Hi Christoph
The output of the gdb backtrace is:
#0 std::operator<< <char, std::char_traits<char>, std::allocator<char> >
(__os=..., __str=
Traceback (most recent call last):
File
"/usr/local/gcc-4.7.1/lib64/../share/gcc-4.7.1/python/libstdcxx/v6/printers.py",
line 602, in to_string
header = ptr.cast(reptype) - 1
RuntimeError: Cannot access memory at address 0x39
) at
/usr/local/gcc-4.7.1/build/x86_64-unknown-linux-gnu/libstdc++-v3/include/bits/basic_string.h:2755
#1 0x00007ffff7b81335 in votca::csg::GMXTopologyReader::ReadTopology
(this=0x68ddb0, file="topol_nowf.tpr", top=...)
at
/home/mashaya1/Apps/votca/src/csg/src/libcsg/modules/io/gmxtopologyreader.cc:145
#2 0x00007ffff7b47377 in votca::csg::CsgApplication::Run
(this=0x7fffffffcbe0)
at /home/mashaya1/Apps/votca/src/csg/src/libcsg/csgapplication.cc:215
#3 0x00007ffff7844fbc in votca::tools::Application::Exec(int, char**) ()
from /home/mashaya1/Apps/votca/lib/libvotca_tools.so.3
#4 0x000000000044fca8 in main (argc=7, argv=0x7fffffffd078)
at /home/mashaya1/Apps/votca/src/csg/src/tools/csg_stat.cc:116
---
Sikandar
On Thu, Feb 13, 2014 at 10:10 PM, Hossein Motevaselian <
[email protected]> wrote:
> Thank you Christoph,
> I finally installed it without any errors, but as Sikandar said I am
> getting this segment fault error while using the votca commands.
> I will follow your discussions.
> Thanks again
>
> On Thursday, February 13, 2014 3:47:54 PM UTC-6, Christoph Junghans wrote:
>>
>> 2014-02-13 14:34 GMT-07:00 Sikandar Mashayak <[email protected]>:
>> > Hi
>> >
>> > On the same cluster (as Hossein), I was able to successfully install
>> > votca-tools and csg with the cmake option:
>> >
>> > -DBoost_INCLUDE_DIR=/usr/local/boost/boost-1.51.0/include/
>> >
>> > Though, the installation is complete. I get the segmentation faults
>> when I
>> > run any csg application, e.g., csg_stat .
>> >
>> > I am guessing this is related to boost. Am I right? I am not sure how
>> to
>> > trace the cause of the segmentation fault.
>> Build with -DCMAKE_BUILD_TYPE=Debug and then run:
>> $ gdb --args csg_stat options...
>> in gdb type "run", it will run until the segault and then type "bt"
>> (backtrace).
>>
>> Cheers,
>>
>> Christoph
>>
>> >
>> > Thanks
>> > Sikandar
>> >
>> >
>> > On Thu, Feb 13, 2014 at 8:27 PM, Denis Andrienko <
>> [email protected]>
>> > wrote:
>> >>
>> >> You might also need to specify
>> >> -DBoost_FILESYSTEM_LIBRARY=/usr/local/boost/boost-1.51.0/lib/libboost_filesystem.so
>>
>> >>
>> >>
>> >> As I have already mentioned, boost has several bugs in major releases.
>> We
>> >> haven't tested 1.51, but I had to downgrade it in the latest UBUNTU
>> release.
>> >> We know that 1.49 and 1.54 are working. Also make sure that you don't
>> have
>> >> several versions installed at the same time:
>> >>
>> >>
>> >> dpkg -s libboost-dev | grep 'Version'
>> >> or
>> >> cat /usr/include/boost/version.hpp | grep "BOOST_LIB_VERSION"
>> >>
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>> >
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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