CP2K¶
Popis¶
CP2K je softvérový balík pre kvantovú chémiu a fyziku pevných látok, ktorý dokáže vykonávať atomistické simulácie pevných látok, kvapalín, molekulárnych, periodických, materiálových, kryštálových a biologických systémov. CP2K poskytuje všeobecný rámec pre rôzne modelovacie metódy, napríklad DFT s použitím prístupov Gaussian and Plane Waves (GPW) a all-electron GPW (GAPW).
Oficiálna dokumentácia¶
Viac informácií o tutoriáloch a dokumentácii CP2K nájdete v CP2K HOWTOs.
Dostupné verzie¶
Aktuálne sú dostupné nasledujúce verzie CP2K:
- Spúšťacie závislosti:
- Žiadne, požadované knižnice a závislosti sa načítajú automaticky spolu s modulom
CP2K/2022.1-foss-2022a.
- Žiadne, požadované knižnice a závislosti sa načítajú automaticky spolu s modulom
Modul CP2K môžete načítať pomocou nasledujúceho príkazu:
module load CP2K/2022.1-foss-2022a
- Spúšťacie závislosti:
- Žiadne, požadované knižnice a závislosti sa načítajú automaticky spolu s modulom
CP2K/2023.1-foss-2022a.
- Žiadne, požadované knižnice a závislosti sa načítajú automaticky spolu s modulom
Modul CP2K môžete načítať pomocou nasledujúceho príkazu:
module load CP2K/2023.1-foss-2022a
- Spúšťacie závislosti:
- Žiadne, požadované knižnice a závislosti sa načítajú automaticky spolu s modulom
CP2K/2023.1-foss-2022b.
- Žiadne, požadované knižnice a závislosti sa načítajú automaticky spolu s modulom
Modul CP2K môžete načítať pomocou nasledujúceho príkazu:
module load CP2K/2023.1-foss-2022b
CP2K Benchmark¶
Mriežkový výpočet CP2K, ako aj násobenie blokovo riedkych matíc v DBCSR (Cannonov algoritmus), preferujú štvorcové číslo pre celkový počet rankov (2D komunikačný vzor).
Z tohto dôvodu môže byť efektívnejšie nechať niektoré jadrá CPU nevyužité, aby sa dosiahla táto vlastnosť štvorcového čísla, namiesto použitia všetkých jadier s „nepreferovaným“ celkovým počtom rankov. Kontraintuitívne môže byť výhodou aj nerovnomerný počet rankov na uzol (t. j. odlišné počty rankov na socket). Fixovanie (pinning) MPI procesov a umiestňovanie vlákien vyžaduje dodatočnú pozornosť v rámci jednotlivých uzlov, aby sa systém s dvoma socketmi zaťažil vyváženým spôsobom, alebo aby sa medzi rankmi vytvoril priestor pre OpenMP vlákna.
Aby sme lepšie pochopili, ako CP2K využíva dostupný hardvér na Devane a ako dosiahnuť dobrý výkon, môžeme preskúmať vplyv výberu počtu MPI rankov na uzol a OpenMP vlákien na výkon benchmarkov.
Na spustenie benchmarkov bol použitý nasledujúci príkaz:
mpiexec -np $mpi_rank --map-by slot:PE=$omp_thread -x OMP_PLACES=cores -x OMP_PROC_BIND=SPREAD -x OMP_NUM_THREADS=$omp_thread cp2k.psmp -i ${benchmark}.inp > ${benchmark}.out
Pracovný adresár
Jednouzlové benchmarky boli spustené na lokálnom NVMe disku /work/, ktorý je integrovaný
do každého výpočtového uzla a je zvyčajne rýchlejší než zdieľané súborové systémy /home/ a /scratch/.
