Problem when calculate slab model, the memory usage is increased and finally it stops
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Ke Zhou
Oct 30, 2019, 5:08:34 AM10/30/19
to cp2k
Dear Developers,
I have ask the questions of increasing memory usage for several times. Now I can calculate bulk system without stoping.
But now I found the memory usage for cp2k is increased with time (for both of version 5.1 and 6.1)during running when I calculate the slab-model system (water in 2D channel ) . Finally, it stops when the usage reach the upper bound. I also tried cp2k 5.1 and had same problem. But I run it in our old cluster which is 2.5.1 version, it works well.
However, I run one of the example in CP2K package, H2O-64.inp (path: ./test/QS/benchmark), which is bulk water system, using both 6.1 and 5.1, it runs well.
Can you help me?
Is the problem from compile (may be some libs) or the input file?
Best,
Ke
Input file:
########## H2O-64.inp, from example file ##################
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME GTH_BASIS_SETS
POTENTIAL_FILE_NAME POTENTIAL
&MGRID
CUTOFF 280
REL_CUTOFF 30
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
WF_INTERPOLATION PS
EXTRAPOLATION_ORDER 3
&END QS
&SCF
SCF_GUESS ATOMIC
&OT ON
MINIMIZER DIIS
&END OT
&PRINT
&RESTART OFF
&END
&END
# SCF_GUESS RESTART
# EPS_SCF 1.0E-7
&END SCF
&XC
&XC_FUNCTIONAL Pade
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 12.4138 12.4138 12.4138
&END CELL
# 64 H2O (TIP5P,1bar,300K) a = 12.4138
&COORD
O 12.235322 1.376642 10.869880
O 6.445390 3.706940 8.650794
O 0.085977 2.181322 8.276663
O 12.052554 2.671366 2.147199
O 12.250036 4.190930 12.092014
O 7.187422 0.959062 4.733469
O 8.346457 7.210040 4.667644
O 12.361546 11.527875 8.106887
O 3.299984 4.440816 9.193275
O 2.855829 3.759909 6.552815
O 1.392494 6.362753 0.586172
O 1.858645 8.694013 2.068738
O 3.770231 12.094519 8.652183
O 6.432508 3.669828 2.772418
O 1.998724 1.820217 4.876440
O 8.248581 2.404730 6.931303
O 5.753814 3.360029 12.461534
O 11.322212 5.649239 2.236798
O 4.277318 2.113956 10.590808
O 5.405015 3.349247 5.484702
O 6.493278 11.869958 0.684912
O 3.275250 2.346576 2.425241
O 7.981003 6.352512 7.507970
O 5.985990 6.512854 12.194648
O 10.636714 11.856872 12.209540
O 9.312283 3.670384 3.508594
O 1.106885 5.830301 6.638695
O 8.008007 3.326363 10.869818
O 12.403000 9.687405 11.761901
O 4.219782 7.085315 8.153470
O 3.781557 8.203821 11.563272
O 11.088898 4.532081 7.809475
O 10.387548 8.408890 1.017882
O 1.979016 6.418091 10.374159
O 4.660547 0.549666 5.617403
O 8.745880 12.256257 8.089383
O 2.662041 10.489890 0.092980
O 7.241661 10.471815 4.226946
O 2.276827 0.276647 10.810417
O 8.887733 0.946877 1.333885
O 1.943554 8.088552 7.567650
O 9.667942 8.056759 9.868847
O 10.905491 8.339638 6.484782
O 3.507733 4.862402 1.557439
O 8.010457 8.642846 12.055969
O 8.374446 10.035932 6.690309
O 5.635247 6.076875 5.563993
O 11.728434 1.601906 5.079475
O 9.771134 9.814114 3.548703
O 3.944355 10.563450 4.687536
O 0.890357 6.382287 4.065806
O 6.862447 6.425182 2.488202
O 3.813963 6.595122 3.762649
O 6.562448 8.295463 8.807182
O 9.809455 0.143325 3.886553
O 4.117074 11.661225 2.221679
O 5.295317 8.735561 2.763183
