-------------------------------------------------------------------------- By default, for Open MPI 4.0 and later, infiniband ports on a device are not used by default. The intent is to use UCX for these devices. You can override this policy by setting the btl_openib_allow_ib MCA parameter to true. Local host: c002 Local adapter: mlx5_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c002 Local device: mlx5_0 -------------------------------------------------------------------------- -------------------------------------------------------------------------- By default, for Open MPI 4.0 and later, infiniband ports on a device are not used by default. The intent is to use UCX for these devices. You can override this policy by setting the btl_openib_allow_ib MCA parameter to true. Local host: c002 Local adapter: mlx5_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c002 Local device: mlx5_0 -------------------------------------------------------------------------- Traceback (most recent call last): File "../../td/ClusterEnergyAndForces__TD_000043093022_003/runner", line 46, in run_lammps lammps_process = subprocess.check_call( File "/usr/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['lammps', '-in', 'output/lammps_inputs/main.lammps.tpl']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "../../td/ClusterEnergyAndForces__TD_000043093022_003/runner", line 256, in run_lammps(infile, logfile) File "../../td/ClusterEnergyAndForces__TD_000043093022_003/runner", line 56, in run_lammps raise Exception("LAMMPS did not exit properly:\n" + extrainfo) Exception: LAMMPS did not exit properly: LAMMPS (23 Jun 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task kim init Sim_LAMMPS_Buckingham_FreitasSantosColaco_2015_SiCaOAl__SM_154093256665_000 metal unit_conversion_mode #=== KIM is looking for 'Portable Models' in these directories === # 1: . # 2: /mmfs1/scratch/bwaters2/bwaters/job-9f6ddc71-1f52-4827-bd37-485b1f3b8ccb-007-57ba88df-9629-4fb3-b64d-b826ae0efdbe/TE_449294764291_003-and-SM_154093256665_000-1689700543/staged_job_files/repository/mo # 3: /home/bwaters2/.kim-api/2.3.0+GNU.GNU.GNU.2023-06-29-17-15-23/portable-models-dir # 4: /usr/local/lib/kim-api/portable-models #=== KIM is looking for 'Simulator Models' in these directories === # 1: . # 2: /mmfs1/scratch/bwaters2/bwaters/job-9f6ddc71-1f52-4827-bd37-485b1f3b8ccb-007-57ba88df-9629-4fb3-b64d-b826ae0efdbe/TE_449294764291_003-and-SM_154093256665_000-1689700543/staged_job_files/repository/sm # 3: /home/bwaters2/.kim-api/2.3.0+GNU.GNU.GNU.2023-06-29-17-15-23/simulator-models-dir # 4: /usr/local/lib/kim-api/simulator-models #=== BEGIN kim init ========================================== # Using KIM Simulator Model : Sim_LAMMPS_Buckingham_FreitasSantosColaco_2015_SiCaOAl__SM_154093256665_000 # For Simulator : LAMMPS 8 Feb 2023 # Running on : LAMMPS 23 Jun 2022 # # Conversion factors from metal to metal: variable _u_mass internal 1.000000000000e+00 variable _u_distance internal 1.000000000000e+00 variable _u_time internal 1.000000000000e+00 variable _u_energy internal 1.000000000000e+00 variable _u_velocity internal 1.000000000000e+00 variable _u_force internal 1.000000000000e+00 variable _u_torque internal 1.000000000000e+00 variable _u_temperature internal 1.000000000000e+00 variable _u_pressure internal 1.000000000000e+00 variable _u_viscosity internal 1.000000000000e+00 variable _u_charge internal 1.000000000000e+00 variable _u_dipole internal 1.000000000000e+00 variable _u_efield internal 1.000000000000e+00 variable _u_density internal 1.000000000000e+00 # units metal neighbor 2.0 bin # Angstroms timestep 1.0e-3 # picoseconds atom_style charge neigh_modify one 4000 #=== END kim init ============================================ boundary f f f variable boxextent equal 25.0 region box block -${boxextent} ${boxextent} -${boxextent} ${boxextent} -${boxextent} ${boxextent} region box block -25 ${boxextent} -${boxextent} ${boxextent} -${boxextent} ${boxextent} region box block -25 