Benchmarky boli zmerané pre nasledujúce systémy:
Ab-initio molekulárna dynamika kvapalnej vody s použitím Born-Oppenheimerovho
prístupu a Quickstep DFT. Sú zvolené nastavenia produkčnej kvality pre sady báz (TZV2P) a cutoff rovinných vĺn (280 Ry) a pre výpočet výmenovo-korelačnej energie sa používa aproximácia lokálnej hustoty (LDA). Konfigurácie boli vygenerované klasickou ekvilibráciou a počiatočný odhad elektrónovej hustoty sa robí na základe atómových orbitálov. Jednouzlový systém obsahuje 64 molekúl vody (192 atómov, 640 elektrónov) v bunke 12.4 ų a cross-node systém obsahuje 256 molekúl vody (768 atómov, 2560 elektrónov) v bunke 19.7 ų. Obe simulácie MD sa spúšťajú na 10 krokov.
??? Example "H2O_64.inp"
&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
EPS_CHECK_DIAG 1.0E-12
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 0.5
TEMPERATURE 300.0
&END MD
&END MOTION
??? Example "H2O_256.inp"
&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
# SCF_GUESS RESTART
# EPS_SCF 1.0E-7
&PRINT
&RESTART OFF
&END
&END
&END SCF
&XC
&XC_FUNCTIONAL Pade
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 19.7340 19.7340 19.7340
&END CELL
# 256 H2O (TIP5P,1bar,300K) a = 19.7340
&COORD
O 3.255901 3.688405 12.233196
O 16.070915 1.855224 2.671883
O 14.430416 11.166566 6.965595
O 3.193559 0.023208 0.578067
O 7.727474 2.923744 1.420645
O 15.625821 12.743272 4.965716
O 5.667053 6.761802 4.274583
O 8.679988 11.155767 16.528346
O 16.437650 6.552064 14.765867
O 9.743913 0.846814 13.583578
O 11.611481 14.073408 17.181213
O 2.334528 14.445330 14.357176
O 6.899834 18.979840 2.401200
O 17.135403 7.948223 18.492081
O 0.301116 19.378486 10.711962
O 3.355849 15.055856 16.761154
O 4.191357 12.923494 13.054658
O 13.404400 2.583312 3.042674
O 11.458216 7.724938 0.083129
O 15.328469 4.825143 16.973443
O 18.377167 2.076604 13.162943
O 5.001031 6.013815 17.632807
O 7.565213 0.635175 10.686386
O 3.071148 15.465948 5.861605
O 7.597675 9.381749 12.966876
O 15.398571 1.942103 8.153702
O 15.773356 18.923564 13.522681
O 11.634086 11.260727 8.426820
O 10.694751 16.707250 4.511765
O 1.520652 7.188747 18.597189
O 9.262206 7.938121 14.412353
O 7.092153 0.477485 14.704975
O 11.418210 7.298544 10.447168
O 12.045829 12.534893 0.989496
O 9.374221 1.210496 5.195853
O 1.383329 19.321531 3.824144
O 7.883681 3.101988 15.246867
O 8.374488 11.428684 11.715591
O 10.662076 10.282190 0.336566
O 3.430752 10.678359 9.683614
O 7.205562 13.589012 16.372127
O 2.853099 0.963068 13.796587
O 19.014248 6.480330 17.094428
O 4.193880 2.828439 9.915639
O 5.482566 7.295503 11.806390
O 19.471724 1.734725 4.307353
O 3.449645 1.415875 2.769827
O 14.090557 3.280133 15.111847
O 15.593729 1.840739 13.443937
O 12.323683 2.367383 10.399977
O 16.924719 16.375867 11.290493
O 17.368333 18.108276 0.486965
O 6.128596 9.141663 5.550795
O 12.865798 16.543055 0.781893
O 18.132650 12.678232 5.868495
O 10.063360 9.352667 9.224044
O 6.851907 12.361788 5.407360
O 3.646807 18.191374 11.344920
O 9.651652 5.146348 14.029226