O 9.971999 5.379339 5.340378
O 12.254708 8.643874 3.957116
O 2.344274 10.761274 6.829162
O 7.013416 0.643488 10.518797
O 5.152349 10.233624 10.359388
O 11.184278 5.884064 10.298279
O 12.252335 8.974142 9.070831
H 12.415139 2.233125 11.257611
H 11.922476 1.573799 9.986994
H 5.608192 3.371543 8.971482
H 6.731226 3.060851 8.004962
H -0.169205 1.565594 7.589645
H -0.455440 2.954771 8.118939
H 12.125168 2.826463 1.205443
H 12.888828 2.969761 2.504745
H 11.553255 4.386613 11.465566
H 12.818281 4.960808 12.067151
H 7.049495 1.772344 4.247898
H 6.353019 0.798145 5.174047
H 7.781850 7.384852 5.420566
H 9.103203 6.754017 5.035898
H 12.771232 11.788645 8.931744
H 12.018035 10.650652 8.276334
H 3.557245 3.792529 9.848846
H 2.543844 4.884102 9.577958
H 2.320235 4.521250 6.329813
H 2.872128 3.749963 7.509824
H 1.209685 7.121391 1.140501
H 2.238885 6.038801 0.894245
H 2.763109 8.856353 2.336735
H 1.329379 9.047369 2.783755
H 4.315639 11.533388 9.203449
H 3.098742 12.433043 9.244412
H 5.987369 3.448974 3.590530
H 5.813096 3.419344 2.086985
H 1.057126 1.675344 4.969379
H 2.248496 2.292119 5.670892
H 8.508264 1.653337 7.464411
H 8.066015 2.034597 6.067646
H 5.197835 2.915542 11.821572
H 6.630900 3.329981 12.079371
H 10.788986 6.436672 2.127933
H 11.657923 5.463602 1.359832
H 3.544476 1.634958 10.977765
H 4.755770 1.455054 10.087655
H 4.465371 3.375459 5.665294
H 5.682663 4.264430 5.524498
H 6.174815 11.778676 1.582954
H 5.713640 12.089924 0.174999
H 3.476076 1.498708 2.028983
H 2.730229 2.134295 3.182949
H 7.119624 5.936450 7.474030
H 8.536492 5.799405 6.958665
H 5.909499 5.717477 11.667621
H 6.125402 6.196758 13.087330
H 11.203499 12.513536 11.804844
H 10.260930 12.300153 12.970145
H 9.985036 3.927685 2.878172
H 8.545584 3.468329 2.972331
H 1.399882 6.620092 7.093246
H 0.963561 6.112523 5.735345
H 8.067363 3.674002 9.979955
H 8.000737 2.375959 10.756190
H 11.821629 10.402510 12.020482
H 12.206854 8.983242 12.379892
H 3.461473 7.606485 7.889688
H 3.844478 6.304711 8.560946
H 3.179884 7.585614 11.148494
H 4.401957 7.652030 12.039573
H 11.573777 5.053211 7.169515
H 10.342076 4.186083 7.320831
H 10.065640 8.919194 1.760981
H 9.629585 8.322499 0.439729
H 1.396302 6.546079 9.625630
H 1.405516 6.479759 11.138049
H 4.024008 1.232518 5.405828
H 4.736858 0.579881 6.571077
H 9.452293 12.313381 8.732772
H 8.976559 11.502788 7.545965
H 1.834701 10.012311 0.153462
H 3.295197 9.836403 -0.204175
H 7.056724 11.401702 4.095264
H 6.499038 10.020287 3.825865
H 1.365541 0.487338 11.013887
H 2.501591 -0.428131 11.417871
H 8.644279 1.812362 1.005409
H 8.142674 0.388030 1.112955
H 1.272659 8.365063 8.191888
H 2.142485 8.877768 7.063867
H 8.961493 7.826192 9.265523
H 9.227102 8.487654 10.601118
H 10.150144 7.758934 6.392768
H 10.596082 9.187988 6.167290
H 3.463106 4.096188 2.129414
H 3.919461 4.539801 0.755791
H 7.418998 9.394959 12.028876
H 7.430413 7.883095 12.106546
H 7.972905 10.220334 5.841196
H 7.675111 9.631498 7.203725
H 5.332446 6.381336 6.419473
H 5.000025 6.434186 4.943466
H 11.575078 2.271167 4.412540
H 11.219802 0.847030 4.783357
H 8.865342 9.721516 3.843998
H 10.000732 10.719285 3.758898
H 3.186196 10.476397 5.265333
H 4.407331 11.335128 5.013723
