-------------------------------------------------------------------------- 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: c402-101 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c402-101 Local device: hfi1_0 -------------------------------------------------------------------------- -------------------------------------------------------------------------- A call to mkdir was unable to create the desired directory: Directory: /tmp/ompi.c402-101.870522/pid.72230 Error: No such file or directory Please check to ensure you have adequate permissions to perform the desired operation. -------------------------------------------------------------------------- [c402-101.stampede2.tacc.utexas.edu:72230] [[52457,0],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 107 [c402-101.stampede2.tacc.utexas.edu:72230] [[52457,0],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 346 -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_session_dir failed --> Returned value Error (-1) instead of ORTE_SUCCESS -------------------------------------------------------------------------- [c402-101.stampede2.tacc.utexas.edu:72192] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 716 [c402-101.stampede2.tacc.utexas.edu:72192] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 172 -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_init failed --> Returned value Unable to start a daemon on the local node (-127) instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: ompi_rte_init failed --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0) -------------------------------------------------------------------------- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [c402-101.stampede2.tacc.utexas.edu:72192] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! 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 (30 Jul 2021) 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 EDIP_LAMMPS_LucasBertolusPizzagalli_2009_SiC__MO_634310164305_000 metal unit_conversion_mode #=== BEGIN kim init ========================================== # 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 This model has 136 mutable parameters. No. | Parameter name | data type | extent ----------------------------------------------------- 1 | A_SiSiSi | "Double" | 1 2 | B_SiSiSi | "Double" | 1 3 | cutoffA_SiSiSi | "Double" | 1 4 | cutoffC_SiSiSi | "Double" | 1 5 | alpha_SiSiSi | "Double" | 1 6 | beta_SiSiSi | "Double" | 1 7 | sigma_SiSiSi | "Double" | 1 8 | rho_SiSiSi | "Double" | 1 9 | gamma_SiSiSi | "Double" | 1 10 | eta_SiSiSi | "Double" | 1 11 | lambda_SiSiSi | "Double" | 1 12 | mu_SiSiSi | "Double" | 1 13 | Q0_SiSiSi | "Double" | 1 14 | u1_SiSiSi | "Double" | 1 15 | u2_SiSiSi | "Double" | 1 16 | u3_SiSiSi | "Double" | 1 17 | u4_SiSiSi | "Double" | 1 18 | A_SiSiC | "Double" | 1 19 | B_SiSiC | "Double" | 1 20 | cutoffA_SiSiC | "Double" | 1 21 | cutoffC_SiSiC | "Double" | 1 22 | alpha_SiSiC | "Double" | 1 23 | beta_SiSiC | "Double" | 1 24 | sigma_SiSiC | "Double" | 1 25 | rho_SiSiC | "Double" | 1 26 | gamma_SiSiC | "Double" | 1 27 | eta_SiSiC | "Double" | 1 28 | lambda_SiSiC | "Double" | 1 29 | mu_SiSiC | "Double" | 1 30 | Q0_SiSiC | "Double" | 1 31 | u1_SiSiC | "Double" | 1 32 | u2_SiSiC | "Double" | 1 33 | u3_SiSiC | "Double" | 1 34 | u4_SiSiC | "Double" | 1 35 | A_SiCSi | "Double" | 1 36 | B_SiCSi | "Double" | 1 37 | cutoffA_SiCSi | "Double" | 1 38 | cutoffC_SiCSi | "Double" | 1 39 | alpha_SiCSi | "Double" | 1 40 | beta_SiCSi | "Double" | 1 41 | sigma_SiCSi | "Double" | 1 42 | rho_SiCSi | "Double" | 1 43 | gamma_SiCSi | "Double" | 1 44 | eta_SiCSi | "Double" | 1 45 | lambda_SiCSi | "Double" | 1 46 | mu_SiCSi | "Double" | 1 47 | Q0_SiCSi | "Double" | 1 48 | u1_SiCSi | "Double" | 1 49 | u2_SiCSi | "Double" | 1 50 | u3_SiCSi | "Double" | 1 51 | u4_SiCSi | "Double" | 1 52 | A_SiCC | "Double" | 1 53 | B_SiCC | "Double" | 1 54 | cutoffA_SiCC | "Double" | 1 55 | cutoffC_SiCC | "Double" | 1 56 | alpha_SiCC | "Double" | 1 57 | beta_SiCC | "Double" | 1 58 | sigma_SiCC | "Double" | 1 59 | rho_SiCC | "Double" | 