Segmentation fault (core dumped) when running minimize_blockmodel_dl(g, overlap=True)
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
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 -- Tiago de Paula Peixoto <tiago@skewed.de>
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 -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/
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. -- Tiago de Paula Peixoto <tiago@skewed.de>
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 <tiago@skewed.de> 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.
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
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? -- Tiago de Paula Peixoto <tiago@skewed.de>
Yes, it compiles without problem with the current git version. thanks On Tue, Nov 7, 2017 at 10:11 PM, Tiago de Paula Peixoto <tiago@skewed.de> 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?
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
participants (4)
-
Alexandre Bovet -
sanja -
Sanja Šćepanović
-
Tiago de Paula Peixoto