Hi,
I recently upgraded to v2.22 (from v2.19) and I noticed that with the new version when I use the roller button on the mouse to zoom in or out, the application crashes with a segmentation fault - this was NOT the case with v2.19.
I was wondering if anybody else has experienced similar issues or have any ideas how to resolve the issue.
Regards, Vaggelis
-- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/
On 22.09.2017 19:21, Evangelos Petsalis wrote:
Hi,
I recently upgraded to v2.22 (from v2.19) and I noticed that with the new version when I use the roller button on the mouse to zoom in or out, the application crashes with a segmentation fault - this was NOT the case with v2.19.
I was wondering if anybody else has experienced similar issues or have any ideas how to resolve the issue.
I've never observed any problems of this kind.
Whenever reporting problems, it is crucial to give some basic background information (e.g. what OS and distribution you are using), and some simple and clear reproduction steps, otherwise it is virtually impossible to help.
Best, Tiago
Tiago,
I am using Ubuntu 16.04 (on a fresh install) and the way I plot the graph is using a GraphWidget that is attached to a Glade-generated GUI. The error I get is a segmentation fault that kills the whole python environment, which leads me to believe that there is something going on with the rendering library - you can see the code dies in the middle of rendering. Note that this happens on v2.22 and v2.23 but NOT on v.2.19.
I know I am not being much more specific than before, but posting the code that currently crashes would be of zero help since it far from the simple example that you are asking.
I was hoping that somebody else on the forum might have observed similar behavior. If not I will spend some time trying to create a simple and self-contained example that captures this behavior.
Regards, Vaggelis
On Fri, Sep 22, 2017 at 11:30 PM, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 22.09.2017 19:21, Evangelos Petsalis wrote:
Hi,
I recently upgraded to v2.22 (from v2.19) and I noticed that with the new version when I use the roller button on the mouse to zoom in or out, the application crashes with a segmentation fault - this was NOT the case
with
v2.19.
I was wondering if anybody else has experienced similar issues or have
any
ideas how to resolve the issue.
I've never observed any problems of this kind.
Whenever reporting problems, it is crucial to give some basic background information (e.g. what OS and distribution you are using), and some simple and clear reproduction steps, otherwise it is virtually impossible to help.
Best, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
On 27.09.2017 00:29, Evangelos Petsalis wrote:
I am using Ubuntu 16.04 (on a fresh install) and the way I plot the graph is using a GraphWidget that is attached to a Glade-generated GUI. The error I get is a segmentation fault that kills the whole python environment, which leads me to believe that there is something going on with the rendering library - you can see the code dies in the middle of rendering. Note that this happens on v2.22 and v2.23 but NOT on v.2.19.
I know I am not being much more specific than before, but posting the code that currently crashes would be of zero help since it far from the simple example that you are asking.
Without a specific example, there is virtually zero that anything can be done, unfortunately. I don't observe any crashes when doing said operations, so it must be tied to the specific way you are doing things, and it is difficult to guess blindly...
Tiago,
Here a small example that causes the graph to crash on v2.23:
from graph_tool.all import * import graph_tool as gt g = gt.collection.data["celegansneural"] interactive_window(g)
Once the window comes up, make sure you maximize it, and then start moving the roller up and down to zoom in/out rapidly.
The crash behavior is very erratic, in the sense that sometimes it crashes immediately, and some other times you have to keep zooming in/out for a few seconds. But it is important to maximize your window (on smaller windows it does not happen).
Coincidentally, is there a way to install previous versions of graph-tool using apt-get?
Regards, Vaggelis
On Wed, Sep 27, 2017 at 1:35 AM, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 27.09.2017 00:29, Evangelos Petsalis wrote:
I am using Ubuntu 16.04 (on a fresh install) and the way I plot the
graph is
using a GraphWidget that is attached to a Glade-generated GUI. The error
I
get is a segmentation fault that kills the whole python environment,
which
leads me to believe that there is something going on with the rendering library - you can see the code dies in the middle of rendering. Note that this happens on v2.22 and v2.23 but NOT on v.2.19.
I know I am not being much more specific than before, but posting the
code
that currently crashes would be of zero help since it far from the simple example that you are asking.
Without a specific example, there is virtually zero that anything can be done, unfortunately. I don't observe any crashes when doing said operations, so it must be tied to the specific way you are doing things, and it is difficult to guess blindly...
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
On 27.09.2017 17:09, Evangelos Petsalis wrote:
Tiago,
Here a small example that causes the graph to crash on v2.23:
from graph_tool.all import * import graph_tool as gt g = gt.collection.data["celegansneural"] interactive_window(g)
Once the window comes up, make sure you maximize it, and then start moving the roller up and down to zoom in/out rapidly.
