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

[Sean Marks]

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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
> --
> 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