H 0.558187 7.255936 3.859331
H 0.341672 5.789383 3.552346
H 7.459933 6.526049 3.229193
H 6.696228 5.483739 2.440372
H 3.864872 6.313007 2.849385
H 2.876419 6.621201 3.953862
H 5.631529 8.079145 8.753997
H 7.003296 7.568245 8.367822
H 9.615413 0.527902 3.031755
H 8.962985 0.109366 4.332162
H 3.825854 11.139182 1.474087
H 4.063988 11.063232 2.967211
H 5.784391 7.914558 2.708486
H 4.780461 8.655167 3.566110
H 10.880659 5.444664 5.046607
H 9.593331 4.687991 4.797350
H 11.562317 8.960134 3.376765
H 11.926084 8.816948 4.839320
H 2.856874 11.297981 7.433660
H 1.492332 11.195517 6.786033
H 7.145820 0.090200 9.749009
H 7.227275 0.077690 11.260665
H 4.662021 9.538430 10.798155
H 5.994537 9.833472 10.142985
H 10.544299 6.595857 10.301445
H 11.281750 5.653082 9.374494
H 12.103020 8.841164 10.006916
H 11.491592 8.576221 8.647557
&END COORD
&KIND H
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PADE-q1
&END KIND
&KIND O
BASIS_SET TZV2P-GTH
POTENTIAL GTH-PADE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT H2O-64
RUN_TYPE MD
PRINT_LEVEL LOW
&TIMINGS
THRESHOLD 0.000001
&END
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10000000
TIMESTEP 0.5
TEMPERATURE 300.0
&END MD
&END MOTION
########## H2O-64.inp, from example file ##################
########## my input file, the memory usage for cp2k is increased with time ##################
########## the system is water + graphene walls ##################
#@SET SYSTEM G-WT
&GLOBAL
PROJECT G-WT
RUN_TYPE MD
PRINT_LEVEL low
EXTENDED_FFT_LENGTHS T
&END GLOBAL
&FORCE_EVAL
! the electronic structure part of CP2K is named Quickstep
METHOD Quickstep
STRESS_TENSOR ANALYTICAL
&DFT
! basis sets and pseudopotential files can be found in cp2k/data
BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
POTENTIAL_FILE_NAME ./POTENTIAL
WFN_RESTART_FILE_NAME ./G-WT-RESTART.wfn
&MGRID
! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.
! certain calculations (e.g. geometry optimization, vibrational frequencies,
! NPT and cell optimizations, need higher cutoffs)
CUTOFF [Ry] 500
##REL_CUTOFF [Ry] 50
&END
&QS
! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).
METHOD GPW
! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,
! sets reasonable values for all other thresholds.
EPS_DEFAULT 1.0E-10
! used for MD, the method used to generate the initial guess.
MAP_CONSISTENT TRUE
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 4
&END
&POISSON
PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and a wavelet solver
&END
&PRINT
! output atomic charge
&MULLIKEN
## FILENAME ${SYSTEM}
&EACH
MD 10
&END EACH
&END MULLIKEN
! output others
&END
! use the OT METHOD for robust and efficient SCF, suitable for all non-metallic systems.
&SCF
SCF_GUESS RESTART #ATOMIC ! can be used to RESTART an interrupted calculation
MAX_SCF 1000
EPS_SCF 1.0E-7 #1.0E-7 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7
&OUTER_SCF ! repeat the inner SCF cycle 10 times
MAX_SCF 10
EPS_SCF 1.0E-7 #1.0E-7 ! must match the above
&END
####### for OT #######
CHOLESKY OFF
&OT
#CHOLESKY OFF
! an accurate preconditioner suitable also for larger systems
PRECONDITIONER FULL_ALL
! the most robust choice (DIIS might sometimes be faster, but not as stable).
