[QE-users] Neb.x Error

Abdul Shaik arshaik at asu.edu
Thu Feb 7 05:51:45 CET 2019


Hi,
I am trying to run neb calculation to get diffusion barrier for Cadmium
interstitial in CdTe. The simulation runs for the first iteration but stops
after that with an error message " Error in routine read_wfc (29):  cannot
open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading"

The complete out log is as shown below


     Program NEB v.6.3MaX starts on  6Feb2019 at 18:47: 2

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
         "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details
at
     http://www.quantum-espresso.org/quote

     Parallel version (MPI & OpenMP), running on     247 processor cores
     Number of MPI processes:               247
     Threads/MPI process:                     1

     MPI processes distributed on    16 nodes
     path-images division:  nimage    =      13
     R & G space division:  proc/nbgrp/npool/nimage =      19

     parsing_file_name: ./cdte_cdi.neb.in
     Reading input from pw_1.in
Warning: card &IONS ignored
Warning: card / ignored
               file Cd.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 4D
renormalized
               file Te.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 5P
renormalized
     Reading input from pw_2.in
Warning: card &IONS ignored
Warning: card / ignored
               file Cd.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 4D
renormalized
               file Te.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 5P
renormalized
     Reading input from pw_3.in
Warning: card &IONS ignored
Warning: card / ignored
               file Cd.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 4D
renormalized
               file Te.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S 5P
renormalized

     initial path length           = 10.6539 bohr
     initial inter-image distance  =  0.8878 bohr

     string_method                 =    neb
     restart_mode                  =    from_scratch
     opt_scheme                    =    broyden
     num_of_images                 =    13
     nstep_path                    =    20
     CI_scheme                     =    auto
     first_last_opt                =    T
     use_freezing                  =    F
     ds                            =    2.0000 a.u.
     k_max                         =    0.3000 a.u.
     k_min                         =    0.2000 a.u.
     suggested k_max               =    0.1542 a.u.
     suggested k_min               =    0.1028 a.u.
     path_thr                      =    0.1000 eV / A

     ------------------------------ iteration   1
------------------------------

     cpu =  0   tcpu =      6.6    self-consistency for image   1

     activation energy (->) =   1.492073 eV
     activation energy (<-) =   1.490791 eV

     image        energy (eV)        error (eV/A)        frozen

         1    -324446.4150866            0.572621            F
         2    -324446.0677089            1.007237            F
         3    -324445.4389185            1.592099            F
         4    -324444.9245675            2.036232            F
         5    -324444.9326045            1.788934            F
         6    -324445.4894297            1.188030            F
         7    -324445.8776389            0.602238            F
         8    -324445.4887571            1.187911            F
         9    -324444.9338041            1.788777            F
        10    -324444.9230138            2.036543            F
        11    -324445.4398085            1.592535            F
        12    -324446.0679420            1.007259            F
        13    -324446.4138049            0.571477            F

     climbing image = 10

     path length          = 10.654 bohr
     inter-image distance =  0.888 bohr

     ------------------------------ iteration   2
------------------------------

     cpu =  0   tcpu =   2422.2    self-consistency for image   1






 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine read_wfc (29):
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...








 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine read_wfc (29):
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine read_wfc (29):
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
     Error in routine read_wfc (29):
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     Error in routine read_wfc (29):
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     Error in routine read_wfc (29):
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     Error in routine read_wfc (29):
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading
     Error in routine read_wfc (29):
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     cannot open restart file
/scratch/arshaik/CdTe_neb_OUT/CdTe_NEB_7/CdTe_NEB.save/wfc5 for reading



     stopping ...
     stopping ...
     stopping ...
     stopping ...
     stopping ...

     stopping ...
     stopping ...
     stopping ...




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     stopping ...
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     stopping ...
     stopping ...
     stopping ...
     stopping ...

     stopping ...

     stopping ...
     stopping ...

