[Openmd-users] Segmentation fault using openmd

[Dan Gezelter]

Philipp,

  I think we've got a fix -- it is checked in to the 2.4 development branch on github. We are going to release 2.4 in the next month or two, but if you want to jump ahead and use 2.4 now, you can get a copy on github:

git clone https://github.com/OpenMD/OpenMD.git

If you are interested in the details, the qhull 2015 versions have three distinct ways the qhull routines can be called:

  1) The "reentrant" method which passes the qh_qh pointer in all the functions
  2) Using a dynamically-allocated pointer to the qh_qh object
  3) Using static libraries

The package installed on Ubuntu has the headers for reentrant and pointer-based calls, but only the library for the second method.  We had been assuming the static libraries were always present, so we had to be a bit more careful on the build process.

 --Dan  


> On Jul 13, 2016, at 5:32 AM, Hans Philipp <philipp.hans at tuwien.ac.at> wrote:
> 
> 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
> 
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*************************************************************
 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
*************************************************************