[CP2K-user] [CP2K:12430] Re: Stop Jobs Because Increasing Memory Usage
Ke Zhou
zhouk... at gmail.com
Wed Oct 30 02:01:42 UTC 2019
Dear Nam,
Thanks for your suggestion. I use the 2018 version, the memory usage is
still increasing.
I gauss the problem is from some of libs. But I don't know which the libs
cause the problem.
Best,
Ke
Nam Tran <trann... at gmail.com> 于2019年10月28日周一 下午3:44写道：
> 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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