[CP2K-user] Stop Jobs Because Increasing Memory Usage
Nam Tran
trann... at gmail.com
Mon Oct 28 07:44:46 UTC 2019
Hi,
I am not sure about your case but I have a similar problem when I updated
to intel compiler and mkl 2019. Maybe I made something wrong during the
installation but downgrade to 2018 version solved my problem.
Nam
On Monday, 28 October 2019 18:35:15 UTC+11, Ke Zhou wrote:
>
> Dear Developers,
>
> Now I am running cp2k 6.1 on our new cluster.
> The *memory usage for cp2k is increased with time *during running.
> 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, bulk water), using both 6.1 and 5.1, it runs well.
>
> Can you help me?
> Is the problem from compile 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 bulk water + one Cl ion
> ##################
>
>
> @SET SYSTEM Bulk
>
> &GLOBAL
> PROJECT ${SYSTEM}
> RUN_TYPE MD
> PRINT_LEVEL low
> EXTENDED_FFT_LENGTHS T
> &END GLOBAL
>
> &FORCE_EVAL
> ! the electronic structure part of CP2K is named Quickstep
> METHOD Quickstep
> STRESS_TENSOR ANALYTICAL
> &DFT
> ! basis sets and pseudopotential files can be found in cp2k/data
> BASIS_SET_FILE_NAME ./GTH_BASIS_SETS
> POTENTIAL_FILE_NAME ./POTENTIAL
> WFN_RESTART_FILE_NAME ./${SYSTEM}-RESTART.wfn
>
> ! Charge and multiplicity
> CHARGE -1
> # LSD
> # MULTIPLICITY 1
> # Two times the total spin plus one. Specify 3 for a triplet, 4 for
> a quartet, and so on.
> # Default is 1 (singlet) for an even number and 2 (doublet) for an odd
> number of electrons.
> #
>
> &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
>
> ###### for diagonalization #######
> # ADDED_MOS 100
> # CHOLESKY OFF #INVERSE
> # &SMEAR ON
> # METHOD FERMI_DIRAC
> # ELECTRONIC_TEMPERATURE [K] 300
> # &END SMEAR
> # &DIAGONALIZATION
> # ALGORITHM STANDARD
> # EPS_ADAPT 0.01
> # &END DIAGONALIZATION
>
> &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] 12.42 12.42 12.42
> &END CELL
>
> ! atom coordinates can be in the &COORD section,
> ! or provided as an external file.
> # &TOPOLOGY
> # COORD_FILE_NAME Na.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
> &KIND Cl
> BASIS_SET DZVP-MOLOPT-SR-GTH ## TZV2P-GTH ##DZVP-GTH-PBE
> POTENTIAL GTH-PBE-q7
> &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
> # COMVEL_TOL 0.00001
>
> &THERMOSTAT
> # REGION MOLECULE
> # REGION GLOBAL
> # REGION MASSIVE
> 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
> &EACH
> MD 1
> &END EACH
> FORMAT XYZ
> &END TRAJECTORY
> &VELOCITIES
> &EACH
> MD 1
> &END EACH
> FORMAT XYZ
> &END VELOCITIES
> &FORCES
> &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 ./Bulk-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 ##################
>
>
>
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