MINIMIZER DIIS ## CG
N_DIIS 5
ENERGY_GAP 1.0E-5
&END OT
&MIXING
METHOD BROYDEN_MIXING
ALPHA 0.2
BETA 1.5
NBROYDEN 8
&END MIXING
&END SCF
! specify the exchange and correlation treatment
&XC
! use a PBE functional
&XC_FUNCTIONAL PBE
&PBE
PARAMETRIZATION revPBE
#SCALE_C 0.0
&END PBE
&VWN
&END VWN
&END XC_FUNCTIONAL
! adding Grimme's D3 correction (by default without C9 terms)
&VDW_POTENTIAL
POTENTIAL_TYPE PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
#CALCULATE_C9_TERM T
#REFEREBCE_C9_TERM T
#LONG_RANGE_CORRECTION T
PARAMETER_FILE_NAME dftd3.dat
REFERENCE_FUNCTIONAL revPBE
R_CUTOFF [angstrom] 11
&END
&END VDW_POTENTIAL
&END XC
&END DFT
! description of the system
&SUBSYS
&CELL
! unit cells that are orthorhombic are more efficient with CP2K
ABC [angstrom] 12.825000 12.340862 20.0
&END CELL
! atom coordinates can be in the &COORD section,
! or provided as an external file.
# &TOPOLOGY
# COORD_FILE_NAME 29WT.xyz
# COORD_FILE_FORMAT XYZ
# &END
! MOLOPT basis sets are fairly costly,
! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements
! their contracted nature makes them suitable
! for condensed and gas phase systems alike.
&KIND C
BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH ###DZVP-GTH-PBE
POTENTIAL GTH-PBE-q6
&END KIND
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH ##DZVP-GTH-PBE
POTENTIAL GTH-PBE-q1
&END KIND
&END SUBSYS
&END FORCE_EVAL
! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section
&MOTION
&MD
ENSEMBLE NVT ! sampling the canonical ensemble, accurate properties might need NVE
TEMPERATURE [K] 330
TIMESTEP [fs] 0.5
STEPS 40000 # 20 ps
&THERMOSTAT
TYPE NOSE
&NOSE
LENGTH 4 # CPMD
YOSHIDA 9 # 3 5 7 9 15 25 125#
TIMECON 100
MTS 2
&END NOSE
&END THERMOSTAT
&END MD
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 1..120
&END FIXED_ATOMS
&END CONSTRAINT
&PRINT
&TRAJECTORY
# FILENAME=${SYSTEM}-1.xyz
&EACH
MD 1
&END EACH
FORMAT XYZ
&END TRAJECTORY
&VELOCITIES
# FILENAME=${SYSTEM}-1.vel
&EACH
MD 1
&END EACH
FORMAT XYZ
&END VELOCITIES
&FORCES
# FILENAME=${SYSTEM}-1.force
&EACH
MD 5
&END EACH
&END FORCES
&RESTART
&EACH
MD 20
&END
&END
&MIXED_ENERGIES
&EACH
MD 5
&END EACH
&END MIXED_ENERGIES
&CELL
&EACH
MD 1
&END EACH
&END CELL
&STRESS
&EACH
MD 10
&END EACH
&END STRESS
&RESTART_HISTORY
&EACH
MD 50
&END EACH
&END RESTART_HISTORY
&END PRINT
&END MOTION
&EXT_RESTART
RESTART_FILE_NAME ./G-WT-1.restart
RESTART_POS
RESTART_VEL
RESTART_CELL
RESTART_CONSTRAINT F
&END EXT_RESTART
########## my input file, the memory usage for cp2k is increased with time ##################
Бранислав Миловановић
Nov 30, 2019, 9:47:39 AM11/30/19
to cp2k
Dear Ke, Developers,
I have the same problem with increasing memory usage over time, with the following input used:
&GLOBAL
PROJECT Na+_G_quad_wannier
RUN_TYPE MD
PRINT_LEVEL LOW
PREFERRED_FFT_LIBRARY FFTSG
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME /home/branislavm/Projects/Programs/Potentials/BASIS_SET
POTENTIAL_FILE_NAME /home/branislavm/Projects/Programs/Potentials/GTH_POTENTIALS
