2017-06-26 7:33 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Hello, > > This is from gdb: > > [Thread debugging using libthread_db enabled] > warning: File "/gpfs/fs1/sfw/gcc/5.3.0/lib64/libstdc++.so.6.0.21-gdb.py" > auto-loading has been declined by your `auto-load safe-path' set to > "/usr/share/gdb/auto-load:/usr/ > lib/debug:/usr/bin/mono-gdb.py". > To enable execution of this file add > add-auto-load-safe-path > /gpfs/fs1/sfw/gcc/5.3.0/lib64/libstdc++.so.6.0.21-gdb.py > line to your configuration file "/home/mchakra2/.gdbinit". > To completely disable this security protection add > set auto-load safe-path / > line to your configuration file "/home/mchakra2/.gdbinit". > For more information about this security protection see the > "Auto-loading safe path" section in the GDB manual. E.g., run from the > shell: > info "(gdb)Auto-loading safe path" > Reading file topol.tpr, VERSION 5.1.3 (single precision) > I have 6000 beads in 1000 molecules > I have 2000 beads in 1000 molecules for the coarsegraining > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > Reading frame 20 time 20.000 Number of spline functions for the > interaction A-A:35 > Number of spline functions for the interaction B-B:35 > Number of spline functions for the interaction A-B:35 > > You are using VOTCA! > > hey, somebody wants to forcematch! > > Using simple Least Squares! > > Program received signal SIGSEGV, Segmentation fault. > 0x00002aaaaef1da6a in LAPACKE_dge_nancheck () from > /software/intel/2016.0515/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so > Missing separate debuginfos, use: debuginfo-install > expat-2.0.1-11.el6_2.x86_64 glibc-2.12-1.166.el6_7.7.x86_64 > sqlite-3.6.20-1.el6.x86_64 zlib-1.2.3-29.el6.x86_64 > (gdb) bt > #0 0x00002aaaaef1da6a in LAPACKE_dge_nancheck () from > /software/intel/2016.0515/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so Hmm, that seems to be inside mkl.
Can you try to build VOTCA without mkl (option -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON) and use gsl instead to see if the problem persists? Christoph > #1 0x00002aaaaef22cb2 in LAPACKE_dgels () from > /software/intel/2016.0515/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so > #2 0x00002aaaaadaf5fc in > votca::tools::linalg_qrsolve(boost::numeric::ublas::vector<double, > boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, > boo > st::numeric::ublas::matrix<double, > boost::numeric::ublas::basic_row_major<unsigned long, long>, > boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, > boost::numeric::ublas::vector<double, > boost::numeric::ublas::unbounded_array<double, std::allocator<double> > >&, > boost::numeric::ublas::vector<double, boost::numeric::ubla > s::unbounded_array<double, std::allocator<double> > >*) () from > /software/votca/b2/lib/libvotca_tools.so.5 > #3 0x000000000040bcd6 in CGForceMatching::FmatchAccumulateData() () > #4 0x000000000040d0ef in > CGForceMatching::EvalConfiguration(votca::csg::Topology*, > votca::csg::Topology*) () > #5 0x00002aaaaaaec044 in > votca::csg::CsgApplication::ProcessData(votca::csg::CsgApplication::Worker*) > () from /software/votca/b2/lib/libvotca_csg.so.5 > #6 0x00002aaaaaaec06a in votca::csg::CsgApplication::Worker::Run() () from > /software/votca/b2/lib/libvotca_csg.so.5 > #7 0x00002aaaaaaedd8c in votca::csg::CsgApplication::Run() () from > /software/votca/b2/lib/libvotca_csg.so.5 > #8 0x00002aaaaad7f05b in votca::tools::Application::Exec(int, char**) () > from /software/votca/b2/lib/libvotca_tools.so.5 > #9 0x000000000041a1d3 in main () > (gdb) quit > > > Thanks. > > ~M. Chakraborty > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
