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October 18, 2022 07:15
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Errors: MBX-0.7/plugins/lammps/examples/na+_bulk/1atm/298K
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(work) 298K > mpirun -np 2 lmp_mpi_mbx -in lammps.in | |
-------------------------------------------------------------------------- | |
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: login-0-0 | |
Local adapter: mlx4_0 | |
Local port: 1 | |
-------------------------------------------------------------------------- | |
-------------------------------------------------------------------------- | |
WARNING: There was an error initializing an OpenFabrics device. | |
Local host: login-0-0 | |
Local device: mlx4_0 | |
-------------------------------------------------------------------------- | |
LAMMPS (29 Sep 2021 - Update 3) | |
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) | |
using 1 OpenMP thread(s) per MPI task | |
Reading data file ... | |
orthogonal box = (-0.040444797 -0.040444797 -0.040444797) to (20.348405 20.348405 20.348405) | |
1 by 1 by 2 MPI processor grid | |
reading atoms ... | |
832 atoms | |
reading velocities ... | |
832 velocities | |
scanning bonds ... | |
2 = max bonds/atom | |
scanning angles ... | |
1 = max angles/atom | |
reading bonds ... | |
554 bonds | |
reading angles ... | |
277 angles | |
Finding 1-2 1-3 1-4 neighbors ... | |
special bond factors lj: 0 0 0 | |
special bond factors coul: 0 0 0 | |
2 = max # of 1-2 neighbors | |
1 = max # of 1-3 neighbors | |
1 = max # of 1-4 neighbors | |
2 = max # of special neighbors | |
special bonds CPU = 0.000 seconds | |
read_data CPU = 0.022 seconds | |
ERROR on proc 1: Unsupported molecule type in MBX (../fix_mbx.cpp:2312) | |
Last command: fix 2 all mbx 2 1 na 277 h2o json mbx.json | |
ERROR on proc 0: Unsupported molecule type in MBX (../fix_mbx.cpp:2312) | |
Last command: fix 2 all mbx 2 1 na 277 h2o json mbx.json | |
-------------------------------------------------------------------------- | |
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD | |
with errorcode 1. | |
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. | |
You may or may not see output from other processes, depending on | |
exactly when Open MPI kills them. | |
-------------------------------------------------------------------------- | |
[login-0-0.um.edu.mo:300915] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2079 | |
[login-0-0.um.edu.mo:300915] 1 more process has sent help message help-mpi-btl-openib.txt / ib port not selected | |
[login-0-0.um.edu.mo:300915] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages | |
[login-0-0.um.edu.mo:300915] 1 more process has sent help message help-mpi-btl-openib.txt / error in device init | |
[login-0-0.um.edu.mo:300915] 1 more process has sent help message help-mpi-api.txt / mpi-abort |
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