[gmx-users] grompp is using a very large amount of memory on a modestly-sized system

Justin Lemkul jalemkul at vt.edu
Fri Mar 8 18:28:03 CET 2019



On 3/8/19 11:04 AM, Sean Marks wrote:
> Hi, everyone,
>
> I am running into an issue where grompp is using a tremendous amount of
> memory and crashing, even though my system is not especially large (63976
> atoms).
>
> I am using GROMACS 2016.3.
>
> My system consists of liquid water (7,930 molecules) next to a block of ice
> (8,094 molecules). The ice oxygens are restrained to their lattice position
> with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am using
> the TIP4P/Ice model, which is a rigid 4-site model with a negative partial
> charge located on a virtual site rather than the oxygen.
>
> My goal is to systematically reduce the electrostatic interactions between
> the water molecules and the position-restrained ice, while leaving
> water-water and ice-ice interactions unaffected.
>
> To accomplish this, I am modeling all of the ice molecules using a single
> moleculetype so that I can take advantages of GROMACS' FEP features to
> selectively scale interactions. I explicitly specify all constraints and
> exclusions in the topology file. This moleculetype contains one virtual
> site, 3 constraints, and 4 exclusions per "residue" (ice molecule).
>
> When I run grompp, I receive the following error, which I think means that
> a huge block of memory (~9 GB) was requested but could not be allocated:
>
> =====
> Command line:
>    gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r
> initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top
>
> ...
>
> Generated 21 of the 21 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 21 of the 21 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'ICE'
> turning H bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'SOL'
> turning H bonds into constraints...
> Coupling 1 copies of molecule type 'ICE'
> Setting gen_seed to 1021640799
> Velocities were taken from a Maxwell distribution at 273 K
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removing all charge groups because cutoff-scheme=Verlet
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2016.3
> Source file: src/gromacs/utility/smalloc.cpp (line 226)
>
> Fatal error:
> Not enough memory. Failed to realloc -8589934588 bytes for il->iatoms,
> il->iatoms=25e55010
> (called from file
> /home/semarks/source/gromacs/2016.3/icc/serial/gromacs-2016.3/src/gromacs/
> gmxpreprocess/convparm.cpp,
> line 565)
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> =======
>
> In the hope that it helps with diagnosing the problem, here is my mdp file:

The problem is this:
> couple-intramol = no    ; don't adjust ice-ice interactions
>
This setting causes the creation of a large exclusion matrix, which in 
your case is approximately 32,376 x 32,376 elements. For small 
molecules, this generally isn't an issue, but since you're trying to 
modulate a large number of molecules within a much larger 
[moleculetype], the memory requirement goes up exponentially.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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