O 14.702155 19.318694 7.337933
O 4.704722 3.557252 14.693143
O 4.439323 12.293040 16.213110
O 2.950685 3.495988 4.653586
O 17.645646 11.885171 16.078799
O 3.867803 12.784598 2.985852
O 1.516840 3.465029 17.959152
O 17.051930 2.450441 17.079846
O 19.052576 18.154859 2.542852
O 18.539634 15.742451 5.369952
O 16.941509 4.797414 12.127366
O 18.108998 8.014378 8.914854
O 11.735772 15.618760 10.583048
O 6.527237 16.638142 6.817835
O 4.739175 17.241359 1.712942
O 15.763694 16.015069 15.125115
O 14.633659 8.502790 5.979803
O 17.990406 19.186138 6.711449
O 17.087648 19.261891 4.235336
O 6.438457 14.158798 13.659355
O 8.637943 5.975711 5.714379
O 3.696492 13.367660 10.371699
O 10.713109 4.276733 19.458257
O 12.191594 14.267573 3.227457
O 19.620798 1.745324 15.930104
O 14.840105 15.130419 3.594617
O 18.535909 1.843986 7.833154
O 19.534650 16.625726 16.461936
O 1.134677 12.883140 2.503369
O 17.911147 17.356065 14.336023
O 19.065729 19.177456 17.261382
O 13.413726 3.933294 18.936849
O 19.375578 9.292636 2.168931
O 10.273633 16.549201 1.711851
O 8.525888 3.117505 11.428861
O 9.322632 19.294095 3.039398
O 2.624955 11.554152 7.372725
O 6.487449 16.945619 15.216364
O 10.806371 18.628583 16.498068
O 14.276748 6.232826 10.342518
O 6.455733 10.037931 15.344037
O 17.423747 15.481898 0.065549
O 8.401200 10.434403 6.762831
O 4.351816 16.028540 9.836889
O 16.612817 16.655486 7.064014
O 12.198466 7.918098 4.815168
O 0.404921 14.904948 18.786777
O 5.119635 16.880267 17.731520
O 5.140209 6.557387 0.772534
O 18.903965 17.397377 9.161172
O 5.258866 19.604276 12.726662
O 13.924546 13.731471 13.576097
O 14.594605 8.826509 11.807322
O 6.365614 19.580663 17.233310
O 14.491966 18.128083 16.449138
O 16.341737 11.986195 0.479400
O 12.906412 19.058193 1.577441
O 9.023452 7.055536 19.384766
O 9.828802 8.369960 6.418495
O 6.593163 4.547219 12.793384
O 16.368425 18.507138 9.479435
O 5.820127 11.058639 0.460154
O 12.570333 18.481994 4.177579
O 10.782149 4.942074 16.398826
O 6.041042 15.272321 0.787093
O 10.159136 16.780419 8.748393
O 2.565982 17.474942 7.802971
O 2.372918 4.158929 8.049443
O 1.618699 1.588523 7.208223
O 14.218329 18.236910 11.272203
O 8.393945 14.735975 8.457569
O 7.233905 10.745578 9.156340
O 4.501307 3.466444 18.763272
O 14.961867 10.294275 9.565178
O 15.587410 13.498738 16.827908
O 17.819941 0.938842 10.397867
O 15.152387 15.624832 9.191503
O 1.301035 4.830551 3.069971
O 13.466662 7.437013 14.296970
O 7.793273 10.322016 3.724300
O 15.396563 7.909817 8.319641
O 4.096870 6.633955 8.484160
O 5.458836 8.937566 9.749795
O 18.564046 4.273689 18.472243
O 0.507789 9.863045 19.419463
O 8.536523 16.508306 19.314851
O 10.573013 11.348021 4.370387
O 11.173137 11.525483 12.506452
O 6.526180 5.975264 15.410860
O 4.666320 13.234851 6.675427
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H 12.794009 1.143401 5.991878
H 12.457694 0.259767 4.809517
H 17.146495 3.397125 5.813066
H 17.077995 2.048396 6.497270
H 8.109698 19.492632 17.916208
H 8.603322 18.468007 18.915395
H 18.872490 11.781930 4.618143
