-------------------------------------------------------------------------- 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 is at least non-excluded one OpenFabrics device found, but there are no active ports detected (or Open MPI was unable to use them). This is most certainly not what you wanted. Check your cables, subnet manager configuration, etc. The openib BTL will be ignored for this job. Local host: c002 -------------------------------------------------------------------------- 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-89658c66-c6f2-431f-b547-48fbf0326f74-007-ad2dabee-5d33-4c94-b09c-a7018603e241/TE_362002298404_003-and-SM_154093256665_000-1689700548/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-89658c66-c6f2-431f-b547-48fbf0326f74-007-ad2dabee-5d33-4c94-b09c-a7018603e241/TE_362002298404_003-and-SM_154093256665_000-1689700548/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 ${boxextent} region box block -25 25 -25 25 -25 25 create_box 1 box Created orthogonal box = (-25 -25 -25) to (25 25 25) 1 by 1 by 1 MPI processor grid read_dump output/lammps_inputs/cluster.xyz 0 x y z box no add yes format xyz Scanning dump file ... Reading snapshot from dump file ... orthogonal box = (-25 -25 -25) to (25 25 25) 0 atoms before read 5 atoms in snapshot 0 atoms purged 0 atoms replaced 0 atoms trimmed 5 atoms added 5 atoms after read group all region box 5 atoms in group all variable mass1_converted equal 28.0855*${_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 ${kim_cutoff} pair_style buck/coul/cut 10.0 86.6025403784439 set type 1 charge 2.4 Setting atom values ... 5 settings made for charge pair_coeff 1 1 0.0 1.00000 0.00 #=== END kim interactions ==================================== # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*${_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) = 6.156 | 6.156 | 6.156 Mbytes v_pe_metal 327.52576 ERROR: Lost atoms: original 5 current 1 (src/thermo.cpp:481) Last command: minimize 1e-10 ${ftol} 2000 100000 Command exited with non-zero status 1 {"realtime":3.76,"usertime":1.22,"systime":5.00,"memmax":58920,"memavg":0}