The crash behavior is very erratic, in the sense that sometimes it crashes immediately, and some other times you have to keep zooming in/out for a few seconds. But it is important to maximize your window (on smaller windows it does not happen).
Sorry, it seems I forgot to answer you.
I can't reproduce this behavior... I get no crashes, regardless of how fast I zoom in and out.
Coincidentally, is there a way to install previous versions of graph-tool using apt-get?
You just have to download the .deb file and install it using dpkg.
Best, Tiago
FYI, a compiled version of Graph-Tool v2.25 on Ubuntu 17.04 does not exhibit the crash when zooming in/out.
On Thu, Oct 5, 2017 at 2:46 PM, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 27.09.2017 17:09, Evangelos Petsalis wrote:
Tiago,
Here a small example that causes the graph to crash on v2.23:
from graph_tool.all import * import graph_tool as gt g = gt.collection.data["celegansneural"] interactive_window(g)Once the window comes up, make sure you maximize it, and then start
moving
the roller up and down to zoom in/out rapidly.
The crash behavior is very erratic, in the sense that sometimes it
crashes
immediately, and some other times you have to keep zooming in/out for a
few
seconds. But it is important to maximize your window (on smaller windows
it
does not happen).
Sorry, it seems I forgot to answer you.
I can't reproduce this behavior... I get no crashes, regardless of how fast I zoom in and out.
Coincidentally, is there a way to install previous versions of graph-tool using apt-get?
You just have to download the .deb file and install it using dpkg.
Best, Tiago
-- Tiago de Paula Peixoto tiago@skewed.de _______________________________________________ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
Hi,
I tried to compile the v2.23 code to see if it will exhibit the same behavior as the pre-compiled one since the v2.19 was compiled on my computer.
I got the following error. Any suggestions what might be wrong?
Thanks in advance, Vaggelis
========================================================================== CONFIGURATION SUMMARY
========================================================================== Using python version: 3.5.2 Python interpreter: /usr/bin/python3.5 Installation path: /usr/lib/python3/dist-packages/graph_tool
C++ compiler (CXX): g++ -std=gnu++14 C++ compiler version: 5.4.0
Prefix: /usr/local 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_coroutine Numpy CPP flags: -I/home/labuser/.local/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 ================================================================================
============================================================ ERROR MESSAGE ============================================================
^ layers/../overlap/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::add_vertices(Vlist&, Blist&)’: layers/../overlap/../blockmodel/graph_blockmodel.hh:760:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ In file included from layers/graph_blockmodel_layers_overlap_mcmc_bundled.cc:24:0: layers/../overlap/graph_blockmodel_overlap.hh: In lambda function: layers/../overlap/graph_blockmodel_overlap.hh:289:32: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ CXX layers/graph_blockmodel_layers_overlap_multicanonical.lo In file included from layers/../overlap/graph_blockmodel_overlap_util.hh:24:0, from layers/graph_blockmodel_layers_overlap_multicanonical.cc:23: layers/../overlap/../blockmodel/graph_blockmodel.hh: In lambda function: layers/../overlap/../blockmodel/graph_blockmodel.hh:300:29: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ layers/../overlap/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::remove_vertices(Vlist&)’: layers/../overlap/../blockmodel/graph_blockmodel.hh:667:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ layers/../overlap/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::add_vertices(Vlist&, Blist&)’: layers/../overlap/../blockmodel/graph_blockmodel.hh:760:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ In file included from layers/graph_blockmodel_layers_overlap_multicanonical.cc:24:0: layers/../overlap/graph_blockmodel_overlap.hh: In lambda function: layers/../overlap/graph_blockmodel_overlap.hh:289:32: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ make[4]: *** No rule to make target 'layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.cc', needed by 'layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.lo'. Stop. make[4]: Leaving directory '/media/sf_junk/graph-tool-2.23/src/graph/inference' Makefile:751: recipe for target 'all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory '/media/sf_junk/graph-tool-2.23/src/graph' Makefile:422: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/media/sf_junk/graph-tool-2.23/src' Makefile:604: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/media/sf_junk/graph-tool-2.23' Makefile:491: recipe for target 'all' failed make: *** [all] Error 2
On Wed, Sep 27, 2017 at 1:35 AM, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 27.09.2017 00:29, Evangelos Petsalis wrote:
I am using Ubuntu 16.04 (on a fresh install) and the way I plot the
graph is
using a GraphWidget that is attached to a Glade-generated GUI. The error
I
get is a segmentation fault that kills the whole python environment,
which
leads me to believe that there is something going on with the rendering library - you can see the code dies in the middle of rendering. Note that this happens on v2.22 and v2.23 but NOT on v.2.19.
