[Openmd-users] Segmentation fault using openmd

[Philipp Hans]

Dear Dan,

I am thrilled by your fast solution.
I will try to build the new version; I hope it works.
I am already exited if what I planned will be working. So I thank you very
much, also for your explanations about what the problem presumably was.


best regards,
Philipp


Dan Gezelter <gezelter at nd.edu> schrieb am Mi., 20. Juli 2016 21:55:

> 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
> >
> > _______________________________________________
> > Openmd-users mailing list
> > Openmd-users at openmd.org
> > http://openmd.org/mailman/listinfo.cgi/openmd-users
>
> *************************************************************
>  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
> *************************************************************
>
>
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