25 -${boxextent} ${boxextent} -${boxextent} ${boxextent} region box block -25 25 -25 ${boxextent} -${boxextent} ${boxextent} region box block -25 25 -25 25 -${boxextent} ${boxextent} region box block -25 25 -25 25 -25 ${boxextent} region box block -25 25 -25 25 -25 25 create_box 1 box Created orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid read_dump output/lammps_inputs/cluster.xyz 0 x y z box no add yes format xyz Scanning dump file ... Reading snapshot from dump file ... orthogonal box = (-25 -25 -25) to (25 25 25) 0 atoms before read 3 atoms in snapshot 0 atoms purged 0 atoms replaced 0 atoms trimmed 3 atoms added 3 atoms after read group all region box 3 atoms in group all variable mass1_converted equal 28.0855*${_u_mass} variable mass1_converted equal 28.0855*1 mass 1 ${mass1_converted} mass 1 28.0855 change_box all x scale ${_u_distance} y scale ${_u_distance} z scale ${_u_distance} remap change_box all x scale 1 y scale ${_u_distance} z scale ${_u_distance} remap change_box all x scale 1 y scale 1 z scale ${_u_distance} remap change_box all x scale 1 y scale 1 z scale 1 remap Changing box ... orthogonal box = (-25 -25 -25) to (25 25 25) orthogonal box = (-25 -25 -25) to (25 25 25) orthogonal box = (-25 -25 -25) to (25 25 25) atom_modify sort 0 0 kim interactions Si #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 0 if "${kim_periodic} != 0" then "pair_style buck/coul/long 10.0" if "${kim_periodic} != 0" then "kspace_style pppm 1.0e-5" if "${kim_periodic} == 0" then "kspace_style none" kspace_style none if "${kim_periodic} == 2" then "kspace_modify slab 3.0" if "${kim_periodic} == 0" then "variable kim_cutoff equal ((lx+xy+xz)^2+(ly+yz)^2+(lz)^2)^(1/2)" variable kim_cutoff equal ((lx+xy+xz)^2+(ly+yz)^2+(lz)^2)^(1/2) if "${kim_periodic} == 0" then "pair_style buck/coul/cut 10.0 ${kim_cutoff}" pair_style buck/coul/cut 10.0 ${kim_cutoff} pair_style buck/coul/cut 10.0 86.6025403784439 set type 1 charge 2.4 Setting atom values ... 3 settings made for charge pair_coeff 1 1 0.0 1.00000 0.00 #=== END kim interactions ==================================== # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} nsq neighbor 2 nsq # Variables used to rescale the positions and forces so that the quantities in the # dumpfile are in the original metal units (angstrom and eV/angstrom) even if we're # running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable x_metal atom x/${_u_distance} variable x_metal atom x/1 variable y_metal atom y/${_u_distance} variable y_metal atom y/1 variable z_metal atom z/${_u_distance} variable z_metal atom z/1 variable fx_metal atom fx/${_u_force} variable fx_metal atom fx/1 variable fy_metal atom fy/${_u_force} variable fy_metal atom fy/1 variable fz_metal atom fz/${_u_force} variable fz_metal atom fz/1 dump dumpid all custom 1 output/lammps_dump/lammps.dump id type v_x_metal v_y_metal v_z_metal v_fx_metal v_fy_metal v_fz_metal dump_modify dumpid sort id format line "%d %d %16.7f %16.7f %16.7f %16.7f %16.7f %16.7f" thermo_style custom v_pe_metal # Define minimization (note that etol is actually unitless, but ftol has units of force) min_style cg variable dmax equal 0.1*${_u_distance} variable dmax equal 0.1*1 min_modify dmax ${dmax} min_modify dmax 0.1 variable ftol equal 1e-10*${_u_force} variable ftol equal 1e-10*1 minimize 1e-10 ${ftol} 2000 100000 minimize 1e-10 1e-10 2000 100000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/SM_154093256665_000#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 88.60254 ghost atom cutoff = 88.60254 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair buck/coul/cut, perpetual attributes: half, newton on pair build: half/nsq/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 6.155 | 6.155 | 6.155 Mbytes v_pe_metal 103.31368 ERROR: Lost atoms: original 3 current 1 (src/thermo.cpp:481) Last command: minimize 1e-10 ${ftol} 2000 100000 Command exited with non-zero status 1 {"realtime":3.45,"usertime":0.20,"systime":0.67,"memmax":57300,"memavg":0}