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Re: [lammps-users] LAMMPS and sparse dump files
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Re: [lammps-users] LAMMPS and sparse dump files


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 27 Nov 2017 09:01:08 -0500

i should add to my statement, that i am assuming that you are using the native text mode LAMMPS dump style (atom or custom).
LAMMPS supports a large variety of output formats and dump styles, but since you didn't mention anything specific it implies the standard format.

if you are using a format based on MPI-IO, you may want to update your LAMMPS version in order to make certain, you have all bugfixes on those, since those use more complex ways to perform i/o. that said, it is still most likely that you have exposed a problem in your local systems file system code, or are using the machine in an unsupported way.

axel.


On Mon, Nov 27, 2017 at 7:01 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Mon, Nov 27, 2017 at 6:06 AM, Michael Bareford <m.bareford@...33....5775...> wrote:
Hello, 

Does anyone know if there are certain situations that could cause LAMMPS to produce
sparse dump files? I’m using the lammps-30Jul16 version with a custom potential model.

Occasionally, our LAMMPS simulations produce TB-sized dump files.
Closer investigation revealed that these were in fact apparent sizes: the actual file
sizes were in the 10 GB range, as expected.

What’s odd is that sometimes the simulations produce dump files that are non-sparse
(normal behaviour) and at other times these files are sparse. There seems to be a
non-deterministic element to this problem. This seems like a potential bug, however, I
couldn’t find a description of a known bug that matches the issue I’m seeing

​this is more likely a bug/problem with the file system hosting the files than with LAMMPS.
LAMMPS is using standard i/o functions from the stdio library part of the c library.

axel.

 

Thanks in advance,
Michael

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
Dr. Axel Kohlmeyer  akohlmey@...92......  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.