[gmx-users] Seg Fault with Gromacs gmx grompp command - Intel compiler

[Mark Abraham]

Hi,

If the environment is sufficiently well constructed to do the necessary
dynamic linking, then things like gmx -version and gmx editconf should not
segfault. Do they? My guess is that the appropriate Intel libraries, or
perhaps the gcc libstdc++ libraries that icc requires are actually not
available in the environment.

Mark

On Thu, 5 Dec 2019 at 21:36, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu>
wrote:

> Thanks for the quick response. I do have the environment properly prepare
> via modules.
>
> GW
>
>
> > On Dec 5, 2019, at 3:24 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > Hi,
> >
> > I suspect you need to prepare the intel environment at run time like you
> > did before compilation. Probably you (or a module you loaded) source-d a
> > compilervars.sh file, and that's probably what you need here.
> >
> > Mark
> >
> > On Thu, 5 Dec 2019 at 20:22, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu
> <mailto:gwolosh at njit.edu>>
> > wrote:
> >
> >>
> >> Also posted on the intel forum:
> >>
> >> This problem is consistent with the following gromacs/compiler versions:
> >>
> >> Gromacs 2019.4/Intel Parallel Studio 2019.4
> >>
> >> Gromacs 2019.4/Intel 2017.2
> >>
> >> Gromacs 2018.2/Intel Parallel Studio 2019.4
> >>
> >> Gromacs 2018.5/Intel Parallel Studio 2019.4
> >>
> >> The command to build and install gromacs in all cases is
> >>
> >> export CC=icc
> >> export CXX=icpc
> >> export FC=ifort
> >>
> >> cmake ..  -DGMX_FFT_LIBRARY=mkl \
> >>                  -DCMAKE_INSTALL_PREFIX=$HOME/sw/gromacs/intel/<version>
> >> &&  make VERBOSE=1 && make install
> >>
> >> The gcc version in the PATH is 5.4.0
> >>
> >> The OS is:
> >>
> >> Scientific Linux release 6.10 (Carbon)
> >>
> >> I am running the lysozyme tutorial:
> >> http://www.mdtutorials.com/gmx/lysozyme/ <
> >> http://www.mdtutorials.com/gmx/lysozyme/ <
> http://www.mdtutorials.com/gmx/lysozyme/>>
> >> The command that seg faults is
> >>
> >> gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
> -maxwarn 2
> >>
> >> The gmx grompp command succeeds when using a version of gromacs compiled
> >> with GCC
> >>
> >> Any help would be greatly appreciated.
> >>
> >>
> >> GW
> >> --
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