[Openmd-users] Segmentation fault using openmd

[Dan Gezelter]

Dear Philipp,

That's a new bug.  I just upgraded one of our ubuntu machines to 16.04, so I'll investigate.   Can you 
verify a few things for me?  

1) Find the installed version of the qhull library, do this:   dpkg -s libqhull-dev  
2) See if there are any differences between the MPI compiler and the compiler you used:

   mpicxx --version
   /usr/bin/c++ --version


Best regards,

 --Dan Gezelter

> On Jul 15, 2016, at 10:41 AM, Hans Philipp <philipp.hans at tuwien.ac.at> wrote:
> 
> Dear Mr Gezelter,
> 
> I sent something to the mailing-list some days ago but did not get any confirmation or notice of receipt. I forward you my message.
> Pleasant weekend,
> Philipp Hans
> 
> 
> Von: Hans Philipp
> Gesendet: Mittwoch, 13. Juli 2016 11:32
> An: openmd-users at openmd.org
> Betreff: Segmentation fault using openmd
>  
> Hello,
> 
> I wanted to use the openmd-program.
> But during compil    ​ation I had to add some options and the program exits with an error.
> 
> ====================================================================================================
> System: Ubuntu 16.04.
> 
> At about 82% of compilation process during linking. Had to add the following:
> -lmpi -lmpi_cxx
> 
> to:
> 
> /usr/bin/c++   -O3 -DNDEBUG   CMakeFiles/openmd_MPI.dir/src/applications/openmd/openmd.cpp.o  -o bin/openmd_MPI -rdynamic -lqhull -lz -lfftw3 lib/libopenmd_parallel.a lib/libopenmd_core.a lib/libopenmd_parallel.a lib/libopenmd_core.a -lqhull -lz -lfftw3 -lmpi -lmpi_cxx
> ------------------------------------------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------------------------------------------
> 
> 
> When trying to run one of the examples, calling
> 
> openmd NP15.md
> 
> leads to:
> Segmentation fault (core dumped)
> 
> 
> The problem seems to lie here:
> 
> Program received signal SIGSEGV, Segmentation fault.
> 0x00000000004a9eda in OpenMD::ConvexHull::computeHull(std::vector<OpenMD::StuntDouble*, std::allocator<OpenMD::StuntDouble*> >) ()
> (gdb) where
> #0  0x00000000004a9eda in OpenMD::ConvexHull::computeHull(std::vector<OpenMD::StuntDouble*, std::allocator<OpenMD::StuntDouble*> >) ()
> #1  0x0000000000646200 in OpenMD::LangevinHullForceManager::LangevinHullForceManager(OpenMD::SimInfo*) ()
> #2  0x00000000006161ae in OpenMD::LangevinHullDynamics::LangevinHullDynamics(OpenMD::SimInfo*) ()
> #3  0x0000000000515411 in OpenMD::IntegratorBuilder<OpenMD::LangevinHullDynamics>::create(OpenMD::SimInfo*) const ()
> #4  0x00000000004610c4 in main ()
> (gdb) quit
> ====================================================================================================
> 
> Thank you in advance.
> best regrads,
> Philipp
> 
> 

*************************************************************
 J. Daniel Gezelter
 Professor and Director of Undergraduate Studies
 Department of Chemistry and Biochemistry
 251 Nieuwland Science Hall
 University of Notre Dame
 Notre Dame, IN 46556-5670

 gezelter at nd.edu | (574) 631-7595 | http://gezelterlab.org
*************************************************************