[CP2K-user] [CP2K:17489] CI-NEB out of memory
Hasan Al-Mahayni
hasanalmahayni at gmail.com
Mon Aug 15 22:07:17 UTC 2022
Hello Matthias,
I would like to first thank you as my NEB is now working. I have two small
questions now that I am running it :)
1) The energies of my first and last image (my inputs) are different in the
NEB simulation than my previous normal GEO_OPT simulations. How do people
usually deal with that? Do they consider only energy differences of the NEB
simulation? Because my thermodynamic energy difference between initial and
final state is 0.18eV while in NEB it is 0.43 eV!
2) One of my NEB simulations ran for 24 hours at 512 cpus and it doesn't
seem to add any iterations to my overall RESULTS file. This does not happen
to my other NEB simulations... So I am wondering how I can figure out if it
is stuck or just taking a long time (which I doubt). For this question I
attach the xyz files, input file and a screenshot of the end of the output
file after 24 hours.
[image: image.png]
I deeply appreciate your help!
Hasan Al-Mahayni
On Fri, Jul 29, 2022 at 7:54 PM Krack Matthias (PSI) <matthias.krack at psi.ch>
wrote:
> Hi Hasan
>
>
>
> Your system is too large to run each of the 5 frames only on one CPU core.
> Increase NPROC_REP from 1 to a larger value depending on the CPU resources
> available (e.g. 16 or better more like 64 which requires 5*64=320 cores
> total).
>
>
>
> Matthias
>
>
>
> *From: *"cp2k at googlegroups.com" <cp2k at googlegroups.com> on behalf of
> Hasan Al-Mahayni <hasanalmahayni at gmail.com>
> *Reply to: *"cp2k at googlegroups.com" <cp2k at googlegroups.com>
> *Date: *Friday, 29 July 2022 at 15:17
> *To: *"cp2k at googlegroups.com" <cp2k at googlegroups.com>
> *Subject: *Re: [CP2K:17414] CI-NEB out of memory
>
>
>
> Hello Matthias,
>
>
>
> Thank you for your reply. I commented out the kpoints, I still get the out
> of memory error. Do I have to remove something else in my input file other
> than kpoints?
>
>
>
>
>
> Hasan Al-Mahayni
>
>
>
>
>
> On Fri, Jul 29, 2022 at 9:45 AM Krack Matthias (PSI) <
> matthias.krack at psi.ch> wrote:
>
> Hi Hasan
>
>
>
> You are running a CI-NEB band calculation with 4x4x1 k points which might
> explain the large number of output files. I am not sure, if that
> combination of features has been sufficiently tested or even validated at
> all, since all NEB test files are Gamma point only runs.
>
>
>
> Best regards
>
>
>
> Matthias
>
>
>
> *From: *"cp2k at googlegroups.com" <cp2k at googlegroups.com> on behalf of
> Hasan Al-Mahayni <hasanalmahayni at gmail.com>
> *Reply to: *"cp2k at googlegroups.com" <cp2k at googlegroups.com>
> *Date: *Friday, 29 July 2022 at 01:36
> *To: *"cp2k at googlegroups.com" <cp2k at googlegroups.com>
> *Subject: *[CP2K:17409] CI-NEB out of memory
>
>
>
> Hello All,
>
>
>
> This is the first time I am running BAND calculation for Climbing image
> NEB. I attach the my input file and my two xyz files. I am getting a huge
> number of output files (639!). I don't think this is normal but I don't see
> what I did wrong in my input file. I only requested 5 image replicas. I
> gave the job a lot of memory/CPUS but it fails after 1 minute telling me
> its out of memory. Can someone help me with this?
>
>
>
>
>
> Thanks in advance,
>
>
>
> Hasan.
>
>
>
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&EXT_RESTART
RESTART_FILE_NAME cp2k-1.restart
&END
&GLOBAL
RUN_TYPE BAND
EXTENDED_FFT_LENGTHS .TRUE.
