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

[Glenn (Gedaliah) Wolosh]

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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