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

Fri Mar 8 21:43:57 CET 2019

Hi,

I don't have a solution for the question at hand, but it'd be great to have
your inputs attached to a new issue at https://redmine.gromacs.org, so that
we can have such an input case to test with, so that we can improve the
simplistic implementation! Please upload it if you can.

Mark

On Fri., 8 Mar. 2019, 19:24 Sean Marks, <semarks at seas.upenn.edu> wrote:

> Scratch that comment about sparseness. I am short on sleep, and for a
> moment thought I was talking about constraints, not electrostatics.
>
> On Fri, Mar 8, 2019 at 1:12 PM Sean Marks <semarks at seas.upenn.edu> wrote:
>
> > I understand now, thank you for the prompt response. While the matrix
> > would actually be quite sparse (since the constraints are localized to
> each
> > ice molecule), I take it that memory is being allocated for a dense
> matrix.
> >
> > That aside, is it feasible to accomplish my stated goal of scaling
> > ice-water electrostatics while leaving other interactions unaffected? One
> > alternative I considered was manually scaling down the charges
> themselves,
> > but doing this causes the lattice to lose its form.
> >
> > On Fri, Mar 8, 2019 at 12:28 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> 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
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
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> >>
> >
> >
> > --
> > Sean M. Marks
> > PhD Candidate
> > Dept. of Chemical and Biomolecular Engineering
> > University of Pennsylvania
> > SeanMarks1123 at gmail.com
> >
>
>
> --
> Sean M. Marks
> PhD Candidate
> Dept. of Chemical and Biomolecular Engineering
> University of Pennsylvania
> SeanMarks1123 at gmail.com
> --
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