H 19.913825 10.742030 4.973282
H 1.214036 15.979527 0.836383
H 1.358359 17.476442 1.010481
H 2.390286 7.445471 2.260321
H 2.070305 5.973095 2.113291
H 15.509428 8.772084 18.297736
H 14.251371 8.011575 17.936053
H 2.164986 6.318148 11.182179
H 3.218966 6.327193 10.095468
H 9.055148 19.771841 9.009256
H 9.994340 20.234355 7.915686
H 12.887272 16.221041 7.145561
H 13.828504 15.375449 7.976796
H 2.782034 7.729455 17.572501
H 3.478506 9.069249 17.463992
H 0.813913 9.013662 9.540298
H 0.907873 9.602664 10.931751
H 1.611663 10.370613 6.955031
H 1.426892 8.881297 6.755797
H 11.569319 2.792807 15.834785
H 10.368580 2.168582 16.513362
H 5.660933 13.928780 19.380332
H 5.737997 12.426877 19.206427
H 0.134365 19.072616 -0.724483
H -0.018751 19.090477 0.781549
H 9.201732 12.872141 2.496357
H 9.456298 12.897033 3.988494
H 16.788628 11.234043 12.209613
H 17.574313 11.332952 10.919337
H 2.746213 8.702709 4.195199
H 2.996867 9.918216 3.328245
H 10.211565 17.359740 15.621149
H 9.823198 16.689417 14.320482
H -0.294761 18.824715 14.202086
H 0.286922 19.149038 12.842544
H 1.384509 14.589709 6.577245
H 0.307892 13.569111 6.879193
H 1.242724 17.700491 6.564055
H 0.746944 18.238717 5.238759
H 9.172808 13.568159 7.618389
H 10.267378 13.419830 6.583106
H 6.019270 16.037783 4.023368
H 6.476663 17.413259 3.586613
H 19.101092 13.949106 14.346483
H 19.460268 14.606258 15.662173
H 0.193689 5.364865 9.707939
H -0.331513 5.489025 8.293498
H 13.069212 4.037530 6.941364
H 13.596349 4.590316 8.248441
H 14.866541 3.817586 11.220490
H 15.187136 2.384994 11.590347
H 2.696486 -0.156487 8.971264
H 1.897491 0.322033 10.164797
H 10.768963 8.712303 13.572688
H 11.639620 9.727058 12.862672
H 3.501892 4.510997 15.512460
H 2.701112 5.785656 15.673371
H 6.068482 4.004972 8.090542
H 6.434687 2.581410 8.452840
H 10.191143 4.829692 3.291673
H 11.315558 5.528156 4.026340
H 14.742475 10.800365 0.641681
H 14.007409 9.598574 0.087362
H 17.315275 7.546781 2.288857
H 18.350716 7.962460 1.265642
H 3.318725 7.996834 13.657551
H 3.155054 8.071880 15.160706
H 17.078145 14.851875 2.881938
H 18.256853 15.393690 3.662309
H 8.557198 14.442603 16.925776
H 9.424718 15.602840 16.486280
H 8.707486 18.696053 11.054040
H 10.173925 18.847305 11.398385
H 12.706339 5.161491 12.738368
H 13.661237 6.012986 13.547701
H 15.179902 5.118546 6.759066
H 15.651428 5.033294 5.322999
H 10.902058 14.438185 14.348341
H 11.548813 13.604605 15.434043
H 18.050841 9.667340 14.218656
H 17.258525 10.892508 14.622504
H 1.899104 16.425197 10.842568
H 1.224070 15.182656 10.301906
H 9.376583 3.418369 18.259202
H 9.054424 1.939153 18.264452
H 15.443399 0.743778 1.484981
H 14.331590 -0.076126 0.865680
H 1.170328 4.320504 14.465003
H 1.806394 3.577476 13.309484
H 1.849435 15.794035 13.157208
H 2.458467 16.993748 13.851227
H 11.991111 7.382537 17.978253
H 11.795238 6.330900 16.906998
H 18.068558 7.977711 5.490581
H 17.587746 6.674374 6.092268
H 17.116471 5.541781 1.601614
H 17.641490 4.207059 2.086141
H 12.153990 13.553634 4.815617