CHARGE 1
&MGRID
CUTOFF 320
REL_CUTOFF 50
NGRIDS 4
&END MGRID
&QS
METHOD GPW
EPS_DEFAULT 1.0E-12
&END QS
&SCF
MAX_SCF 100
EPS_SCF 5.0E-7
SCF_GUESS RESTART
&OT ON
MINIMIZER DIIS
N_DIIS 7
PRECONDITIONER FULL_ALL
ENERGY_GAP 0.001
&END OT
&END SCF
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&VDW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
PARAMETER_FILE_NAME /home/branislavm/Projects/Programs/Potentials/dftd3.dat
REFERENCE_FUNCTIONAL BLYP
&END PAIR_POTENTIAL
&END VDW_POTENTIAL
&XC_GRID
XC_SMOOTH_RHO NN10
XC_DERIV SPLINE2_SMOOTH
&END XC_GRID
&END XC
&LOCALIZE
METHOD JACOBI
MAX_ITER 10000
&PRINT
&WANNIER_CENTERS
IONS+CENTERS
FILENAME =WANNIER_CENTERS.xyz
&EACH
MD 1
&END
&END WANNIER_CENTERS
&END PRINT
&END LOCALIZE
&END DFT
&SUBSYS
&CELL
ABC 25.0 25.0 25.0
PERIODIC NONE
&END CELL
&COORD
N 10.4441985755 7.2694831234 12.5073686365
C 11.7536307003 7.7158627265 12.7113477991
. . . .
. . . .
. . . .
Na 12.4370558895 12.2824472182 12.9521881866
&END COORD
&KIND H
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND C
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND Na
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q9
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE REFTRAJ
STEPS 20000
&REFTRAJ
EVAL_ENERGY_FORCES
TRAJ_FILE_NAME REFTRAJ.xyz
&END REFTRAJ
&END MD
&PRINT
&RESTART
ADD_LAST NUMERIC
&EACH
MD 500
&END
&END RESTART
&END PRINT
&END MOTION
I run:
CP2K version 5.1
SVN source code revision svn:18091
cp2kflags: libint fftw3 libxc parallel mpi3 scalapack libderiv_max_am1=5 libint_max_am=6
on the machine with:
AMD Ryzen Threadripper 1950X 16-Core Processor
G.skill DDR4 2x16GB 3200MHz RipJaws V CL15, F4-3200C15D-32GVK
When I used older cp2k version (2.5.1) I never had similar problems.
Best,
Branislav
среда, 30. октобар 2019. 10.08.34 UTC+1, Ke Zhou је написао/ла:
Dear Developers,I have ask the questions of increasing memory usage for several times. Now I can calculate bulk system without stoping.
But now I found the memory usage for cp2k is increased with time (for both of version 5.1 and 6.1)during running when I calculate the slab-model system (water in 2D channel ) . Finally, it stops when the usage reach the upper bound. I also tried cp2k 5.1 and had same problem. But I run it in our old cluster which is 2.5.1 version, it works well.However, I run one of the example in CP2K package, H2O-64.inp (path: ./test/QS/benchmark), which is bulk water system, using both 6.1 and 5.1, it runs well.Can you help me?Is the problem from compile (may be some libs) or the input file?
Lucas Lodeiro
Dec 1, 2019, 2:12:11 PM12/1/19
to cp...@googlegroups.com
I have the same problem a year ago. I can fix it changing the compiler. First, I use the new intel compiler, and with an older intel compiler the problem disappear.
But, in my case the memory increase problem was in each calculation, regardless of the calculation nature.
regards
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