... yes
checking for exit in -lboost_graph... yes
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking for __gmpz_init in -lgmp... yes
checking for __gmpz_init in -lgmp... (cached) yes
checking whether CGAL is available in /usr... yes
checking whether to enable cgal debbuging with valgrind... no
checking python module: numpy... yes
checking for numpy/arrayobject.h... yes
checking for cairomm-1.0... yes
checking python module: cairo... yes
checking pycairo/py3cairo.h usability... yes
checking pycairo/py3cairo.h presence... yes
checking for pycairo/py3cairo.h... yes
checking whether to enable sparsehash... yes
checking for libsparsehash... no
not found by pkgconfig, trying default...
checking sparsehash/dense_hash_set usability... yes
checking sparsehash/dense_hash_set presence... yes
checking for sparsehash/dense_hash_set... yes
configure: pkgconfig directory is ${libdir}/pkgconfig
checking our pkgconfig libname... graph-tool-py3.5
checking our pkgconfig version... 2.25
checking our pkgconfig_libdir... ${libdir}/pkgconfig
expanded our pkgconfig_libdir... /home/abovet/graphtoolenv/lib/pkgconfig
checking our pkgconfig_libfile... graph-tool-py3.5.pc
checking our package / suffix... graph-tool /
checking our pkgconfig description... graph-tool Python library
checking our pkgconfig requires...
checking our pkgconfig ext libs... -L/usr/lib -lpython3.5m -lboost_python-py35
checking our pkgconfig cppflags... -I/home/abovet/graphtoolenv/lib/python3.5/site-packages/graph_tool/include -I/home/abovet/graphtoolenv/lib/python3.5/site-packages/graph_tool/include/boost-workaround -I/usr/include/python3.5m -pthread -I/usr/include -I/home/abovet/graphtoolenv/lib/python3.5/site-packages/numpy/core/include
checking our pkgconfig ldflags...
noninstalled pkgconfig -L /home/abovet/local/graph-tool-2.25/src/.libs
noninstalled pkgconfig -I /home/abovet/local/graph-tool-2.25/.
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/graph/Makefile
config.status: creating src/graph/centrality/Makefile
config.status: creating src/graph/clustering/Makefile
config.status: creating src/graph/correlations/Makefile
config.status: creating src/graph/draw/Makefile
config.status: creating src/graph/flow/Makefile
config.status: creating src/graph/generation/Makefile
config.status: creating src/graph/inference/Makefile
config.status: creating src/graph/layout/Makefile
config.status: creating src/graph/search/Makefile
config.status: creating src/graph/spectral/Makefile
config.status: creating src/graph/stats/Makefile
config.status: creating src/graph/topology/Makefile
config.status: creating src/graph/util/Makefile
config.status: creating src/graph_tool/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing graph-tool-py3.5.pc commands
config.status: creating graph-tool-py3.5.pc.in
config.status: creating graph-tool-py3.5.pc
config.status: creating graph-tool-py3.5-uninstalled.pc
config.status: creating graph-tool-py3.5-uninstalled.sh
================================================================================
                             CONFIGURATION SUMMARY                             
================================================================================
Using python version:   3.5.2
Python interpreter:     /home/abovet/graphtoolenv/bin/python
Installation path:      /home/abovet/graphtoolenv/lib/python3.5/site-packages/graph_tool

C++ compiler (CXX):     g++ -std=gnu++14
C++ compiler version:   5.4.0

Prefix:                 /home/abovet/graphtoolenv
Pkgconfigdir:           ${libdir}/pkgconfig

Python CPP flags:       -I/usr/include/python3.5m
Python LD flags:        -L/usr/lib -lpython3.5m
Boost CPP flags:        -pthread -I/usr/include
Boost LD flags:         -lboost_iostreams -lboost_python-py35 -lboost_regex -lboost_context -lboost_coroutine
Numpy CPP flags:        -I/home/abovet/graphtoolenv/lib/python3.5/site-packages/numpy/core/include
Sparsehash CPP flags:  
CGAL CPP flags:         -I/usr/include
CGAL LD flags:          -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread -lpthread
Expat CPP flags:        -I/usr/include
Expat LD flags:         -L/usr/lib -lexpat
Cairomm CPP flags:       -I/usr/include/cairomm-1.0 -I/usr/lib/x86_64-linux-gnu/cairomm-1.0/include -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/freetype2 -I/usr/include/libpng12 -I/usr/include/sigc++-2.0 -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include
Cairomm LD flags:       -lcairomm-1.0 -lcairo -lsigc-2.0
OpenMP compiler flags:  -fopenmp
OpenMP LD flags:       
Extra CPPFLAGS:         -DNDEBUG
Extra CXXFLAGS:         -fopenmp -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra -ftemplate-backtrace-limit=0
Extra LDFLAGS:         

