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Error while using IBRION=8
Posted: Fri Jan 22, 2021 12:51 pm
by 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:
Code: Select all
-----------------------------------------------------------------------------
| |
| 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.
Re: Error while using IBRION=8
Posted: Fri Jan 22, 2021 1:05 pm
by henrique_miranda
Have you tried removing NPAR from the INCAR as suggested in the error?
Re: Error while using IBRION=8
Posted: Sat Jan 23, 2021 9:01 am
by abdul_jaleel1
yes I have tried to remove NPAR but after this job stops on
Code: Select all
| 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
Code: Select all
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
Code: Select all
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!!! <---- |
| |
-----------------------------------------------------------------------------
Re: Error while using IBRION=8
Posted: Sat Jan 23, 2021 9:08 am
by abdul_jaleel1
Please further information regarding the executed job is given below:
KPOINTS
Code: Select all
KPT-Resolved Value to Generate K-Mesh: 0.020
0
Monkhorst-Pack
2 2 1
0.0 0.0 0.0
POSCAR
Code: Select all
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
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
Re: Error while using IBRION=8
Posted: Sun Jan 24, 2021 11:36 pm
by henrique_miranda
In this INCAR file you've posted NPAR=2 can you please try to run without this line?
Re: Error while using IBRION=8
Posted: Wed Feb 17, 2021 7:05 am
by 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
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)
===================================================================================
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)
Re: Error while using IBRION=8
Posted: Wed Feb 17, 2021 3:11 pm
by 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
Re: Error while using IBRION=8
Posted: Wed Feb 17, 2021 5:41 pm
by abdul_jaleel1
bashrc
Code: Select all
#source activate py36
# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
ulimit -s
Code: Select all
#!/bin/bash
#PBS -q batch
#PBS -N testing
#PBS -l nodes=1:ppn=36
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=1
mpirun -np 36 /home/abdul/VASP/vasp.6.1.2.fixcell/bin/vasp_std > vasprun.log
I have also try to use " ulimited -s unlimited" but problem still exsists.
Thanks in advance
Regards
Re: Error while using IBRION=8
Posted: Wed Feb 17, 2021 9:33 pm
by henrique_miranda
Please read the post I sent you carefully:
forum/viewtopic.php?t=13253#p13298
if your account has hard-set stack size limits, please add the following line to your .bashrc:
ulimit -s unlimited
Re: Error while using IBRION=8
Posted: Thu Feb 18, 2021 6:35 am
by abdul_jaleel1
sorry, how can I check? "hard-set stack size limits"
Re: Error while using IBRION=8
Posted: Thu Feb 18, 2021 11:36 am
by henrique_miranda
please check what get if you type
in the terminal of your computer.
Re: Error while using IBRION=8
Posted: Thu Feb 18, 2021 11:51 am
by abdul_jaleel1
I have checked the following commands in the terminal:
Code: Select all
[abdul@physics test]$ 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
Re: Error while using IBRION=8
Posted: Thu Feb 18, 2021 12:04 pm
by henrique_miranda
Now if you type:
you will see that the stack size limit was changed.
Once you set this in your
.bashrc your calculations should be able to run.
Re: Error while using IBRION=8
Posted: Thu Feb 18, 2021 12:17 pm
by 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)
===================================================================================
Re: Error while using IBRION=8
Posted: Thu Feb 18, 2021 2:37 pm
by henrique_miranda
Did you also try adding:
in your PBS submission script?
Before the mpirun vasp command.