[Pw_forum] QE-5.1.2: NEB.X Crashes with MPI errors
Mauro Sgroi
maurofrancesco.sgroi at gmail.com
Mon Jun 15 16:13:30 CEST 2015
Dear All,
I'm trying to submit a NEB calculation on the Mn3/4Co1/4PO4 system to
calculate the Lithium energy barrier for diffusion. The baseline
calculation on MnPO4 went fine.
Inserting the cobalt atoms neb.x crashes during the calculation on the
second image.
No error is printed in the log but in the standard output I obtain:
2 2 INTERMEDIATE_IMAGE
[t12node084:17231] 55 more processes have sent help message
help-mpi-btl-openib.txt / reg mem limit low
[t12node084:17231] Set MCA parameter "orte_base_help_aggregate" to 0 to see
all help / error messages
[t12node082:28692] *** An error occurred in MPI_Bcast
[t12node082:28692] *** on communicator MPI COMMUNICATOR 9 SPLIT FROM 7
[t12node082:28692] *** MPI_ERR_TRUNCATE: message truncated
[t12node082:28692] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
--------------------------------------------------------------------------
mpiexec has exited due to process rank 31 with PID 28692 on
node t12node082 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
[t12node084:17231] 8 more processes have sent help message
help-mpi-errors.txt / mpi_errors_are_fatal
Is my input in some way wrong, it's a problem of compilation of the code or
it is a bug? My code is compiled with gcc/gfortran and OpenMPI.
I'm reporting my input for reference below.
Thanks lot in advance and best regards,
Mauro Sgroi.
Centro Ricerche FIAT, Italy.
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch'
string_method = 'neb',
nstep_path = 200,
ds = 1.D0,
opt_scheme = "broyden2",
num_of_images = 7,
k_max = 0.3D0,
k_min = 0.2D0,
CI_scheme = "auto",
path_thr = 0.1D0,
first_last_opt = .true.
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
pseudo_dir='/data5/sgroi/DATABASE/ESPRESSO',
prefix='mnpo4_121_gamma',
outdir='/net/manager/remote/qespresso/mnpo4_121_gamma',
wf_collect=.false.,
disk_io='none',
/
&SYSTEM
ibrav=8,
nat=49,
ntyp=5,
ecutwfc=78,
ecutrho=355,
nbnd=240,
occupations='smearing',
degauss=1d-10,
smearing='mv',
nspin=2,
starting_magnetization(1)=0.9,
starting_magnetization(2)=0.9,
lda_plus_u=.true.,
Hubbard_U(1)= 4.5,
Hubbard_U(2)=5.695,
celldm(1)=18.49395,
celldm(2)=1.21346602537586616163,
celldm(3)=0.49381770795314143273
/
&ELECTRONS
conv_thr=1.0d-9,
electron_maxstep=200,
mixing_beta=0.5,
scf_must_converge=.false.
/
ATOMIC_SPECIES
Mn 54.9381 Mn.pbesol-spn-kjpaw_psl.0.3.1.UPF
Co 58.933195 Co.pbesol-n-kjpaw_psl.0.2.3.UPF
P 30.9737 P.pbesol-n-kjpaw_psl.0.1.UPF
O 15.9994 O.pbesol-n-kjpaw_psl.0.1.UPF
Li 6.941 Li.pbesol-s-kjpaw_psl.0.2.1.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { crystal }
Li 0.5 0.25 0.5
Co 0.29072591 0.12500000 0.91347261
Co 0.29072591 0.62500000 0.91347261
Mn 0.70927409 0.87500000 0.08652739
Mn 0.70927409 0.37500000 0.08652739
Mn 0.20927409 0.87500000 0.41347261
Mn 0.20927409 0.37500000 0.41347261
Mn 0.79072591 0.12500000 0.58652739
Mn 0.79072591 0.62500000 0.58652739
P 0.10084365 0.12500000 0.40451768
P 0.10084365 0.62500000 0.40451768
P 0.89915635 0.87500000 0.59548232
