CP2K¶
Description¶
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the Gaussian and Plane Waves (GPW) and the all-electron GPW (GAPW) approaches.
User guide¶
For more information about the CP2K tutorials and documentation, refer to the CP2K HOWTOs.
Available Versions¶
The following versions of CP2K are currently available:
- Runtime dependencies:
- None, required libraries and dependencies are loaded automatically with the
CP2K/2022.1-foss-2022amodule.
- None, required libraries and dependencies are loaded automatically with the
You can load the CP2K module with the following command:
module load CP2K/2022.1-foss-2022a
- Runtime dependencies:
- None, required libraries and dependencies are loaded automatically with the
CP2K/2023.1-foss-2022amodule.
- None, required libraries and dependencies are loaded automatically with the
You can load the CP2K module with the following command:
module load CP2K/2023.1-foss-2022a
- Runtime dependencies:
- None, required libraries and dependencies are loaded automatically with the
CP2K/2023.1-foss-2022bmodule.
- None, required libraries and dependencies are loaded automatically with the
You can load the CP2K module with the following command:
module load CP2K/2023.1-foss-2022b
Benchmarking CP2K¶
CP2K's grid-based calculation as well as DBCSR's block sparse matrix multiplication (Cannon algorithm) prefer a square number for the total rank-count (2D communication pattern).
It can be more efficient to leave CPU cores unused in order to achieve this square number property rather than using all cores with a "non-preferred" total rank-count. Counter-intuitively, even an unbalanced rank-count per node (i.e. different rank-counts per socket) can be an advantage. Pinning MPI processes and placing threads requires extra care to be taken on a per-node basis to load a dual-socket system in a balanced fashion or to set up space between ranks for the OpenMP threads.
In order to better understand how CP2K utilises the available hardware on Devana and how to get good performance we can examine the effect on benchmark performance of the choice of the number of MPI ranks per node and OpenMP threads.
The following command has been used to run the benchmarks:
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
Working directory
Single-node benchmarks have been run on local /work/ storage native to each compute node, which is generally faster than the shared storage hosting the /home/ and /scratch/ directories.
Benchmarks have been made on the following systems:
Ab-initio molecular dynamics of liquid water using the Born-Oppenheimer approach,
using Quickstep DFT. Production quality settings for the basis sets (TZV2P) and the planewave cutoff (280 Ry) are chosen, and the Local Density Approximation (LDA) is used for the calculation of the Exchange-Correlation energy. The configurations were generated by classical equilibration, and the initial guess of the electronic density is made based on Atomic Orbitals. The single-node system contains 64 water molecules (192 atoms, 640 electrons) in a 12.4 ų cell and the cross-node system contains 256 water molecules (768 atoms, 2560 electrons) in a 19.7 ų cell. Both MDs are run for 10 steps.
??? 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
O 6.402945 13.151964 8.883378
O 14.376039 10.834261 14.016712
O 12.414962 17.952195 7.781521
O 15.010477 14.767335 19.167546
O 19.030000 14.611263 12.585150
O 13.687862 10.891629 16.670175
O 18.228913 4.485968 7.304354
O 19.452020 4.604955 11.192355
O 5.551354 0.465377 8.319775
O 6.508259 14.411282 3.238631
O 12.221639 13.029840 10.583593
O 4.066102 9.924226 13.111459
O 8.562132 5.495116 1.808549
O 14.811554 4.923188 3.636113
O 6.258811 19.338925 5.522351
O 11.344385 1.682912 8.058418
O 16.546534 19.702995 18.030429
O 3.531111 10.317432 18.943618
O 6.491499 16.121738 11.637543
O 7.528156 8.090478 1.871301
O 7.387113 2.962459 5.373266
O 14.786713 13.534978 11.094518
O 18.969830 3.106882 2.108279
O 8.837248 18.119152 6.081332
O 16.662775 8.466431 3.953000
O 13.082313 10.454414 3.258637
O 8.800684 5.165380 8.265621
O 8.354846 7.754998 16.924572
O 2.636580 7.693780 6.195845
O 13.379317 6.797664 1.827698
O 8.112212 10.301131 19.156016
O 8.384419 14.074378 11.889330
O 0.625772 5.501543 5.762600
O 0.501632 7.576243 11.607246
O 13.137721 19.687247 14.749134
O 3.370547 15.420721 3.067192
O 19.618824 8.184412 14.661511
O 12.307864 1.134825 5.167365
O 17.083367 2.459190 5.632717
O 8.896659 19.204160 18.378493
O 19.462806 11.137648 4.227427
O 1.457609 16.646983 1.477792
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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
Single node Performance | Cross-node Performance
:------------------------------:|:----------------------------:
 | 
???+ Note "System change"
The system was changed for the cross-node benchmarks because the system selected for the single-node calculations is relatively small.
This is a short molecular dynamics run of 1000 time steps in a NPT ensemble at 300K.
It consists of 28000 atoms - a 10³ supercell with 28 atoms of iron silicate (Fe2SiO4, also known as Fayalite) per unit cell. The simulation employs a classical potential (Morse with a hard-core repulsive term and 5.5 Å cutoff) with long-range electrostatics using Smoothed Particle Mesh Ewald (SPME) summation. While CP2K does support classical potentials via the Frontiers In Simulation Technology (FIST) module, this is not a typical calculation for CP2K but is included to give an impression of the performance difference between machines for the MM part of a QM/MM calculation.
??? 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
Single node Performance | Cross-node Performance
:------------------------------:|:----------------------------:
 | 
???+ Note "Shared storage usage"
Performance drop from single node performance table on left and cross-node performance measured for one node is caused by different disks used during calculations, i.e., single node performance was calculated using local **/work/** disk, while cross-node performance was calculated on shared **/scratch/** storage.
This is a single-point energy calculation using linear-scaling DFT.
It consists of 6144 atoms in a 39 Å3 box (2048 water molecules in total). An LDA functional is used with a DZVP MOLOPT basis set and a 300 Ry cut-off. For large systems the linear-scaling approach for solving Self-Consistent-Field equations will be much cheaper computationally than using standard DFT and allows scaling up to 1 million atoms for simple systems. The linear scaling cost results from the fact that the algorithm is based on an iteration on the density matrix. The cubically-scaling orthogonalisation step of standard Quickstep DFT using OT is avoided and the key operation is sparse matrix-matrix multiplications, which have a number of non-zero entries that scale linearly with system size. These are implemented efficiently in the DBCSR library.
??? 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
Single node Performance | Cross-node Performance
:------------------------------:|:----------------------------:
 | 
Because of the above-mentioned complexity, a script for planning MPI/OpenMP-hybrid execution, CP2K_plan.sh, is made available to users in /storage-apps/scripts/. For a system with 64 cores per node (two sockets, disabled hyperthreading), setting up the "system metric" looks like:
./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
Example run script¶
You can copy and modify this script as cp2k_run.sh and submit the job to a compute node with the command 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
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