H 12.628689 13.729582 6.242361
H 16.330014 11.257761 2.165161
H 16.012891 11.631772 3.597447
H 5.154880 5.535489 5.673787
H 4.083021 4.471601 5.779412
H 18.907168 10.704097 18.781072
H 17.714610 9.822259 18.477658
H 4.292349 2.437911 17.515194
H 4.417532 2.288417 16.013903
H 18.092840 11.250951 7.403555
H 19.457826 10.873239 7.938383
H 11.016838 3.957561 5.893053
H 10.498074 4.550537 7.185786
H 0.569907 12.683934 9.938953
H 1.892871 13.377656 10.184739
H 16.319546 8.197457 11.874214
H 17.326178 8.138060 10.745029
H 11.219209 5.423499 11.032984
H 11.008719 3.976127 11.423757
H 15.358390 17.250274 5.862108
H 15.560717 18.244485 4.738496
H 1.379228 13.224549 19.106095
H 1.673674 12.701482 20.495914
H 6.597693 2.328303 2.660352
H 6.543056 2.250890 4.171285
H 12.891746 -0.427390 11.378358
H 12.707398 0.214358 12.737060
H 10.121466 0.512996 0.091711
H 11.417784 0.369505 0.860387
H 9.739829 16.900826 12.072975
H 10.868091 15.940402 12.383629
H 12.075983 16.443348 17.478504
H 13.273916 17.360268 17.605422
H 11.155873 9.209976 17.069162
H 10.357259 10.489696 16.940996
&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-256
RUN_TYPE MD
PRINT_LEVEL LOW
EPS_CHECK_DIAG 1.0E-12
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 0.5
TEMPERATURE 300.0
&END MD
&END MOTION
Výkon na jednom uzle | Výkon na viacerých uzloch
:------------------------------:|:----------------------------:
 | 
???+ Note "Zmena systému"
Systém bol pre cross-node benchmarky zmenený, pretože systém zvolený pre jednouzlové výpočty je relatívne malý.
Ide o krátku simuláciu molekulárnej dynamiky s 1000 časovými krokmi v NPT
ensemble pri 300 K. Zostáva z 28000 atómov – 10³ superbunky so 28 atómami železného silikátu (Fe2SiO4, tiež známy ako Fayalite) na jednocčkovú bunku. Simulácia používa klasický potenciál (Morse s repulzným členom s cutoff 5.5 Å) s elektrostatičkým pôsobením na dlhé vzdialenosti pomocou súčtu Smoothed Particle Mesh Ewald (SPME). Hoci CP2K podporuje klasické potenciály prostredníctvom modulu Frontiers In Simulation Technology (FIST), nejde o typický výpočet pre CP2K, je však zahrnutý, aby dal predstavu o rozdieli výkonu medzi strojmí pre MM časť QM/MM výpočtu.
??? Example "Fayalite.inp"
&GLOBAL
PROJECT_NAME fayalite_pedone_md
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&FORCE_EVAL
METHOD FIST
STRESS_TENSOR ANALYTICAL
&MM
&FORCEFIELD
&CHARGE
ATOM Fe
CHARGE 1.2
&END CHARGE
&CHARGE
ATOM Si
CHARGE 2.4
&END CHARGE
&CHARGE
ATOM O
CHARGE -1.2
&END CHARGE
IGNORE_MISSING_CRITICAL_PARAMS
&NONBONDED
&GENPOT
ATOMS Fe O
FUNCTION D*((1-exp(-A*(X-R)))^2 - 1) + C/(X^12)
PARAMETERS D A R C
RCUT 5.5
VALUES 0.078171 1.822638 2.658163 2.0
UNITS eV angstrom^-1 angstrom eV*angstrom^12
VARIABLES X
&END GENPOT
&GENPOT
ATOMS Si O
FUNCTION D*((1-exp(-A*(X-R)))^2 - 1) + C/(X^12)
PARAMETERS D A R C
RCUT 5.5
VALUES 0.340554 2.006700 2.100000 1.0
UNITS eV angstrom^-1 angstrom eV*angstrom^12
VARIABLES X
&END GENPOT
&GENPOT
ATOMS O O
FUNCTION D*((1-exp(-A*(X-R)))^2 - 1) + C/(X^12)
PARAMETERS D A R C
RCUT 5.5