Using OpenMP:           yes
Using sparsehash:       yes
Using cairo:            yes
================================================================================














$ make
make  all-recursive
make[1]: Entering directory '/home/abovet/local/graph-tool-2.25'
Making all in src
make[2]: Entering directory '/home/abovet/local/graph-tool-2.25/src'
Making all in graph
make[3]: Entering directory '/home/abovet/local/graph-tool-2.25/src/graph'
Making all in centrality
make[4]: Entering directory '/home/abovet/local/graph-tool-2.25/src/graph/centrality'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/home/abovet/local/graph-tool-2.25/src/graph/centrality'
Making all in clustering
make[4]: Entering directory '/home/abovet/local/graph-tool-2.25/src/graph/clustering'
  CXX      graph_motifs.lo
In file included from graph_motifs.cc:26:0:
../../../src/graph/graph_python_interface.hh: In constructor ‘graph_tool::CoroGenerator::CoroGenerator(Dispatch&)’:
../../../src/graph/graph_python_interface.hh:94:18: error: ‘fixedsize_stack’ is not a member of ‘graph_tool::coroutines’
                 (coroutines::fixedsize_stack(BOOST_COROUTINE_STACK_SIZE),
                  ^
Makefile:520: recipe for target 'graph_motifs.lo' failed
make[4]: *** [graph_motifs.lo] Error 1
make[4]: Leaving directory '/home/abovet/local/graph-tool-2.25/src/graph/clustering'
Makefile:751: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/home/abovet/local/graph-tool-2.25/src/graph'
Makefile:422: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/abovet/local/graph-tool-2.25/src'
Makefile:603: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/abovet/local/graph-tool-2.25'
Makefile:490: recipe for target 'all' failed
make: *** [all] Error 2





On Tue, Oct 31, 2017 at 7:36 PM, Tiago de Paula Peixoto <[hidden email]> wrote:
On 31.10.2017 18:22, sanja wrote:
> Hi,
>
> I am unable to install the version 2.25.
>
> After configuring I receive a make error as below:
>
> In file included from graph_motifs.cc:26:0:
> ../../../src/graph/graph_python_interface.hh: In constructor
> ‘graph_tool::CoroGenerator::CoroGenerator(Dispatch&)’:
> ../../../src/graph/graph_python_interface.hh:94:18: error: ‘fixedsize_stack’
> is not a member of ‘graph_tool::coroutines’
>                  (coroutines::fixedsize_stack(BOOST_COROUTINE_STACK_SIZE),
>

Please provide information regarding the operating system you are using, and
the boost version you have installed. Also, please include the entire output
of the configure and make commands (not only excerpts), as well as the
entire contents of the config.log file.

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Re: Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

Tiago Peixoto
Administrator
On 07.11.2017 18:43, Alexandre Bovet wrote:
>
> Sorry for hijacking this thread, but I have the same problem when trying to
> compile graph-tool under Linux Mint 18.1 Serena with python3.5. I don't use
> the graph-tool ubuntu package because I want to install it in a virtual env.

Could you please try with the current git version?

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Re: Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)

Alexandre Bovet
Yes, it compiles without problem with the current git version.

thanks

On Tue, Nov 7, 2017 at 10:11 PM, Tiago de Paula Peixoto <[hidden email]> wrote:
On 07.11.2017 18:43, Alexandre Bovet wrote:
>
> Sorry for hijacking this thread, but I have the same problem when trying to
> compile graph-tool under Linux Mint 18.1 Serena with python3.5. I don't use
> the graph-tool ubuntu package because I want to install it in a virtual env.

Could you please try with the current git version?

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