FFTW_PLAN_TYPE ESTIMATE
PREFERRED_FFT_LIBRARY FFTW3
PROJECT cp2k
PRINT_LEVEL LOW
&TIMINGS SILENT
THRESHOLD 1e-08
&END TIMINGS
&END GLOBAL
&MOTION
&BAND
NUMBER_OF_REPLICA 5
K_SPRING 0.02
&OPTIMIZE_BAND
OPT_TYPE DIIS
&DIIS
MAX_STEPS 1000
&END
&END
&CONVERGENCE_CONTROL
MAX_FORCE 0.0045
RMS_FORCE 0.0003
MAX_DR 0.0005
RMS_DR 0.0001
&END
ROTATE_FRAMES FALSE
NPROC_REP 64
BAND_TYPE CI-NEB
&CI_NEB
NSTEPS_IT 5
&END
&REPLICA
COORD_FILE_NAME slab1.xyz
&END
&REPLICA
COORD_FILE_NAME slab2.xyz
&END
&PROGRAM_RUN_INFO
INITIAL_CONFIGURATION_INFO
&END
&CONVERGENCE_INFO
&EACH
BAND 1
REPLICA_EVAL 1
&END
&END
&END BAND
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 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
&END FIXED_ATOMS
&END CONSTRAINT
&GEO_OPT
MAX_ITER 400
OPTIMIZER BFGS
MAX_DR 5e-04
!RESTART_FILE_NAME cp2k-BFGS.Hessian
&END GEO_OPT
&PRINT
&TRAJECTORY
FORMAT XYZ
&END TRAJECTORY
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD Quickstep
STRESS_TENSOR ANALYTICAL
&PRINT
&STRESS_TENSOR ON
&END STRESS_TENSOR
&END PRINT
&DFT
UKS .TRUE.
CHARGE 0
WFN_RESTART_FILE_NAME cp2k-RESTART.kp
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&MGRID
NGRIDS 5
RELATIVE_CUTOFF 50
CUTOFF 550
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
METHOD GPW
EXTRAPOLATION USE_GUESS
&END QS
&SCF
EPS_SCF 1.0E-10
SCF_GUESS RESTART
ADDED_MOS 200
CHOLESKY OFF
MAX_SCF 100
&OUTER_SCF F
EPS_SCF 1.0E-10
MAX_SCF 100
&END OUTER_SCF
&SMEAR T
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE 3.0000000000000000E+02
&END SMEAR
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 4.0000000000000002E-01
BETA 1.5000000000000000E+00
NMIXING 5
NBUFFER 8
&END MIXING
&END SCF
&XC
FUNCTIONAL_ROUTINE NEW
DENSITY_CUTOFF 1.0e-12
GRADIENT_CUTOFF 1.0e-12
TAU_CUTOFF 1.0e-12
&XC_FUNCTIONAL
&PBE
&END PBE
&END XC_FUNCTIONAL
&XC_GRID
USE_FINER_GRID .TRUE.
&END XC_GRID
&VDW_POTENTIAL ! ... dispersion interactions
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3 ! computed with the DFTD3 method
REFERENCE_FUNCTIONAL PBE
! that requires the following parameters (in external file, specified here)
PARAMETER_FILE_NAME ./dftd3.dat
R_CUTOFF 15 ! cutoff raddius for the dispersion interactions
&END PAIR_POTENTIAL
&END
&END XC
&POISSON
POISSON_SOLVER PERIODIC
PERIODIC XYZ
&END POISSON
&KPOINTS
SCHEME GAMMA
FULL_GRID .TRUE.
&END KPOINTS
&LS_SCF
MAX_SCF 100
&END LS_SCF
&END DFT
&SUBSYS
&CELL
ABC 12.91530535837229 12.91530535837229 35.4795
ALPHA_BETA_GAMMA 90 90 90
PERIODIC XYZ
&END CELL
&KIND Cu
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND N
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&TOPOLOGY
COORD_FILE_FORMAT XYZ
COORD_FILE_NAME slab1.xyz
CONN_FILE_FORMAT off
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
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