[ase-users] Problems with LAMMPSlib interface for >8 CPUs
Andrew Logsdail
LogsdailA at cardiff.ac.uk
Sat May 11 15:46:59 CEST 2019
Dear Ask
On 11 May 2019, at 11:49, Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>> wrote:
Dear Andrew,
Am Fr., 10. Mai 2019 um 09:51 Uhr schrieb Andrew Logsdail via
ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>:
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://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%7Cc39abe27de0f4d06a9a208d6d5fe5e44%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=S27tc8u9HqCYelAXk3mpuvmL6BoFVUtfV09wYG4KJv0%3D&reserved=0 (too big for mailing list; it’d be good to have this on the examples page for LAMMPS maybe?).
I use the lammps package provided by Debian, but it does not come with
lammpslib so I have never tested it. How exactly does the
installation work?
Good question, and not one I can easily answer; What exactly do you mean by “how does it work”? I’ve been primarily led by the ASE guide notes and my own sys admin so far (who provided the work test harness) - I have contacted the LAMMPS mailing list, but as the calculation works with the test harness this was deemed probably an ASE LAMMPSlib issue, rather than that of the LAMMPS Python library.
All the best,
Andy
Best regards
Ask
I look forward to your feedback.
Andy
—
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: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flogsdail.github.io&data=01%7C01%7CLogsdailA%40cardiff.ac.uk%7Cc39abe27de0f4d06a9a208d6d5fe5e44%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=QvZ0OQ5%2FGeHK3XLv0J6uIMaw9TgN6TrWH9swy1Ibj1g%3D&reserved=0
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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: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flogsdail.github.io&data=01%7C01%7CLogsdailA%40cardiff.ac.uk%7Cc39abe27de0f4d06a9a208d6d5fe5e44%7Cbdb74b3095684856bdbf06759778fcbc%7C1&sdata=QvZ0OQ5%2FGeHK3XLv0J6uIMaw9TgN6TrWH9swy1Ibj1g%3D&reserved=0
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The University welcomes correspondence in Welsh or English.
Mae'r Brifysgol yn croesawu gohebiaeth yn Gymraeg neu'n Saesneg.
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—
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
The University welcomes correspondence in Welsh or English.
Mae'r Brifysgol yn croesawu gohebiaeth yn Gymraeg neu'n Saesneg.
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