2014-02-14 12:59 GMT-07:00 Sikandar Mashayak <[email protected]>: > 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 This line 145 has been there for a long time, but my guess is that something goes wrong with the residue numbers: top.getResidue(res_offset + bead->getResnr())->getName()
Can you check with gmdump, if the Residue numbers in your tpr start with 0 and are contiguous. Christoph > #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" >>> >> >>> >> -- >>> >> You received this message because you are subscribed to the Google >>> >> Groups >>> >> "votca" group. >>> >> To unsubscribe from this group and stop receiving emails from it, send >>> >> an >>> >> email to [email protected]. >>> >> To post to this group, send email to [email protected]. >>> >> Visit this group at http://groups.google.com/group/votca. >>> >> For more options, visit https://groups.google.com/groups/opt_out. >>> > >>> > >>> > -- >>> > You received this message because you are subscribed to the Google >>> > Groups >>> > "votca" group. >>> > To unsubscribe from this group and stop receiving emails from it, send >>> > an >>> > email to [email protected]. >>> > To post to this group, send email to [email protected]. >>> > Visit this group at http://groups.google.com/group/votca. >>> > For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at http://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/groups/opt_out. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
