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

[Glenn (Gedaliah) Wolosh]

> On Dec 6, 2019, at 8:46 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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 :)


Just to be clear. I’m a sysadmin responsible for the building, installation and testing of GROMACS. Your tutorial has been extremely valuable for this purpose. The reason I put in maxwarn was that the command :

gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr 

failed due to a waring.


WARNING 1 [file topol.top, line 18409]:
  You are using Ewald electrostatics in a system with net charge. This can
  lead to severe artifacts, such as ions moving into regions with low
  dielectric, due to the uniform background charge. We suggest to
  neutralize your system with counter ions, possibly in combination with a
  physiological salt concentration.

In the next step of the tutorial the counter ions are added.

For my testing purposes, I just needed to get past the warning.

GW



> 
> -Justin
> 
> -- 
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> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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