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

[Mark Abraham]

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>
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/>
> 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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