The input file for the neb.x is as given below

BEGIN
BEGIN_PATH_INPUT
&PATH
  restart_mode      = 'from_scratch'
  string_method     = 'neb',
  nstep_path        = 20,
  ds                = 2.D0,
  opt_scheme        = "broyden",
  num_of_images     = 13,
  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
  prefix         = "CdTe_NEB"
  outdir         = "/scratch/arshaik/CdTe_neb_OUT",
  pseudo_dir     =
"/home/arshaik/qeProjs/CdTe/CdTe_pbesol_paw/CdTe/../../../pseudo",
  restart_mode   = 'from_scratch'
/
&SYSTEM
  ibrav                  = 0,
  nat                    = 65,
  ntyp                   = 2,
  ecutwfc                = 60.0D0,
  ecutrho                = 240.0D0,
!  occupations            = "smearing",
!  degauss                = 0.03D0,
/
&ELECTRONS
  conv_thr    = 1.D-6,
  mixing_beta = 0.3D0,
  startingwfc = 'random'
/
&IONS
/
ATOMIC_SPECIES
 Cd 112.411  Cd.pbesol-n-kjpaw_psl.1.0.0.UPF
 Te 127.6    Te.pbesol-n-kjpaw_psl.1.0.0.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS angstrom
Cd    6.51    0    0
Te    8.1375    1.6275    1.6275
Cd    9.765    3.255    0
Te    11.3925    4.8825    1.6275
Cd    9.765    0    3.255
Te    11.3925    1.6275    4.8825
Cd    0    0    0
Te    1.6275    1.6275    1.6275
Cd    3.255    3.255    0
Te    4.8825    4.8825    1.6275
Cd    6.51    6.51    0
Te    8.1375    8.1375    1.6275
Cd    9.765    9.765    0
Te    11.3925    11.3925    1.6275
Cd    3.255    0    3.255
Te    4.8825    1.6275    4.8825
Cd    6.51    3.255    3.255
Te    8.1375    4.8825    4.8825
Cd    9.765    6.51    3.255
Te    11.3925    8.1375    4.8825
Cd    6.51    0    6.51
Te    8.1375    1.6275    8.1375
Cd    9.765    3.255    6.51
Te    11.3925    4.8825    8.1375
Cd    9.765    0    9.765
Te    11.3925    1.6275    11.3925
Cd    0    6.51    0
Te    1.6275    8.1375    1.6275
Cd    3.255    9.765    0
Te    4.8825    11.3925    1.6275
Cd    0    3.255    3.255
Te    1.6275    4.8825    4.8825
Cd    3.255    6.51    3.255
Te    4.8825    8.1375    4.8825
Cd    6.51    9.765    3.255
Te    8.1375    11.3925    4.8825
Cd    0    0    6.51
Te    1.6275    1.6275    8.1375
Cd    3.255    3.255    6.51
Te    4.8825    4.8825    8.1375
Cd    6.51    6.51    6.51
Te    8.1375    8.1375    8.1375
Cd    9.765    9.765    6.51
Te    11.3925    11.3925    8.1375
Cd    3.255    0    9.765
Te    4.8825    1.6275    11.3925
Cd    6.51    3.255    9.765
Te    8.1375    4.8825    11.3925
Cd    9.765    6.51    9.765
Te    11.3925    8.1375    11.3925
Cd    0    9.765    3.255
Te    1.6275    11.3925    4.8825
Cd    0    6.51    6.51
Te    1.6275    8.1375    8.1375
Cd    3.255    9.765    6.51
Te    4.8825    11.3925    8.1375
Cd    0    3.255    9.765
Te    1.6275    4.8825    11.3925
Cd    3.255    6.51    9.765
Te    4.8825    8.1375    11.3925
Cd    6.51    9.765    9.765
Te    8.1375    11.3925    11.3925
Cd    0    9.765    9.765
Te    1.6275    11.3925    11.3925
Cd      4.8825  4.8825  4.8825
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
Cd    6.51    0    0
Te    8.1375    1.6275    1.6275
Cd    9.765    3.255    0
Te    11.3925    4.8825    1.6275
Cd    9.765    0    3.255
Te    11.3925    1.6275    4.8825
Cd    0    0    0
Te    1.6275    1.6275    1.6275
Cd    3.255    3.255    0
Te    4.8825    4.8825    1.6275
Cd    6.51    6.51    0
Te    8.1375    8.1375    1.6275
Cd    9.765    9.765    0
Te    11.3925    11.3925    1.6275
Cd    3.255    0    3.255
Te    4.8825    1.6275    4.8825
Cd    6.51    3.255    3.255
Te    8.1375    4.8825    4.8825
Cd    9.765    6.51    3.255
Te    11.3925    8.1375    4.8825
Cd    6.51    0    6.51
Te    8.1375    1.6275    8.1375
Cd    9.765    3.255    6.51
Te    11.3925    4.8825    8.1375
Cd    9.765    0    9.765
Te    11.3925    1.6275    11.3925
Cd    0    6.51    0
Te    1.6275    8.1375    1.6275
Cd    3.255    9.765    0
Te    4.8825    11.3925    1.6275
Cd    0    3.255    3.255
Te    1.6275    4.8825    4.8825
Cd    3.255    6.51    3.255