VALUES 0.042395 1.379316 3.618701 22.0
UNITS eV angstrom^-1 angstrom eV*angstrom^12
VARIABLES X
&END GENPOT
&END NONBONDED
&SPLINE
EMAX_SPLINE [eV] 100
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
GMAX 15 33 19
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 4.8195 10.4788 6.0873
MULTIPLE_UNIT_CELL 10 10 10
&END CELL
&TOPOLOGY
MULTIPLE_UNIT_CELL 10 10 10
&END TOPOLOGY
&COORD
SCALED
! Fe1 and symmetric images
Fe 0.0 0.0 0.0
Fe 0.5 0.5 0.5
Fe 0.0 0.0 0.5
Fe 0.5 0.5 0.0
! Fe2
Fe 0.98598 0.28026 0.25
Fe 0.51402 0.78026 0.25
Fe 0.01402 0.71974 0.75
Fe 0.48698 0.21974 0.75
! Si
Si 0.43122 0.09765 0.25
Si 0.06878 0.59765 0.25
Si 0.56878 0.90235 0.75
Si 0.93122 0.40235 0.75
! O1
O 0.76814 0.09217 0.25
O 0.73186 0.59217 0.25
O 0.23186 0.90783 0.75
O 0.26814 0.40783 0.75
! O2
O 0.20895 0.45365 0.25
O 0.29015 0.95365 0.25
O 0.79105 0.54635 0.75
O 0.70895 0.04635 0.75
! O3 (8 symmetric images)
O 0.28897 0.16563 0.03643
O 0.21103 0.66563 0.46357
O 0.71103 0.83437 0.53643
O 0.78897 0.33437 0.96357
O 0.71103 0.83437 0.96357
O 0.78897 0.33437 0.53643
O 0.28897 0.16563 0.46357
O 0.21103 0.66563 0.03643
&END COORD
&END SUBSYS
&END FORCE_EVAL
&MOTION
&MD
ENSEMBLE NPT_I
STEPS 1000
TEMPERATURE 300
TIMESTEP 2.0
&BAROSTAT
PRESSURE 1.0
&END BAROSTAT
&THERMOSTAT
&NOSE
&END NOSE
&END THERMOSTAT
&END MD
&END MOTION
Výkon na jednom uzle | Výkon na viacerých uzloch
:------------------------------:|:----------------------------:
 | 
???+ Note "Zdieľaný súborový systém"
Klesajúci výkon v porovnaní s tabuľkou výkonu na jednom uzle vľavo a cross-node výkonom
nameraným pre jeden uzol je spôsobený odlišnými diskami použitými počas výpočtov, t.j.
výkon na jednom uzle bol vypočítaný s použitím lokálneho disku **/work/**, zatiaľ čo cross-node
výkon bol vypočítaný na zdieľanom súborovom systéme **/scratch/**.
Ide o single-point výpočet energie s použitím lineárne škálovaného DFT.
Zostáva z 6144 atómov v boxe 39 Å3 (celkovo 2048 molekúl vody). Používa sa LDA funkcionál s bázou DZVP MOLOPT a cutoff 300 Ry. Pre veľké systémy bude lineárne škálovací prístup k riešeniu Self-Consistent-Field rovnic výpočtovo oveľa lacnejší než použitie štandardného DFT a umožňuje škálovanie až na 1 milión atómov pre jednoduché systémy. Náklady lineárneho škálovania vyplývajú z toho, že algoritmus je založený na iterácii nad maticou hustoty. Kubicky škálovací krok ortonormalizácie štandardného Quickstep DFT s použitím OT sa vynechá a kľúčovou operáciou je násobenie riedkych, ktoré majú počet nenulových položiek škálovaný lineárne s veľkosťou systému. Tieto sú efektívne implementované v knižnici DBCSR.
??? Example "H2O_dft_ls.inp"
! size can be tuned by setting NREP
! molecular clustering is an interesting parameter
@SET NREP 2
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME POTENTIAL
&PRINT
&MULLIKEN OFF
&END MULLIKEN
&END PRINT
&MGRID
CUTOFF 300
&RS_GRID
MAX_DISTRIBUTED_LEVEL 5
&END
SKIP_LOAD_BALANCE_DISTRIBUTED
&END MGRID
&QS
EPS_DEFAULT 1.0E-10
LS_SCF
&DISTRIBUTION
BASIC_OPTIMIZATION .FALSE.
