-------------------------------------------------------------------------- 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: c401-054 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c401-054 Local device: hfi1_0 -------------------------------------------------------------------------- Traceback (most recent call last): File "../../td/TriclinicPBCEnergyAndForces__TD_892847239811_003/runner", line 45, 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', 'isolated_atom.lammps.Si.in']' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "../../td/TriclinicPBCEnergyAndForces__TD_892847239811_003/runner", line 207, in isolated_atom_energies[symbol] = get_isolated_atom_energy( File "../../td/TriclinicPBCEnergyAndForces__TD_892847239811_003/runner", line 71, in get_isolated_atom_energy run_lammps(templated_input, lammps_output) File "../../td/TriclinicPBCEnergyAndForces__TD_892847239811_003/runner", line 55, 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: /work2/08773/bwaters/stampede2/bwaters/job-07b2b70e-1c6f-4ef1-8318-18da6e7a886b-007-67f4351f-79ee-42ca-9446-fcfa86874a6e/TE_068509008767_003-and-SM_154093256665_000-1688584357/staged_job_files/repository/mo # 3: /home1/08773/bwaters/.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: /work2/08773/bwaters/stampede2/bwaters/job-07b2b70e-1c6f-4ef1-8318-18da6e7a886b-007-67f4351f-79ee-42ca-9446-fcfa86874a6e/TE_068509008767_003-and-SM_154093256665_000-1688584357/staged_job_files/repository/sm # 3: /home1/08773/bwaters/.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 create_atoms 1 single 0.0 0.0 0.0 Created 1 atoms using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25) create_atoms CPU = 0.000 seconds 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 ${_u_distance} remap change_box all x scale 1 y scale 1 z scale 1 remap Changing box ... orthogonal box = (-25 -25 -25) to (25 25 25) orthogonal box = (-25 -25 -25) to (25 25 25) orthogonal box = (-25 -25 -25) to (25 25 25) variable mass_converted equal 28.0855*${_u_mass} variable mass_converted equal 28.0855*1 mass 1 ${mass_converted} mass 1 28.0855 atom_modify sort 0 0 kim interactions Si #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 0 if "${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 ${kim_cutoff} pair_style buck/coul/cut 10.0 86.6025403784439 set type 1 charge 2.4 Setting atom values ... 1 settings made for charge #=== END kim interactions ==================================== # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*${_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" thermo_style custom v_pe_metal run 0 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: No fixes with time integration, atoms won't move (src/verlet.cpp:60) ERROR: All pair coeffs are not set (src/pair.cpp:246) Last command: run 0 Command exited with non-zero status 1 {"realtime":4.85,"usertime":3.51,"systime":10.43,"memmax":62408,"memavg":0}