Re: Periodic cell too small with GPUs, not with pur CPUs

From: Francesco Pietra (
Date: Mon Jul 17 2017 - 09:09:20 CDT

Dear Dave:
I got the impression that problems with such poor GPUs like my GTX680 are
exacerbated with version 12 of namd, or at least with the night build that
I mentioned on previous mail.

I am now at a larger box for the same system that I mentioned (just to
allow the protein tumbling). Minimization on a 4 core desktop gave no
problems. Gradual heating on the GTX680 box led to chaining of the TIP3P
waters. Again no problem with the desktop, at its very low speed
(rigidbonds water, ts=1.0fs, margin 0)

NPT (based on the heating output) on the GTX680 box could not be run by
even going to ts=0.1fs, larger margin).

Again no problems on the desktop (the nextScale cluster in under tuning of
nam12 with knl, presently very poor performance).

I had no similar problems with previous versions of namd on the same GTX680


On Wed, Jul 5, 2017 at 6:02 PM, David Hardy <> wrote:

> Dear Francesco,
> This issue shouldn't have anything to do with the "wrapall" option, since
> this just affects the output of atom coordinates to the DCD file.
> The "periodic cell became too small" error occurs when using a barostat
> that shrinks the periodic cell to the point where the patch size along a
> dimension becomes smaller than the extended cutoff distance, which is why
> increasing "margin" is helping.
> Overall, your problem between running on GPUs vs CPUs is most likely due
> to differences in the calculation of the virial, which then affects the
> barostat. The virial appears to be, numerically speaking, not a well
> conditioned quantity to compute, so the use of single precision (GPUs)
> versus double precision (CPUs) in its calculation is probably at the root
> of your issue.
> In terms of using NAMD on GPUs, increasing the "margin," as Josh
> recommends, is probably your best course of action. Increasing the margin
> to 10 seems to me to be really extreme, as this will impede performance.
> Ask yourself: Is your periodic cell really expected to shrink as much as
> (minimum number of patches along a given dimension)*margin? Maybe first
> try setting it more modestly to 1 or 2 to see if you can then successfully
> run.
> Best regards,
> Dave
> --
> David J. Hardy, Ph.D.
> Theoretical and Computational Biophysics
> Beckman Institute, University of Illinois
> On Jul 5, 2017, at 9:39 AM, Joshua . <> wrote:
> Hello Francesco,
> I am new to NAMD, but I had a similar problem "periodic cell became too
> small" and resolved it by setting margin to 10 (while keeping wrapAll on).
> Documentation from 2.6 says to leave it alone unless trying to optimize
> performance, but it solved the issue for me immediately: http://www.ks.
> Josh
> On Wed, Jul 5, 2017 at 3:09 AM, Francesco Pietra <>
> wrote:
>> Hallo:
>> I am at an unbiased MD with a large protein containing organic ligands in
>> a TIP3P box that (wrapall on) gave no troubles on a Nextscale cluster on
>> 264 pure CPUs along a 58.2ns simulation, ts=1.0fs.
>> On trying to continue the simulation with my workstation with a couple of
>> GTX680, I am facing immediate "periodic cell became too small" under either
>> "wrapall on" or "wrapall no" (I used successfully this hardware for MD up
>> to this case). NAMD_CVS_2017-05-25_Linux-x86_64_multicore-CUDA.
>> In contrast, the simulation continues without problems (albeit very
>> slowly) on pure CPUs with a desktop, either "wrapall no" (which was the
>> reason for continuing the simulation in order to safely measure the
>> distances between the centers of mass of protein and ligands) or "wrapall
>> on".
>> francesco pietra

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