[ase-users] Problems with LAMMPSlib interface for >8 CPUs

[Andrew Logsdail]

On 10 May 2019, at 14:18, Noam Bernstein <noam.bernstein at nrl.navy.mil<mailto:noam.bernstein at nrl.navy.mil>> wrote:

On May 10, 2019, at 3:18 AM, Andrew Logsdail via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:

Dear ASE-users,

I have been having problems with the LAMMPSlib interface and wonder if anyone has experience/knowledge of this interface and its implementation? (Or can scrutinise my use and spot some obvious mistake I’m making!)

My problem is that, with the EAM example input provided for NiH, I cannot get the LAMMPSlib calculation to run on >8 CPUs without receiving a “Lost Atoms” error from LAMMPS (it works fine for =< 8 CPUs). I can get the calculation to run successfully for >8 CPUs with LAMMPSrun, i.e. writing input files and performing a system call. I can also take the input files generated from this LAMMPSrun approach and use a basic Python test harness to run the LAMMPS executable, again on >8 CPUs. So the problem seems to be isolated to LAMMPSlib in ASE, rather than the LAMMPS python library itself.

Any input would be welcomed, and/or if anyone can attempt a testrun with LAMMPSlib on my behalf that would also be welcomed! It has been challenging to work this out (and also get compatible LAMMPSlib/LAMMPSrun commands setup) and I’ve updated the ASE documentation to help with this in the future.

Files from my testing are attached, with EAM potential file downloadable from here:https://www.dropbox.com/s/9hqs00cwkjs8yy8/NiAlH_jea.eam.alloy?dl=0<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2F9hqs00cwkjs8yy8%2FNiAlH_jea.eam.alloy%3Fdl%3D0&data=01%7C01%7CLogsdailA%40cardiff.ac.uk%7C296bc107e90944cff7ae08d6d549facb%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=GAmG2mPSS9GPo5vhGYw02RkXD8fH6vpIl8H9%2BXu%2FQm8%3D&reserved=0> (too big for mailing list; it’d be good to have this on the examples page for LAMMPS maybe?).


I don’t know how well those have been tested with parallel LAMMPS, but you may want to contact Ellad Tadmor of the OpenKIM project (tadmor at umn.edu<mailto:tadmor at umn.edu>) who I know has been working on updating/debugging LAMMPSlib.

Noam

Thanks Noam. Unfortunately Ellad is unfamiliar with the parallel implementation of LAMMPSlib - if you have any other suggestions then do let me know!

All the best,

Andy





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U.S. NAVAL
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_RESEARCH_
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LABORATORY

Noam Bernstein, Ph.D.
Center for Materials Physics and Technology
U.S. Naval Research Laboratory
T +1 202 404 8628  F +1 202 404 7546
https://www.nrl.navy.mil<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nrl.navy.mil&data=01%7C01%7CLogsdailA%40cardiff.ac.uk%7C296bc107e90944cff7ae08d6d549facb%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=0ZkMeezUZL4ntlPRUFEoCB5eiOEpjEhs8EiBgfdkpGA%3D&reserved=0>


—

Dr. Andrew Logsdail

School of Chemistry,
Cardiff University,
Main Building,
Park Pl,
Cardiff CF10 3AT

T: +44 2922 510 162
E: LogsdailA at cardiff.ac.uk<mailto:LogsdailA at cardiff.ac.uk>
W: http://logsdail.github.io
@: http://www.twitter.com/a_logsdail

Yr Ysgol Cemeg,
Prifysgol Caerdydd,
Y Prif Adeilad,
Plas-y-Parc,
Caerdydd,
CF10 3AT

F: +44 2922 510 162
E: LogsdailA at cardiff.ac.uk<mailto:LogsdailA at cardiff.ac.uk>
W: http://logsdail.github.io
@: http://www.twitter.com/a_logsdail

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