[gmx-users] Out of memory error for g_density and trjconv

[Justin Lemkul]

On 1/15/16 11:24 AM, Wheeler S.R. wrote:
> I've run an atomistic simulation of 2048 DOPC and 65,536 waters; so ~500,000 atoms in total.  I'd like to produce an electron density plot of the bilayer so I tried to use g_density but immediately got the error message:
>
> Fatal error:
> Not enough memory. Failed to calloc -1082130432 elements of size 4 for grps[j].nm_ind (called from file /local/software/gromacs/5.0.4/source/gromacs-5.0.4/src/gromacs/fileio/tpxio.c, line 2510)
>
> As I get the same message even if I try to analyse the last frame of the trajectory (using the -b flag), I assume the problem is the number of atoms rather than the length of the trajectory. However I'm not sure how to proceed given that I also get the same error message immediately if I try to use trjconv to, for example, strip the waters out of the trajectory.
>
> I have a couple of questions:
> 1) Does the error message mean that it requires 1082130432 * 4bytes (ie ~4.5GB)? If so,I'm confused why I get this message even when I'm running on a node that has 8GB per processor (256GB for a whole 32 processor node)?  How much memory is it asking for?

Note that calloc is showing a negative number, which is nonsense, so it's an 
overflow and wraparound problem.

> 2) Is there any way of stripping down this trajectory (other than trjconv!) as it currently stands in order to get round the memory issue or is it just a case that these simulations are effectively wasted because I can't analyse them?
>

trjconv is the only means to strip atoms out of a trajectory.  500k atoms is not 
that large, though.  I've done plenty of simulations that size.  What about 
upgrading to 5.1.1 and trying again?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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