1 60 | gamma_SiCC | "Double" | 1 61 | eta_SiCC | "Double" | 1 62 | lambda_SiCC | "Double" | 1 63 | mu_SiCC | "Double" | 1 64 | Q0_SiCC | "Double" | 1 65 | u1_SiCC | "Double" | 1 66 | u2_SiCC | "Double" | 1 67 | u3_SiCC | "Double" | 1 68 | u4_SiCC | "Double" | 1 69 | A_CSiSi | "Double" | 1 70 | B_CSiSi | "Double" | 1 71 | cutoffA_CSiSi | "Double" | 1 72 | cutoffC_CSiSi | "Double" | 1 73 | alpha_CSiSi | "Double" | 1 74 | beta_CSiSi | "Double" | 1 75 | sigma_CSiSi | "Double" | 1 76 | rho_CSiSi | "Double" | 1 77 | gamma_CSiSi | "Double" | 1 78 | eta_CSiSi | "Double" | 1 79 | lambda_CSiSi | "Double" | 1 80 | mu_CSiSi | "Double" | 1 81 | Q0_CSiSi | "Double" | 1 82 | u1_CSiSi | "Double" | 1 83 | u2_CSiSi | "Double" | 1 84 | u3_CSiSi | "Double" | 1 85 | u4_CSiSi | "Double" | 1 86 | A_CSiC | "Double" | 1 87 | B_CSiC | "Double" | 1 88 | cutoffA_CSiC | "Double" | 1 89 | cutoffC_CSiC | "Double" | 1 90 | alpha_CSiC | "Double" | 1 91 | beta_CSiC | "Double" | 1 92 | sigma_CSiC | "Double" | 1 93 | rho_CSiC | "Double" | 1 94 | gamma_CSiC | "Double" | 1 95 | eta_CSiC | "Double" | 1 96 | lambda_CSiC | "Double" | 1 97 | mu_CSiC | "Double" | 1 98 | Q0_CSiC | "Double" | 1 99 | u1_CSiC | "Double" | 1 100 | u2_CSiC | "Double" | 1 101 | u3_CSiC | "Double" | 1 102 | u4_CSiC | "Double" | 1 103 | A_CCSi | "Double" | 1 104 | B_CCSi | "Double" | 1 105 | cutoffA_CCSi | "Double" | 1 106 | cutoffC_CCSi | "Double" | 1 107 | alpha_CCSi | "Double" | 1 108 | beta_CCSi | "Double" | 1 109 | sigma_CCSi | "Double" | 1 110 | rho_CCSi | "Double" | 1 111 | gamma_CCSi | "Double" | 1 112 | eta_CCSi | "Double" | 1 113 | lambda_CCSi | "Double" | 1 114 | mu_CCSi | "Double" | 1 115 | Q0_CCSi | "Double" | 1 116 | u1_CCSi | "Double" | 1 117 | u2_CCSi | "Double" | 1 118 | u3_CCSi | "Double" | 1 119 | u4_CCSi | "Double" | 1 120 | A_CCC | "Double" | 1 121 | B_CCC | "Double" | 1 122 | cutoffA_CCC | "Double" | 1 123 | cutoffC_CCC | "Double" | 1 124 | alpha_CCC | "Double" | 1 125 | beta_CCC | "Double" | 1 126 | sigma_CCC | "Double" | 1 127 | rho_CCC | "Double" | 1 128 | gamma_CCC | "Double" | 1 129 | eta_CCC | "Double" | 1 130 | lambda_CCC | "Double" | 1 131 | mu_CCC | "Double" | 1 132 | Q0_CCC | "Double" | 1 133 | u1_CCC | "Double" | 1 134 | u2_CCC | "Double" | 1 135 | u3_CCC | "Double" | 1 136 | u4_CCC | "Double" | 1 #=== 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 = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) 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 = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) 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 ${_u_distance} remap change_box all x scale 1 y scale 1 z scale 1 remap Changing box ... orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) variable mass_converted equal 28.0855*${_u_mass} variable mass_converted equal 28.0855*1 mass 1 ${mass_converted} mass 1 28.0855 atom_modify sort 0 0 kim interactions Si #=== BEGIN kim interactions ================================== pair_style kim EDIP_LAMMPS_LucasBertolusPizzagalli_2009_SiC__MO_634310164305_000 pair_coeff * * Si #=== END kim interactions ==================================== # Use nsq neighlist method instead of binning since this is a small system variable neigh_skin equal 2.0*${_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/MO_634310164305_000#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.941586 ghost atom cutoff = 4.941586 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 4.941586 pair build: full/nsq stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 0.4051 | 0.4051 | 0.4051 Mbytes v_pe_metal 0 Loop time of 8.63e-06 on 1 procs for 0 steps with 1 atoms 81.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.63e-06 | | |100.00 Nlocal: 1.00000 ave 1 max 1 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0.0000000 Neighbor list builds = 0 Dangerous builds = 0 print "Isolated atom energy: ${pe_metal} eV" Isolated atom energy: 0 eV Total wall time: 0:00:00 Command exited with non-zero status 1 {"realtime":3.03,"usertime":3.30,"systime":10.42,"memmax":45376,"memavg":0}