Te    4.8825    8.1375    4.8825
Cd    6.51    9.765    3.255
Te    8.1375    11.3925    4.8825
Cd    0    0    6.51
Te    1.6275    1.6275    8.1375
Cd    3.255    3.255    6.51
Te    4.8825    4.8825    8.1375
Cd    6.51    6.51    6.51
Te    8.1375    8.1375    8.1375
Cd    9.765    9.765    6.51
Te    11.3925    11.3925    8.1375
Cd    3.255    0    9.765
Te    4.8825    1.6275    11.3925
Cd    6.51    3.255    9.765
Te    8.1375    4.8825    11.3925
Cd    9.765    6.51    9.765
Te    11.3925    8.1375    11.3925
Cd    0    9.765    3.255
Te    1.6275    11.3925    4.8825
Cd    0    6.51    6.51
Te    1.6275    8.1375    8.1375
Cd    3.255    9.765    6.51
Te    4.8825    11.3925    8.1375
Cd    0    3.255    9.765
Te    1.6275    4.8825    11.3925
Cd    3.255    6.51    9.765
Te    4.8825    8.1375    11.3925
Cd    6.51    9.765    9.765
Te    8.1375    11.3925    11.3925
Cd    0    9.765    9.765
Te    1.6275    11.3925    11.3925
Cd      3.255   3.255   3.255
LAST_IMAGE
ATOMIC_POSITIONS angstrom
Cd    6.51    0    0
Te    8.1375    1.6275    1.6275
Cd    9.765    3.255    0
Te    11.3925    4.8825    1.6275
Cd    9.765    0    3.255
Te    11.3925    1.6275    4.8825
Cd    0    0    0
Te    1.6275    1.6275    1.6275
Cd    3.255    3.255    0
Te    4.8825    4.8825    1.6275
Cd    6.51    6.51    0
Te    8.1375    8.1375    1.6275
Cd    9.765    9.765    0
Te    11.3925    11.3925    1.6275
Cd    3.255    0    3.255
Te    4.8825    1.6275    4.8825
Cd    6.51    3.255    3.255
Te    8.1375    4.8825    4.8825
Cd    9.765    6.51    3.255
Te    11.3925    8.1375    4.8825
Cd    6.51    0    6.51
Te    8.1375    1.6275    8.1375
Cd    9.765    3.255    6.51
Te    11.3925    4.8825    8.1375
Cd    9.765    0    9.765
Te    11.3925    1.6275    11.3925
Cd    0    6.51    0
Te    1.6275    8.1375    1.6275
Cd    3.255    9.765    0
Te    4.8825    11.3925    1.6275
Cd    0    3.255    3.255
Te    1.6275    4.8825    4.8825
Cd    3.255    6.51    3.255
Te    4.8825    8.1375    4.8825
Cd    6.51    9.765    3.255
Te    8.1375    11.3925    4.8825
Cd    0    0    6.51
Te    1.6275    1.6275    8.1375
Cd    3.255    3.255    6.51
Te    4.8825    4.8825    8.1375
Cd    6.51    6.51    6.51
Te    8.1375    8.1375    8.1375
Cd    9.765    9.765    6.51
Te    11.3925    11.3925    8.1375
Cd    3.255    0    9.765
Te    4.8825    1.6275    11.3925
Cd    6.51    3.255    9.765
Te    8.1375    4.8825    11.3925
Cd    9.765    6.51    9.765
Te    11.3925    8.1375    11.3925
Cd    0    9.765    3.255
Te    1.6275    11.3925    4.8825
Cd    0    6.51    6.51
Te    1.6275    8.1375    8.1375
Cd    3.255    9.765    6.51
Te    4.8825    11.3925    8.1375
Cd    0    3.255    9.765
Te    1.6275    4.8825    11.3925
Cd    3.255    6.51    9.765
Te    4.8825    8.1375    11.3925
Cd    6.51    9.765    9.765
Te    8.1375    11.3925    11.3925
Cd    0    9.765    9.765
Te    1.6275    11.3925    11.3925
Cd      1.6275  4.8825  1.6275
END_POSITIONS
K_POINTS automatic
2 2 2 0 0 0
CELL_PARAMETERS angstrom
13.02000000000000 0.00000000000000 0.00000000000000
0.00000000000000 13.02000000000000 0.00000000000000
0.00000000000000 0.00000000000000 13.02000000000000
END_ENGINE_INPUT
END

I am calling the neb.x with the following sbatch script

#!/bin/bash

#SBATCH --ntasks=16 --cpus-per-task=16
#SBATCH --qos=normal --mem-per-cpu=2G          # number of nodes
#SBATCH -t 1-12:00                  # wall time (D-HH:MM)
#SBATCH -o slurm.%j.out             # STDOUT (%j = JobId)
#SBATCH -e slurm.%j.err             # STDERR (%j = JobId)
#SBATCH --mail-type=ALL             # Send a notification when the job
starts, stops, or fails
#SBATCH --mail-user=arshaik at asu.edu # send-to address

source /home/arshaik/tools/scripts/load_qe.sh

mpirun -np 247 neb.x -ni 13 -nk 1 -nt 1 -nd 144 -inp ./cdte_cdi.neb.in |
tee cdte_cdi.neb.out

Please help how to resolve this.

Regards
Abdul Rawoof.
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