P 0.89915635 0.37500000 0.59548232
P 0.39915635 0.87500000 0.90451768
P 0.39915635 0.37500000 0.90451768
P 0.60084365 0.12500000 0.09548232
P 0.60084365 0.62500000 0.09548232
O 0.12385174 0.12500000 0.71580776
O 0.12385174 0.62500000 0.71580776
O 0.87614826 0.87500000 0.28419224
O 0.87614826 0.37500000 0.28419224
O 0.37614825 0.87500000 0.21580776
O 0.37614825 0.37500000 0.21580776
O 0.62385174 0.12500000 0.78419224
O 0.62385174 0.62500000 0.78419224
O 0.44624223 0.12500000 0.14543042
O 0.44624223 0.62500000 0.14543042
O 0.55375777 0.87500000 0.85456959
O 0.55375777 0.37500000 0.85456959
O 0.05375777 0.87500000 0.64543041
O 0.05375777 0.37500000 0.64543041
O 0.94624223 0.12500000 0.35456959
O 0.94624223 0.62500000 0.35456959
O 0.82994947 0.47473125 0.74215029
O 0.82994947 0.97473125 0.74215029
O 0.17005053 0.52526875 0.25784971
O 0.17005053 0.02526875 0.25784971
O 0.67005053 0.52526875 0.24215029
O 0.67005053 0.02526875 0.24215029
O 0.32994947 0.47473125 0.75784971
O 0.32994947 0.97473125 0.75784971
O 0.32994947 0.77526875 0.75784971
O 0.32994947 0.27526875 0.75784971
O 0.67005053 0.72473125 0.24215029
O 0.67005053 0.22473125 0.24215029
O 0.17005053 0.72473125 0.25784971
O 0.17005053 0.22473125 0.25784971
O 0.82994947 0.77526875 0.74215029
O 0.82994947 0.27526875 0.74215029
LAST_IMAGE
ATOMIC_POSITIONS { crystal }
Li 0.5 0.5 0.5
Co 0.29072591 0.12500000 0.91347261
Co 0.29072591 0.62500000 0.91347261
Mn 0.70927409 0.87500000 0.08652739
Mn 0.70927409 0.37500000 0.08652739
Mn 0.20927409 0.87500000 0.41347261
Mn 0.20927409 0.37500000 0.41347261
Mn 0.79072591 0.12500000 0.58652739
Mn 0.79072591 0.62500000 0.58652739
P 0.10084365 0.12500000 0.40451768
P 0.10084365 0.62500000 0.40451768
P 0.89915635 0.87500000 0.59548232
P 0.89915635 0.37500000 0.59548232
P 0.39915635 0.87500000 0.90451768
P 0.39915635 0.37500000 0.90451768
P 0.60084365 0.12500000 0.09548232
P 0.60084365 0.62500000 0.09548232
O 0.12385174 0.12500000 0.71580776
O 0.12385174 0.62500000 0.71580776
O 0.87614826 0.87500000 0.28419224
O 0.87614826 0.37500000 0.28419224
O 0.37614825 0.87500000 0.21580776
O 0.37614825 0.37500000 0.21580776
O 0.62385174 0.12500000 0.78419224
O 0.62385174 0.62500000 0.78419224
O 0.44624223 0.12500000 0.14543042
O 0.44624223 0.62500000 0.14543042
O 0.55375777 0.87500000 0.85456959
O 0.55375777 0.37500000 0.85456959
O 0.05375777 0.87500000 0.64543041
O 0.05375777 0.37500000 0.64543041
O 0.94624223 0.12500000 0.35456959
O 0.94624223 0.62500000 0.35456959
O 0.82994947 0.47473125 0.74215029
O 0.82994947 0.97473125 0.74215029
O 0.17005053 0.52526875 0.25784971
O 0.17005053 0.02526875 0.25784971
O 0.67005053 0.52526875 0.24215029
O 0.67005053 0.02526875 0.24215029
O 0.32994947 0.47473125 0.75784971
O 0.32994947 0.97473125 0.75784971
O 0.32994947 0.77526875 0.75784971
O 0.32994947 0.27526875 0.75784971
O 0.67005053 0.72473125 0.24215029
O 0.67005053 0.22473125 0.24215029
O 0.17005053 0.72473125 0.25784971
O 0.17005053 0.22473125 0.25784971
O 0.82994947 0.77526875 0.74215029
O 0.82994947 0.27526875 0.74215029
END_POSITIONS
K_POINTS {gamma}
END_ENGINE_INPUT
END
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