Hi Hossein Christoph figured out that the segfault issue, in the above case, occurred because of wrong GROMACS precision specification while building csg.
By default, the csg was built assuming double precision for GROMACS though the precision of an installed GROMACS was single. The precision of GROMACS library while building csg could be set by the cmake option of -DGROMACS_DEFINITIONS= (i) blank (nothing) for single and (ii) -DGMX_DOUBLE for double. The default value was -DGROMACS_DEFINITIONS=-DGMX_DOUBLE, and the gromacs that ./build.sh installed was a single precision. And hence, you get a segmentation fault! This issue is fixed by Christoph. Now cmake tries to guess the precision from the actual installed GROMACS library, instead of assuming it to be double. So pull the changes and check if it works. If you want to be certain, manually specify the option -DGROMACS_DEFINITIONS when you build csg. I hope it helps. Cheers Sikandar On Sun, Feb 16, 2014 at 2:04 AM, Sikandar Mashayak <[email protected]>wrote: > Hi Christoph > > Segfault is occurring due to, in my particular case, bead->getResnr() is > greater than the top.ResidueCount(). > > I checked topology using gmxdump, it looks fine to me. I am, however, not > yet sure why is there inconsistency > in the resdue counts. > > I have attached the input files for csg_stat, can you please check if you > also get the segfault? > > Thanks > Sikandar > > > > On Fri, Feb 14, 2014 at 9:21 PM, Christoph Junghans <[email protected]>wrote: > >> 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. >> > > -- 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.