BASIC_SPATIAL_OPTIMIZATION .TRUE.
&END
&END QS
&LS_SCF
MAX_SCF 2
EPS_FILTER 1.0E-6
EPS_SCF 1.0E-6
MU 0.15
MIXING_FRACTION 0.45
PURIFICATION_METHOD TRS4
S_PRECONDITIONER MOLECULAR
MATRIX_CLUSTER_TYPE MOLECULAR
REPORT_ALL_SPARSITIES OFF
PERFORM_MU_SCAN OFF
&END
&SCF
MAX_SCF 30
EPS_SCF 1.0E-7
&END
&XC
&XC_FUNCTIONAL PADE
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&TOPOLOGY
MULTIPLE_UNIT_CELL ${NREP} ${NREP} ${NREP}
&END
&CELL
ABC 9.8528 9.8528 9.8528
MULTIPLE_UNIT_CELL ${NREP} ${NREP} ${NREP}
&END CELL
# 32 H2O (TIP5P,1bar,300K) a = 9.8528
&COORD
O 2.280398 9.146539 5.088696 H2O
H 1.762019 9.820429 5.528454 H2O
H 3.095987 9.107088 5.588186 H2O
O 1.251703 2.406261 7.769908 H2O
H 0.554129 2.982634 8.082024 H2O
H 1.771257 2.954779 7.182181 H2O
O 1.596302 6.920128 0.656695 H2O
H 2.112148 6.126321 0.798136 H2O
H 1.776389 7.463264 1.424030 H2O
O 2.957518 3.771868 1.877387 H2O
H 3.754249 3.824017 1.349436 H2O
H 3.010580 4.524142 2.466878 H2O
O 0.228972 5.884026 6.532308 H2O
H 0.939475 5.243834 6.571945 H2O
H 0.515723 6.520548 5.877445 H2O
O 9.023431 6.119654 0.092451 H2O
H 9.852960 6.490366 0.393593 H2O
H 8.556008 6.860063 -0.294256 H2O
O 7.256289 8.493641 5.772041 H2O
H 7.886607 7.941321 6.234506 H2O
H 7.793855 9.141028 5.315813 H2O
O 5.090422 9.467016 0.743177 H2O
H 4.467366 9.971162 0.219851 H2O
H 5.758685 10.102795 0.998994 H2O
O 6.330888 7.363471 3.747750 H2O
H 6.652693 7.917443 3.036562 H2O
H 6.711966 7.743594 4.539279 H2O
O 7.763819 8.349367 9.279457 H2O
H 7.751955 8.745180 10.150905 H2O
H 7.829208 9.092212 8.679343 H2O
O 8.280798 3.837153 5.799282 H2O
H 8.312540 3.218330 6.528858 H2O
H 8.508855 4.680699 6.189990 H2O
O 8.878250 2.025797 1.664102 H2O
H 9.742249 1.704975 1.922581 H2O
H 8.799060 2.876412 2.095861 H2O
O 9.160372 0.285100 6.871004 H2O
H 9.505360 1.161677 6.701213 H2O
H 9.920117 -0.219794 7.161006 H2O
O 4.962043 4.134437 0.173376 H2O
H 4.749903 4.186003 -0.758595 H2O
H 5.248010 5.018415 0.403676 H2O
O 2.802896 8.690383 2.435952 H2O
H 3.576065 9.078451 2.026264 H2O
H 2.720238 9.146974 3.273164 H2O
O 9.123223 3.549232 8.876721 H2O
H 9.085561 4.493058 9.031660 H2O
H 9.215391 3.166305 9.749133 H2O
O 1.453702 1.402538 2.358278 H2O
H 1.999705 2.060411 1.927796 H2O
H 1.824184 0.564565 2.081195 H2O
O 6.536550 1.146790 7.609732 H2O
H 7.430334 0.849764 7.438978 H2O
H 6.576029 1.537017 8.482885 H2O
O 2.766709 0.881503 9.544263 H2O
H 2.415851 1.576460 8.987338 H2O
H 2.276957 0.099537 9.289499 H2O
O 0.856426 2.075964 5.010625 H2O
H 1.160987 1.818023 4.140602 H2O
H 0.350256 2.874437 4.860741 H2O
O 6.386036 1.918950 0.242690 H2O
H 5.768804 2.638450 0.375264 H2O
H 7.221823 2.257514 0.563730 H2O
O 2.733023 4.452756 5.850203 H2O
H 3.260797 5.243390 5.962382 H2O
H 3.347848 3.732214 5.988196 H2O
