Help error

[jdgayles16]

I am trying to relax under bias and i get this error.

Code

Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x2aab03087830, rbuf=0x2aab61adfe10, count=258, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(385)...............:
MPIDI_CH3U_Receive_data_found(129): Message from rank 5 and tag 14 truncated; 2000 bytes received but buffer size is 1024
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)..................: MPI_Allreduce(sbuf=0x2aab2e8fcd50, rbuf=0x2aaacfa7de10, count=258, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(385).................:
MPIC_Sendrecv(155)..................:
MPIDI_CH3U_Request_unpack_uebuf(600): Message truncated; 2000 bytes received but buffer size is 512
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x2aab03d80420, rbuf=0x2aab455a3fe0, count=258, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Allreduce(385)...............:
MPIDI_CH3U_Receive_data_found(129): Message from rank 6 and tag 14 truncated; 2000 bytes received but buffer size is 1040

[Nordland]

Hey.

Can you share your script with us? You can just send it to directly to QuantumWise, if it is a secret system

[jdgayles16]

here it is

Code

###############################################################
# Initial State
###############################################################
device_configuration = nlread('CGsupergap05.nc', object_id="gID000")[0]
 
 
###############################################################
# Calculator
###############################################################
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = GGABasis.DoubleZetaPolarized
 
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE
 
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=80.0*Rydberg,
    k_point_sampling=(1, 1, 100),
    )
 
right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=80.0*Rydberg,
    k_point_sampling=(1, 1, 100),
    )
 
device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=80.0*Rydberg,
    )
 
#----------------------------------------
# Iteration Control Settings
#----------------------------------------
left_electrode_iteration_control_parameters = IterationControlParameters(
    tolerance=1e-05,
    )
 
right_electrode_iteration_control_parameters = IterationControlParameters(
    tolerance=1e-05,
    )
 
device_iteration_control_parameters = IterationControlParameters(
    tolerance=1e-05,
    )
 
#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    iteration_control_parameters=left_electrode_iteration_control_parameters,
    )
 
right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    iteration_control_parameters=right_electrode_iteration_control_parameters,
    )
 
#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    iteration_control_parameters=device_iteration_control_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.5*Volt, 0.0*Volt)
    )
 
 
device_configuration = OptimizeGeometry(
        device_configuration,
        maximum_forces=0.05*eV/Ang,
        constraints=[0,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,178,179,180,181,185,186,187,188,194,195,204,205,206,207,211,212,213,214,215,216,218,219,222,223,224,225,230,231,232,233,234,235,238,239,241,242,243,244,246,247,249,250,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404],
        trajectory_filename='CG_05traject.nc',
    )
nlsave('CGsupergap05relax.nc', device_configuration)
device_configuration.setCalculator(calculator,
    initial_state=device_configuration,
)
nlprint(device_configuration)
device_configuration.update()
nlsave('CGsupergap05relax.nc', device_configuration)
nlprint(device_configuration)

[Nordland]

How many CPU are you running on?

[alex_z]

Hey guys,

I have similar problem. I perform geometry optimization. After some time (half an hour or so) my calculation crashes. Here is how I run my job and the log from xterm after the crash:

[user@dirac: parallel_test]$ mpiexec -n 4 /home/user/QuantumWise/atk-10.8.0/atkpython/bin/atkpython run_file.py > run_file.out
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x107c51e0, rbuf=0x108277f0, count=318, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Reduce(759)..................:
MPIR_Reduce_redscat_gather(485)...:
MPIDI_CH3U_Receive_data_found(129): Message from rank 3 and tag 11 truncated; 1280 bytes received but buffer size is 1264
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(773)................: MPI_Allreduce(sbuf=0x15df8b20, rbuf=0x10e33900, count=318, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD) failed
MPIR_Reduce(759)..................:
MPIR_Reduce_redscat_gather(485)...:
MPIDI_CH3U_Receive_data_found(129): Message from rank 3 and tag 11 truncated; 640 bytes received but buffer size is 632

And here are the error lines from output file:

rank 1 in job 3  dirac_57726   caused collective abort of all ranks
  exit status of rank 1: killed by signal 9

I'm running Suse Linux on AMD 64 with 4 cores. My calculator parameters are:

basis_set = GGABasis.DoubleZetaPolarized
exchange_correlation = GGA.PBE
electron_temperature=800.0*Kelvin
k_point_sampling=(1, 1, 100)

The contacts and molecule are composed of carbon and hydrogen with total number of molecules about 100.

[jdgayles16]

im runnin on 10 nodes 1 cpu each with 8 gb of allocated memory, I ran the same system for electronic convergence and had no problem with memory.