Running graph-tool "2.23dev (commit b626e713, Tue Mar 28 22:29:08 2017 +0100)", compiled using GCC 5.4.0 on Ubuntu 16.04 I get a "Segmentation fault (core dumped)" error when running the following:
import graph_tool.all as gt g = gt.collection.data["dolphins"]
This issue does not seem to arise for me when running version "2.22 (commit 44bf2b92, Thu Mar 2 23:08:39 2017 +0000)" (i.e. the latest apt-get release).
Is this an issue caused in the dev version of graph-tool or is this caused by me compiling something incorrectly? Can anybody reproduce this error?
Best,
Philipp
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On 03.04.2017 19:48, P-M wrote:
Running graph-tool "2.23dev (commit b626e713, Tue Mar 28 22:29:08 2017 +0100)", compiled using GCC 5.4.0 on Ubuntu 16.04 I get a "Segmentation fault (core dumped)" error when running the following:
import graph_tool.all as gt g = gt.collection.data["dolphins"]This issue does not seem to arise for me when running version "2.22 (commit 44bf2b92, Thu Mar 2 23:08:39 2017 +0000)" (i.e. the latest apt-get release).
Is this an issue caused in the dev version of graph-tool or is this caused by me compiling something incorrectly? Can anybody reproduce this error?
No, I can't reproduce this.
The git repository has automatic build tests that would easily catch a bug like this, and I've never seen it happening.
I'm skeptical this is an actual bug; it is more likely to be a link-time inconsistency of some sort.
Do you have a backtrace of the segfault?
Best, Tiago
Unfortunately there is no backtrace whatsoever. All I get is Python terminating (if I run it interactively) and the message I posted being displayed. Nothing else appears on my screen.
I am able to use it on my other computer using version "2.23dev (commit 316f8a3d, Tue Mar 28 14:07:46 2017 +0100)" so this issue is by no means critical to me if you have other things to get on with.
Best,
Philipp
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On 04.04.2017 14:52, P-M wrote:
Unfortunately there is no backtrace whatsoever. All I get is Python terminating (if I run it interactively) and the message I posted being displayed. Nothing else appears on my screen.
You have to get a backtrace using GDB; it does not happen automatically. You can google "gdb backtrace" to see how it is done.
I am able to use it on my other computer using version "2.23dev (commit 316f8a3d, Tue Mar 28 14:07:46 2017 +0100)" so this issue is by no means critical to me if you have other things to get on with.
I most certainly have other things to do; but it is up to you if you want to provide the backtrace to investigate further.
Hi Tiago,
The output of gdb is attached ( gdb-python.txt http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4027181/gdb-python.txt ). The issue seems to be:
Thread 1 "python" received signal SIGSEGV, Segmentation fault. 0x00007fffe4248960 in boost::iostreams::detail::gzip_header::reset() () from /home/pmj27/anaconda2/lib/libboost_iostreams.so.1.60.0
Is this of any use?
Best,
Philipp
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Sorry, here is the full output: gdb-python.txt http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4027182/gdb-python.txt
Philipp
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On 04.04.2017 16:12, P-M wrote:
Sorry, here is the full output: gdb-python.txt http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4027182/gdb-python.txt
It seems to be coming from boost-iostreams; not graph-tool.
I see you are using boost 1.60. Maybe you should try upgrading to 1.61, 1.62 or 1.63.
Best, Tiago
It looks like it (though it is funny that the other computer using the same package version doesn't have the issue). It has been a major battle to get all the dependencies to work in Anaconda python so seeing as I have a configuration that currently works I am inclined to stick with the versions I have for now unless other issues also start cropping up. Being able to compile new versions of graph-tool easily is more important to me I think. Thank you for looking into it though!
Best,
Philipp
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P-M -
Tiago de Paula Peixoto