Runtime error in the calculation

[HWLee]

Hi,

I'm trying to calculate PDOS and FatBandstructure with the Planewave calculator in the 114 atoms system.
I added about 15 angstroms for each end, and set the boundary conditions as Neumann/Neumann.
The cutoff is 50 Hartree & I turned on the DFT-D3 correction since its the 2-D materials system.

I was running a calculation on a node with 1 TB of memory, and the calculation stopped in calculating PDOS step with the following error.

______________________________________________________
  File "/opt/synopsys/5.6/tool/QuantumATK/QuantumATK-U-2022.12-SP1/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 879, in __run_atkpython
  File "/home/HW1/QuantumATK/Output/out_WTe2-MoS2/Heterostructure/231119_new_calculation/MoS2+WTe2/PW/PW_MoS2+WTe2_cutoff_50_process_2_231203_EGisbHS4/PW_MoS2+WTe2_cutoff_50_process_2.py", line 272, in <module>
    projected_density_of_states = ProjectedDensityOfStates(
  File "zipdir/NL/Analysis/ProjectedDensityOfStates.py", line 350, in __init__
  File "zipdir/NL/Calculators/DensityFunctionalTheory/PlaneWaveCalculator/Analysis/EigenvaluesAndProjectionWeights.py", line 531, in calculateEigenvaluesAndProjectionWeightsPW
  File "zipdir/NL/Calculators/DensityFunctionalTheory/PlaneWaveCalculator/Analysis/EigensolutionsCalculator.py", line 307, in calculate
  File "zipdir/NL/Calculators/DensityFunctionalTheory/PlaneWaveCalculator/Analysis/EigensolutionsCalculator.py", line 353, in _performKpointTask
  File "zipdir/NL/Calculators/DensityFunctionalTheory/PlaneWaveCalculator/Analysis/EigensolutionsCalculator.py", line 471, in _findEigensolutions
  File "zipdir/NLEngine.py", line 8533, in findEigensolutions
RuntimeError:
** Back Engine Exception : [See the MPI_ERROR field in MPI_Status for the error code] See the MPI_ERROR field in MPI_Status for the error code
** Location of Exception : baseplanewavebasis.cpp:497


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
______________________________________________________

Have you ever encountered any of these errors? and how can I fix them?




The whole input file is as follows:

# %% BulkConfiguration_0

# Set up lattice
vector_a = [10.5579, 0.0, 0.0]*Angstrom
vector_b = [0.0, 6.30359, 0.0]*Angstrom
vector_c = [0.0, 0.0, 70.0]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
...

# Define coordinates
...

# Set up configuration
bulkconfiguration_0 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# Add tags
...


# %% Set PlaneWaveCalculator (1)

# %% PlaneWaveCalculator

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE

correction_extension = GrimmeDFTD3(
    exchange_correlation=exchange_correlation
)

k_point_sampling = MonkhorstPackGrid(
    na=3,
    nb=4,
    nc=1
)

numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=k_point_sampling
)

poisson_solver = MultigridSolver(
    boundary_conditions=[
        [PeriodicBoundaryCondition(), PeriodicBoundaryCondition()],
        [PeriodicBoundaryCondition(), PeriodicBoundaryCondition()],
        [NeumannBoundaryCondition(), NeumannBoundaryCondition()]
    ]
)

checkpoint_handler = NoCheckpointHandler

calculator = PlaneWaveCalculator(
    wave_function_cutoff=50.0*Hartree,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    poisson_solver=poisson_solver,
    correction_extension=correction_extension,
    checkpoint_handler=checkpoint_handler,
    processes_per_kpoint=2
)

nlsave('BulkConfiguration_0_2_results.hdf5', calculator)


# %% Set Calculator

bulkconfiguration_0.setCalculator(calculator)

bulkconfiguration_0.update()

nlsave('BulkConfiguration_0_2_results.hdf5', bulkconfiguration_0)


# %% TotalEnergy (4)

total_energy = TotalEnergy(
    configuration=bulkconfiguration_0
)
nlsave('BulkConfiguration_0_2_results.hdf5', total_energy)


# %% EffectivePotential (4)

effective_potential = EffectivePotential(
    configuration=bulkconfiguration_0
)
nlsave('BulkConfiguration_0_2_results.hdf5', effective_potential)


# %% ChemicalPotential (2)

chemical_potential = ChemicalPotential(
    configuration=bulkconfiguration_0
)
nlsave('BulkConfiguration_0_2_results.hdf5', chemical_potential)


# %% ElectronDensity (3)

electron_density = ElectronDensity(
    configuration=bulkconfiguration_0
)
nlsave('BulkConfiguration_0_2_results.hdf5', electron_density)


# %% ProjectedDensityOfStates

kpoints = MonkhorstPackGrid(
    na=3,
    nb=4,
    nc=1
)

projected_density_of_states = ProjectedDensityOfStates(
    configuration=bulkconfiguration_0,
    kpoints=kpoints,
    projections=ProjectOnTags,
    energies=numpy.linspace(-2.0, 2.0, 2001)*eV
)
nlsave('BulkConfiguration_0_2_results.hdf5', projected_density_of_states)


# %% FatBandstructure

fat_bandstructure = FatBandstructure(
    configuration=bulkconfiguration_0,
    route=('G', 'X', 'C', 'Y', 'G', 'C'),
    points_per_segment=50,
    projections=ProjectOnTags
)
nlsave('BulkConfiguration_0_2_results.hdf5', fat_bandstructure)

[filipr]

That is a weird and rare error. Could be due to a network or system failure. Try to run the calculation again and see if it runs through. If it is reproducible it would be helpful if you could run it a third time but with the environment variable I_MPI_DEBUG=5 set, i.e. in your submission script before atkpython is executed you insert

Code

export I_MPI_DEBUG=5

this will print some MPI debug information to the log file that would be valuable for us to see.

[HWLee]

I appreciate your reply.

I'll retry the calculation and then update it.

[Sakthi@07]

Can you send me the MPI debug information line, included the script file?