Dear Mailing List,
I’m having some problems with running LAMMPS on more than 8 cpus and am hoping for your help. I’m using the python interface with ASE, running the exact example script given on the ASE webpage:
https://wiki.fysik.dtu.dk/ase/ase/calculators/lammps.html#ase.calculators.lammpslib.LAMMPSlib
(An example of the LAMMPS input that is effectively run is given just below the ASE python example on this page). Note this is just a static potential energy calculation, not a dynamic simulation.
The behaviour is as I expect until up to 8 CPUs, despite the following warning because this is only a 5-atom system:
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
However, beyond 8 CPUs I get a seemingly common problem of “Lost atoms”, an example being:
ERROR: Lost atoms: original 5 current 4 (src/thermo.cpp:441)
Given this is a small test system, I thought this was just a domain decomposition problem but if I create a 10x10x10 supercell - so 4001 atoms (1 H dopant in Ni) - I still get exactly the same problem of “Lost Atoms” on >8 CPUs.
Can anyone offer any advice what I might be doing wrong, or ways to isolate the cause of this problem? My executable is managed by a sys admin, built with intel 2018/2 and using Python3.7.0. Attached are the input.py, EAM potential, example submission script and a range of labelled outputs. Thanks in advance for any help you can offer!
All the best,
Andy
input.py (455 Bytes)
input.py (455 Bytes)
16cpu.supercell.log (111 KB)
8cpu.supercell.log (112 KB)
16cpu.default.log (1.77 KB)
8cpu.default.log (2.63 KB)
1cpu.default.log (2.59 KB)
lammps.ase.submission.script.txt (648 Bytes)
NiAlH_jea.eam.alloy.txt (287 KB)