O 4.600039 9.254314 6.575944 H2O
H 5.328688 9.073059 5.982269 H2O
H 5.007063 9.672150 7.334875 H2O
O 3.665373 6.210561 3.158420 H2O
H 4.566850 6.413356 3.408312 H2O
H 3.273115 7.061666 2.963521 H2O
O 3.371648 6.925594 7.476036 H2O
H 3.878372 7.435003 6.843607 H2O
H 3.884673 6.966316 8.283117 H2O
O 5.287920 3.270653 6.155080 H2O
H 5.918240 3.116802 5.451335 H2O
H 5.355924 2.495093 6.711958 H2O
O 5.225237 6.959594 9.582991 H2O
H 5.071858 7.687254 10.185667 H2O
H 6.106394 7.112302 9.241707 H2O
O 0.846293 5.595877 3.820630 H2O
H 1.637363 5.184910 4.169264 H2O
H 0.427645 4.908936 3.301903 H2O
O 9.785620 8.164617 3.657879 H2O
H 9.971698 7.227076 3.709104 H2O
H 10.647901 8.579244 3.629806 H2O
O 8.509982 4.430362 2.679946 H2O
H 8.046808 5.126383 2.213838 H2O
H 7.995317 4.290074 3.474723 H2O
O 1.337625 8.580920 8.272484 H2O
H 1.872601 7.864672 7.930401 H2O
H 0.837635 8.186808 8.987268 H2O
O 8.054437 9.221335 1.991376 H2O
H 8.314696 10.115534 2.212519 H2O
H 8.687134 8.667252 2.448452 H2O
&END COORD
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q1
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PADE-q6
&END KIND
&PRINT
&ATOMIC_COORDINATES OFF
&END
&MOLECULES OFF
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT H2O
RUN_TYPE ENERGY
PRINT_LEVEL MEDIUM
EXTENDED_FFT_LENGTHS
! TRACE
! TRACE_MAX 10000
&END GLOBAL
Výkon na jednom uzle | Výkon na viacerých uzloch
:------------------------------:|:----------------------------:
 | 
Vzhľadom na vyššie spomenutú zložitosť je používateľom v /storage-apps/scripts/ k dispozícii skript na plánovanie hybridného MPI/OpenMP vykonávania, CP2K_plan.sh. Pre systém s 64 jadrovým uzlami (dva sokety, vypnuté hyperthreading) vyzerá nastavenie „system metric“ takto:
./CP2K_plan.sh <num-nodes> <ncores-per-node> <nthreads-per-core> <nsockets-per-node>
./CP2K_plan.sh 1 64 1 2
./CP2K_plan.sh 2 128 1 2
Príklad spúšťacieho skriptu¶
Tento skript si môžete skopírovať a upraviť ako cp2k_run.sh a odoslať úlohu na výpočtový uzol príkazom sbatch cp2k_run.sh.
#!/bin/bash
#SBATCH -J "CP2K" # name of job in SLURM
#SBATCH --account=<your project> # project number
#SBATCH --partition=medium # selected partition (short, medium, long)
#SBATCH --nodes=1 # number of nodes
#SBATCH --ntasks=64 # number of mpi ranks, needs to be tested for the best performance
#SBATCH --cpus-per-task=8 # number of cpus per mpi rank, needs to be tested for the best performance
#SBATCH --time=12:00:00 # time limit for a job
#SBATCH -o stdout.%J.out # standard output
#SBATCH -e stderr.%J.out # error output
# Modules
module load CP2K/2022.1-foss-2022a
# Single launcher: srun (SLURM) is used to launch the MPI job.
srun -n ${SLURM_NTASKS} cp2k.popt -i example.inp > outputfile.out
Created by: