v2.22 crashes when zooming-in or out on graph

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v2.22 crashes when zooming-in or out on graph

Evangelos Petsalis
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



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Re: v2.22 crashes when zooming-in or out on graph

Tiago Peixoto
Administrator
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

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Re: v2.22 crashes when zooming-in or out on graph

Evangelos Petsalis
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 <[hidden email]> wrote:
On <a href="tel:22.09.2017%2019" value="+12209201719">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

--
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_______________________________________________
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[hidden email]
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Re: v2.22 crashes when zooming-in or out on graph

Tiago Peixoto
Administrator
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...

--
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Re: v2.22 crashes when zooming-in or out on graph

Evangelos Petsalis
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 <[hidden email]> wrote:
On <a href="tel:27.09.2017%2000" value="+12709201700">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 <[hidden email]>


_______________________________________________
graph-tool mailing list
[hidden email]
https://lists.skewed.de/mailman/listinfo/graph-tool



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Re: v2.22 crashes when zooming-in or out on graph

Evangelos Petsalis
In reply to this post by Tiago Peixoto
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 <[hidden email]> wrote:
On <a href="tel:27.09.2017%2000" value="+12709201700">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 <[hidden email]>


_______________________________________________
graph-tool mailing list
[hidden email]
https://lists.skewed.de/mailman/listinfo/graph-tool



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Re: v2.22 crashes when zooming-in or out on graph

Evangelos Petsalis
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 <[hidden email]> 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 <[hidden email]> wrote:
On <a href="tel:27.09.2017%2000" value="+12709201700" target="_blank">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 <[hidden email]>


_______________________________________________
graph-tool mailing list
[hidden email]
https://lists.skewed.de/mailman/listinfo/graph-tool




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Re: v2.22 crashes when zooming-in or out on graph

Tiago Peixoto
Administrator
In reply to this post by Evangelos Petsalis
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

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Re: v2.22 crashes when zooming-in or out on graph

Evangelos Petsalis
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 <[hidden email]> wrote:
On <a href="tel:27.09.2017%2017" value="+12709201717">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 <[hidden email]>
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[hidden email]
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