I know I am not being much more specific than before, but posting the
code
that currently crashes would be of zero help since it far from the simple example that you are asking.
Without a specific example, there is virtually zero that anything can be done, unfortunately. I don't observe any crashes when doing said operations, so it must be tied to the specific way you are doing things, and it is difficult to guess blindly...
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
Please ignore the previous email regarding compilation error. I unpacked files in windows and it seems that the maximum path length was reached, and thus the last few characters of the file had been concatenated.
Apologies for the false alarm.
On Thu, Oct 5, 2017 at 12:57 PM, Evangelos Petsalis epetsalis@gmail.com wrote:
Hi,
I tried to compile the v2.23 code to see if it will exhibit the same behavior as the pre-compiled one since the v2.19 was compiled on my computer.
I got the following error. Any suggestions what might be wrong?
Thanks in advance, Vaggelis
========================================================================== CONFIGURATION SUMMARY
========================================================================== Using python version: 3.5.2 Python interpreter: /usr/bin/python3.5 Installation path: /usr/lib/python3/dist-packages/graph_tool
C++ compiler (CXX): g++ -std=gnu++14 C++ compiler version: 5.4.0
Prefix: /usr/local 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_coroutine Numpy CPP flags: -I/home/labuser/.local/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 ============================================================ ====================
============================================================ ERROR MESSAGE ============================================================
^layers/../overlap/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::add_vertices(Vlist&, Blist&)’: layers/../overlap/../blockmodel/graph_blockmodel.hh:760:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ In file included from layers/graph_blockmodel_layers_overlap_mcmc_bundled. cc:24:0: layers/../overlap/graph_blockmodel_overlap.hh: In lambda function: layers/../overlap/graph_blockmodel_overlap.hh:289:32: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ CXX layers/graph_blockmodel_layers_overlap_multicanonical.lo In file included from layers/../overlap/graph_ blockmodel_overlap_util.hh:24:0, from layers/graph_blockmodel_ layers_overlap_multicanonical.cc:23: layers/../overlap/../blockmodel/graph_blockmodel.hh: In lambda function: layers/../overlap/../blockmodel/graph_blockmodel.hh:300:29: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ layers/../overlap/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::remove_vertices(Vlist&)’: layers/../overlap/../blockmodel/graph_blockmodel.hh:667:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ layers/../overlap/../blockmodel/graph_blockmodel.hh: In member function ‘void graph_tool::BlockState<Ts>::add_vertices(Vlist&, Blist&)’: layers/../overlap/../blockmodel/graph_blockmodel.hh:760:21: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ In file included from layers/graph_blockmodel_ layers_overlap_multicanonical.cc:24:0: layers/../overlap/graph_blockmodel_overlap.hh: In lambda function: layers/../overlap/graph_blockmodel_overlap.hh:289:32: warning: attributes at the beginning of statement are ignored [-Wattributes] [[gnu::fallthrough]]; ^ make[4]: *** No rule to make target 'layers/graph_blockmodel_ layers_overlap_multicanonical_multiflip.cc', needed by 'layers/graph_blockmodel_layers_overlap_multicanonical_multiflip.lo'. Stop. make[4]: Leaving directory '/media/sf_junk/graph-tool-2. 23/src/graph/inference' Makefile:751: recipe for target 'all-recursive' failed make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory '/media/sf_junk/graph-tool-2.23/src/graph' Makefile:422: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/media/sf_junk/graph-tool-2.23/src' Makefile:604: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/media/sf_junk/graph-tool-2.23' Makefile:491: recipe for target 'all' failed make: *** [all] Error 2
On Wed, Sep 27, 2017 at 1:35 AM, Tiago de Paula Peixoto tiago@skewed.de wrote:
On 27.09.2017 00:29, Evangelos Petsalis wrote:
I am using Ubuntu 16.04 (on a fresh install) and the way I plot the
graph is
using a GraphWidget that is attached to a Glade-generated GUI. The
error I
get is a segmentation fault that kills the whole python environment,
which
leads me to believe that there is something going on with the rendering library - you can see the code dies in the middle of rendering. Note
that
this happens on v2.22 and v2.23 but NOT on v.2.19.
I know I am not being much more specific than before, but posting the
code
that currently crashes would be of zero help since it far from the
simple
example that you are asking.
Without a specific example, there is virtually zero that anything can be done, unfortunately. I don't observe any crashes when doing said operations, so it must be tied to the specific way you are doing things, and it is difficult to guess blindly...
-- Tiago de Paula Peixoto tiago@skewed.de
graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
-
Evangelos Petsalis -
Tiago de Paula Peixoto