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I used LAMMPS to simulate the thermal conductance for Al2O3/bilayer graphene/Al2O3 system along the z axis. This is my input file.

variable         kb equal 8.617333262e-5
variable         t equal 300.0
variable         th equal 400.0
variable         tc equal 200.0

units            metal
dimension        3
newton           on
boundary         p p p
atom_style       atomic
neighbor         0.3 bin
timestep         0.0005

read_data        atomic_structure_atomic

pair_style       hybrid vashishta lj/cut 12.0 airebo 3.0
pair_coeff       * * vashishta ./Al2O3.vashishta O Al NULL NULL
pair_coeff       * * airebo ./CH.airebo NULL NULL C C
pair_coeff       1 3 lj/cut 0.006199133907248657 3.692748434432002
pair_coeff       1 4 lj/cut 0.006199133907248657 3.692748434432002
pair_coeff       2 3 lj/cut 0.042256836241015484 3.1764162195782846
pair_coeff       2 4 lj/cut 0.042256836241015484 3.1764162195782846

compute          ke1 all ke/atom
variable         tem atom c_ke1/1.5/${kb}

thermo           1000
thermo_style     custom step temp pxx pyy pzz press vol
velocity         all create $t 898758 mom yes rot yes dist gaussian

min_style        cg
minimize         1.0e-8 1.0e-8 1000000 1000000

#1st euqilibrium in NPT ensamble
thermo           2000
thermo_style     custom step temp pe ke etotal vol pxx pyy pzz press
fix              1 all npt temp $t $t 0.05 aniso 0.0 0.0 0.5
dump             xyz_npt all xyz 1000 dump_npt.xyz
dump_modify      xyz_npt element O Al C1 C2
run              1000000
unfix            1
undump           xyz_npt
reset_timestep   0
write_data       atomic_structure_atomic_npt.dat

#2nd equilibrium in NVT ensamble
thermo           2000
thermo_style     custom temp pe ke etotal vol pxx pyy pzz press
fix              2 all nvt temp $t $t 0.05
dump             xyz_nvt all xyz 1000 dump_nvt.xyz
dump_modify      xyz_nvt element O Al C1 C2
run              1000000
unfix            2
undump           xyz_nvt
reset_timestep   0

#Dividing the zone
variable         zbl equal zlo
variable         zbh equal zhi
variable         nla equal 100
variable         sca equal 1/${nla}
variable         len equal ${zbh}-${zbl}
variable         dz equal ${len}/${nla}
variable         zll equal ${zbl}+${dz}*2
variable         zlh equal ${zb1}+${dz}*6
variable         zrl equal ${zbh}-${dz}*6
variable         zrh equal ${zbh}-${dz}*2

region           reg_whole block INF INF INF INF ${zbl} ${zbh} units box
region           lef_fixed INF INF INF INF INF ${zll} units box
region           hot INF INF INF INF ${zll} ${zlh} units box
region           cold INF INF INF INF ${zrl} ${zrh} units box
region           rig_fixed INF INF INF INF ${zrh} INF units box
region           fixed_both union 2 lef_fixed rig_fixed

group            fixed region fixed_both
group            hot region hot
group            cold region cold
group            move subtract all fixed

reset_timestep   0
change_box       p p f

velocity         fixed set 0 0 0
fix              fixed setforce 0 0 0

fix              3 hot langevin ${th} ${th} 0.05 14565 tally yes
fix              4 cold langevin ${tc} ${tc} 0.05 16576 tally yes
fix              5 nve

variable         time equal step
variable         el euqal f_3
variable         er equal f_4

compute          6 all chunk/atom bin/1d z lower ${sca} units reduced
fix              7 all ave/chunk 1 10000 10000 6 v_tem file profile.heat
thermo           2000
thermo_style     custom step temp ke pe etotal press vol
dump             xyz_nve all xyz 1000 dump_nve.xyz
dump_modify      xyz_nve element O Al C1 C2
run              1000000
unfix            7
undump           xyz_nve
reset_timestep   0

fix              8 all ave/chunk 1 10000 10000 6 v_tem file temperature_gredient.dat
fix              eou all print 2000 "${time} ${el} ${er}" file temperature_gredient.dat title "time e1 e2" screen no

thermo           20000
thermo_style     custom step temp ke pe etotal press vol
dump             fin all xyz 20000 fin.xyz
dump_modify      fin element O Al C1 C2
run              2000000

I obtained the following error after I submitted the calculation.

 299.30383     -174318.63      595.75739     -173722.87      99637.124     -3469.2289     -479.26552     -2156.3056     -2034.9333    
 302.72636     -174314.62      602.56985     -173712.05      99637.124     -1293.513      -605.78596     -397.50975     -765.60289    
 297.54946     -174317.68      592.26534     -173725.42      99637.124     -1100.3677     -1671.4191      2695.0301     -25.585573    
Loop time of 10326 on 96 procs for 1000000 steps with 15400 atoms

Performance: 4.184 ns/day, 5.737 hours/ns, 96.843 timesteps/s, 1.491 Matom-step/s
99.1% CPU use with 96 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 296.47     | 2906.7     | 3647.8     |1460.4 | 28.15
Neigh   | 1649.1     | 4300.4     | 5259.4     |1511.1 | 41.65
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 12 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.
--------------------------------------------------------------------------
......
......
......
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 63 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.
--------------------------------------------------------------------------
slurmstepd: error: *** STEP 16827695.0 ON b08r4n08 CANCELLED AT 2024-04-26T23:22:37 ***
Comm    | 650.83     | 2241.6     | 7537srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error:  mpi/pmix_v3: _errhandler: b08r4n08 [0]: pmixp_client_v2.c:211: Error handler invoked: status = -25, source = [slurm.pmix.16827695.0:0]
slurmstepd: error:  mpi/pmix_v3: _errhandler: b08r4n09 [1]: pmixp_client_v2.c:211: Error handler invoked: status = -25, source = [slurm.pmix.16827695.0:43]
slurmstepd: error:  mpi/pmix_v3: _errhandler: b08r4n10 [2]: pmixp_client_v2.c:211: Error handler invoked: status = -25, source = [slurm.pmix.16827695.0:64]
srun: error: b08r4n10: tasks 64-95: Killed
srun: launch/slurm: _step_signal: Terminating StepId=16827695.0
srun: error: b08r4n08: task 0: Exited with exit code 1
srun: error: b08r4n08: tasks 1-31: Killed
srun: error: b08r4n09: tasks 32-63: Killed

I checked the log.lammps file and found that the '#2nd equilibrium in NVT ensamble' in my input file was done; then, the error popped up.

Would anyone please help me revise my input file?

Thank you in advance.

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    $\begingroup$ Others may add more detail, but this looks like a slurm abort rather than a LAMMPS issue. The first things I would check is whether the slurm job ran out of time or out of memory. You can test this by running the same LAMMPS input but on a smaller structure and with fewer steps in each run to see if the job finishes properly. $\endgroup$ Commented Apr 26 at 16:45
  • $\begingroup$ @Andrey Poletayev Thank you for your suggestion. I am checking it again. $\endgroup$
    – Kieran
    Commented Apr 27 at 3:31

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