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

[Justin Lemkul]

On 12/5/19 3:35 PM, Glenn (Gedaliah) Wolosh 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

Sorry to say I have no input on the issue at hand, but PLEASE never use 
-maxwarn with grompp and certainly there is no need to just attach this 
(very dangerous) option to something as simple as my tutorial, which 
should run cleanly without any modification. If you get in this habit, 
you run the risk of performing totally unphysical simulations. grompp 
tries to help - don't ignore it :)

-Justin

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Justin A. Lemkul, Ph.D.
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