Error while using IBRION=8

[abdul_jaleel1]

Dear user, I want to calculate the phonon spectrum using Phonopy. From initial calculations after a single iteration of SCF cycle following error occurs in OUTCAR file:

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-----------------------------------------------------------------------------
|                                                                             |
|     EEEEEEE  RRRRRR   RRRRRR   OOOOOOO  RRRRRR      ###     ###     ###     |
|     E        R     R  R     R  O     O  R     R     ###     ###     ###     |
|     E        R     R  R     R  O     O  R     R     ###     ###     ###     |
|     EEEEE    RRRRRR   RRRRRR   O     O  RRRRRR       #       #       #      |
|     E        R   R    R   R    O     O  R   R                               |
|     E        R    R   R    R   O     O  R    R      ###     ###     ###     |
|     EEEEEEE  R     R  R     R  OOOOOOO  R     R     ###     ###     ###     |
|                                                                             |
|     VASP internal routines have requested a change of the k-point set.      |
|     Unfortunately, this is only possible if NPAR=number of nodes.           |
|     Please remove the tag NPAR from the INCAR file and restart the          |
|     calculation.                                                            |
|                                                                             |
|       ---->  I REFUSE TO CONTINUE WITH THIS SICK JOB ... BYE!!! <----       |
|                                                                             |
 -----------------------------------------------------------------------------

I am running job on 36 cores. I have checked different combination of NPAR and KPAR bur job failed ,also changed to gamma k-meshed but same error exists.

[henrique_miranda]

Have you tried removing NPAR from the INCAR as suggested in the error?

[abdul_jaleel1]

yes I have tried to remove NPAR but after this job stops on

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|     Your generating k-point grid is not commensurate to the symmetry of     |
|     the lattice. This can cause slow convergence with respect to            |
|     k-points for HF-type calculations.                                      |
|     Suggested SOLUTIONS:                                                    |
|      ) If not already the case, use automatic k-point generation.           |
|      ) Shift your grid to Gamma (G) (e.g. required for hex or fcc           |
|     lattice).                                                               |
|                                                                             |
 -----------------------------------------------------------------------------

 POSCAR, INCAR and KPOINTS ok, starting setup
 FFT: planning ...
 WAVECAR not read
 WARNING: random wavefunctions but no delay for mixing, default for NELMDL

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 279555 RUNNING AT physics
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

while using NPAR , KPAR combination at only NPAR=2 its stops after one complete iteration see OSZICAR

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DAV:  32    -0.185331943617E+03   -0.24349E-07   -0.42393E-11   296   0.624E-05    0.632E-05
DAV:  33    -0.185331943625E+03   -0.77926E-08    0.45430E-12   296   0.181E-05
   1 F= -.18533194E+03 E0= -.18533194E+03  d E =-.406046E-05
 Linear response reoptimize wavefunctions
DAV:   1    -0.185331943627E+03   -0.20809E-08    0.29896E-11   296   0.163E-05
DAV:   2    -0.185331943626E+03    0.25466E-09    0.38569E-11   296   0.751E-06
DAV:   3    -0.185331943626E+03    0.22555E-09    0.38014E-11   296   0.722E-06
 Linear response DOF=           6
 Linear response progress:
  Degree of freedom:   1/  6

OUTCAR

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The dynamic configuration has the point symmetry C_1 .


 Subroutine INISYM returns: Found  1 space group operations
 (whereof  1 operations are pure point group operations),
 and found     1 'primitive' translations

 -----------------------------------------------------------------------------
|                                                                             |
|     EEEEEEE  RRRRRR   RRRRRR   OOOOOOO  RRRRRR      ###     ###     ###     |
|     E        R     R  R     R  O     O  R     R     ###     ###     ###     |
|     E        R     R  R     R  O     O  R     R     ###     ###     ###     |
|     EEEEE    RRRRRR   RRRRRR   O     O  RRRRRR       #       #       #      |
|     E        R   R    R   R    O     O  R   R                               |
|     E        R    R   R    R   O     O  R    R      ###     ###     ###     |
|     EEEEEEE  R     R  R     R  OOOOOOO  R     R     ###     ###     ###     |
|                                                                             |
|     VASP internal routines have requested a change of the k-point set.      |
|     Unfortunately, this is only possible if NPAR=number of nodes.           |
|     Please remove the tag NPAR from the INCAR file and restart the          |
|     calculation.                                                            |
|                                                                             |
|       ---->  I REFUSE TO CONTINUE WITH THIS SICK JOB ... BYE!!! <----       |
|                                                                             |
 -----------------------------------------------------------------------------

[abdul_jaleel1]

Please further information regarding the executed job is given below:

KPOINTS

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KPT-Resolved Value to Generate K-Mesh: 0.020
0
Monkhorst-Pack
   2   2   1
0.0  0.0  0.0

POSCAR

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Se Co Ge
   1.0
    12.3480616596812354    0.0000000000000000    0.0000000000000000
    -6.1740308299356625   10.6937350848687416    0.0000000000000000
     0.0000000000000000    0.0000000000000000   22.9647160451495260
  24    8    8
Direct
  0.0000000000000000  0.1952078074177085  0.5651119392351075
  0.5000000000000000  0.1952078074177085  0.5651119392351075
  0.0000000000000000  0.6952078074177086  0.5651119392351075
  0.5000000000000000  0.6952078074177086  0.5651119392351075
  0.0000000000000000  0.3047921925822880  0.4348880607648923
  0.5000000000000000  0.3047921925822880  0.4348880607648923
  0.0000000000000000  0.8047921925822881  0.4348880607648923
  0.5000000000000000  0.8047921925822881  0.4348880607648923
  0.3047921925822916  0.3047921925822880  0.5651119392351075
  0.8047921925822916  0.3047921925822880  0.5651119392351075
  0.3047921925822916  0.8047921925822881  0.5651119392351075
  0.8047921925822916  0.8047921925822881  0.5651119392351075
  0.1952078074177121  0.1952078074177085  0.4348880607648923
  0.6952078074177122  0.1952078074177085  0.4348880607648923
  0.1952078074177121  0.6952078074177086  0.4348880607648923
  0.6952078074177122  0.6952078074177086  0.4348880607648923
  0.1952078074177121  0.0000000000000000  0.5651119392351075
  0.6952078074177122  0.0000000000000000  0.5651119392351075
  0.1952078074177121  0.5000000000000000  0.5651119392351075
  0.6952078074177122  0.5000000000000000  0.5651119392351075
  0.3047921925822916  0.0000000000000000  0.4348880607648923
  0.8047921925822916  0.0000000000000000  0.4348880607648923
  0.3047921925822916  0.5000000000000000  0.4348880607648923
  0.8047921925822916  0.5000000000000000  0.4348880607648923
  0.1666666714999998  0.3333333435000014  0.5000000000000000
  0.6666666714999998  0.3333333435000014  0.5000000000000000
  0.1666666714999998  0.8333333435000014  0.5000000000000000
  0.6666666714999998  0.8333333435000014  0.5000000000000000
  0.3333333134999990  0.1666666564999985  0.5000000000000000
  0.8333333134999990  0.1666666564999985  0.5000000000000000
  0.3333333134999990  0.6666666564999986  0.5000000000000000
  0.8333333134999990  0.6666666564999986  0.5000000000000000
  0.0000000000000000  0.0000000000000000  0.5519950259113526
  0.5000000000000000  0.0000000000000000  0.5519950259113526
  0.0000000000000000  0.5000000000000000  0.5519950259113526
  0.5000000000000000  0.5000000000000000  0.5519950259113526
  0.0000000000000000  0.0000000000000000  0.4480049740886474
  0.5000000000000000  0.0000000000000000  0.4480049740886474
  0.0000000000000000  0.5000000000000000  0.4480049740886474
  0.5000000000000000  0.5000000000000000  0.4480049740886474

INCAR

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PREC = Accurate
  ENCUT = 500
 IBRION = 8
  EDIFF = 1.0e-08
  IALGO = 38
 ISMEAR = 0; SIGMA = 0.1
  LREAL = .FALSE.
ADDGRID = .TRUE.
  LWAVE = .FALSE.
 LCHARG = .FALSE.
NPAR=2
KPAR=1

[henrique_miranda]

In this INCAR file you've posted NPAR=2 can you please try to run without this line?

[abdul_jaleel1]

INCAR

Code: Select all

PREC = Accurate
  ENCUT = 500
 IBRION = 8
  EDIFF = 1.0e-08
  IALGO = 38
 ISMEAR = 0; SIGMA = 0.1
  LREAL = .FALSE.
ADDGRID = .TRUE.
  LWAVE = .FALSE.
 LCHARG = .FALSE.
#NPAR=2
#KPAR=1

vasprun.log

Code: Select all

           W WW W  AAAAAA  RRRRR   N  N N  II  N  N N  G  GGG   !            |
|           WW  WW  A    A  R   R   N   NN  II  N   NN  G    G                |
|           W    W  A    A  R    R  N    N  II  N    N   GGGG   !!!           |
|                                                                             |
|     Your generating k-point grid is not commensurate to the symmetry of     |
|     the lattice. This can cause slow convergence with respect to            |
|     k-points for HF-type calculations.                                      |
|     Suggested SOLUTIONS:                                                    |
|      ) If not already the case, use automatic k-point generation.           |
|      ) Shift your grid to Gamma (G) (e.g. required for hex or fcc           |
|     lattice).                                                               |
|                                                                             |
 -----------------------------------------------------------------------------

 POSCAR, INCAR and KPOINTS ok, starting setup
 FFT: planning ...
 WAVECAR not read
 WARNING: random wavefunctions but no delay for mixing, default for NELMDL

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 423068 RUNNING AT physics
=   KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

OUTCAR stops at:

Code: Select all

 total amount of memory used by VASP MPI-rank0   282661. kBytes
=======================================================================

   base      :      30000. kBytes
   nonl-proj :     115868. kBytes
   fftplans  :      49752. kBytes
   grid      :      74001. kBytes
   one-center:        622. kBytes
   wavefun   :      12418. kBytes

     INWAV:  cpu time    0.0000: real time    0.0000
 Broyden mixing: mesh for mixing (old mesh)
   NGX = 45   NGY = 45   NGZ = 83
  (NGX  =180   NGY  =180   NGZ  =336)
  gives a total of 168075 points

 initial charge density was supplied:
 charge density of overlapping atoms calculated
 number of electron     248.0000000 magnetization
 keeping initial charge density in first step


--------------------------------------------------------------------------------------------------------


 Maximum index for augmentation-charges         4730 (set IRDMAX)

[henrique_miranda]

Seeing this error together with the error you report in:
forum/viewtopic.php?f=4&t=18052

It looks to me like you might have some problem with your compilation or environment settings.
First, have a look at this post:
forum/viewtopic.php?t=13253#p13298

[abdul_jaleel1]

bashrc

Code: Select all

#source activate py36
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

ulimit -s

vasp.pbs script

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#!/bin/bash
#PBS -q batch
#PBS -N testing
#PBS -l nodes=1:ppn=36
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=1
mpirun -np 36 /home/abdul/VASP/vasp.6.1.2.fixcell/bin/vasp_std > vasprun.log

I have also try to use " ulimited -s unlimited" but problem still exsists.
Thanks in advance
Regards

[henrique_miranda]

Please read the post I sent you carefully:
forum/viewtopic.php?t=13253#p13298

if your account has hard-set stack size limits, please add the following line to your .bashrc:
ulimit -s unlimited

[abdul_jaleel1]

sorry, how can I check? "hard-set stack size limits"

[henrique_miranda]

please check what get if you type

Code: Select all

$ ulimit -s

in the terminal of your computer.

[abdul_jaleel1]

I have checked the following commands in the terminal:

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[abdul@physics test]$ ulimit -s
8192
[abdul@physics test]$ ulimit -u
4096
[abdul@physics test]$ ulimit -f
unlimited
[abdul@physics test]$ ulimit -m
unlimited
[abdul@physics test]$ ulimit -v
unlimited

[henrique_miranda]

Now if you type:

Code: Select all

$ ulimit -s unlimited
$ ulimit -s

you will see that the stack size limit was changed.
Once you set this in your .bashrc your calculations should be able to run.

[abdul_jaleel1]

unfortunately the problem still exists,
bashrc

#source activate py36
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions


#export MPI=/opt/intel/compilers_and_libraries_2020.2.254/linux/mpi/intel64/bin
export PATH=/home/abdul/VASP/fftw-3.3.8:$PATH
export LLD_LIBRARY_PATH=/home/abdul/VASP/fftw-3.3.8/lib:$LD_LIBRARY_PATH
#export MANPATH=$MANPATH:$MPI/share/man
#export INFOPATH=$INFOPATH:$MPI/share/man

source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/mkl/bin/mklvars.sh intel64
#export PATH=/home/sarfraz/VASPVSTAT/fftw-3.3.8:$PATH
#export LD_LIBRARY_PATH=/home/sarfraz/VASPVSTAT/fftw-3.3.8/lib:SLD_LIBRARY_PATH
#PATH /opt/conda/envs/env/bin:$PATH
export PATH=/home/abdul/vaspkit/vaspkit.1.2.3/bin:${PATH}
ulimit -s unlimited
ulimit -s


POSCAR, INCAR and KPOINTS ok, starting setup
FFT: planning ...
WAVECAR not read
WARNING: random wavefunctions but no delay for mixing, default for NELMDL

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 125891 RUNNING AT physics
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 125892 RUNNING AT physics
= KILLED BY SIGNAL: 9 (Killed)
===================================================================================

[henrique_miranda]

Did you also try adding:

Code: Select all

ulimit -s unlimited
ulimit -s

in your PBS submission script?
Before the mpirun vasp command.