This benchmark test the performance of CP2K to run calculations of the electronic structure of relatively complex systems containing a million atoms. The input is based on earlier work where the electronic structure of the STMV virus was simulated based on DFT and subsystem DFT. Here, instead, the xTB tight-binding method is employed. The input is realistic in its input settings and might be useful to set up similar systems.
The benchmark exercises in particular the sparse matrix handling and linear scaling algorithms in CP2K. It performs 1 step of geometry optimization, so requires SCF, energy and force calculations. Some properties are computed as well. Given the xTB method, relatively small block sizes dominate in the sparse matrix multiplication.
A typical parallel run will require on the order of 256 nodes, to see completion of the benchmark in a reasonable time, and memory consumption. An invocation with slurm on a system with 32 threads per node (dual socket, Intel(R) Xeon(R) CPU E5-2695 v4 @ 2.10GHz, Piz Daint multi-core) could look like:
export OMP_NUM_THREADS=8
srun --cpu-bind=none --nodes=256 --ntasks=1024 --ntasks-per-node=4 \
--cpus-per-task=8 ./cp2k.psmp -i stmv_xtb.inp -o stmv_xtb.outWhich would need roughly 7Gb per rank (28Gb per node), and would run in in less than 4h. The timing report for this run (based on CP2K 7.0, git:bf104a630):
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 6.012 6.487 8256.073 8256.198
cp_geo_opt 1 2.0 0.041 0.092 8236.532 8236.652
geoopt_lbfgs 1 3.0 0.010 0.074 8236.490 8236.639
cp_opt_gopt_step 1 4.0 0.087 0.285 8236.314 8236.439
cp_eval_at 2 5.0 0.097 0.148 8223.558 8223.698
qs_forces 2 6.0 0.831 1.322 8223.245 8223.380
qs_energies 2 7.0 0.034 0.117 8095.812 8099.994
ls_scf 2 8.0 0.029 0.093 7976.523 7980.780
ls_scf_main 2 9.0 0.016 0.055 7240.555 7240.672
dm_ls_curvy_optimization 47 10.0 0.003 0.076 6583.940 6599.528
dbcsr_multiply_generic 737 13.0 7.232 7.446 6427.778 6579.351
multiply_cannon 737 14.0 41.860 44.498 5883.682 6121.346
optimization_step 47 11.0 0.001 0.015 4866.856 4889.982
multiply_cannon_multrec 23584 15.0 4119.121 4434.655 4133.269 4447.990
compute_direction_newton 16 12.0 0.812 0.870 2530.534 2536.757
update_p_exp 47 12.0 0.009 0.015 2336.108 2359.676
mp_waitall_1 200904 16.1 1041.558 1716.869 1041.558 1716.869
transform_matrix_orth 65 11.0 0.002 0.003 1664.426 1698.501
commutator_symm 170 13.0 0.003 0.004 1413.495 1456.582
purify_mcweeny_orth 50 12.9 0.003 0.065 1312.274 1334.495
multiply_cannon_metrocomm3 23584 15.0 0.125 0.167 294.026 1106.474
multiply_cannon_metrocomm1 23584 15.0 0.172 0.196 596.117 1034.438
dbcsr_new_transposed 417 13.2 32.609 35.757 703.789 824.199
dbcsr_redistribute 417 14.2 379.063 436.415 659.380 776.357
multiply_cannon_metrocomm4 22847 15.0 0.156 0.232 200.626 526.612
mp_irecv_dv 58794 16.3 191.731 503.107 191.731 503.107
calculate_norms 47168 15.0 437.842 473.288 437.842 473.288
ls_scf_init_scf 2 9.0 0.014 0.088 461.141 461.330
ls_scf_init_matrix_S 2 10.0 0.001 0.030 413.455 414.477
ls_scf_dm_to_ks 49 10.0 0.001 0.023 381.400 401.911
matrix_sqrt_Newton_Schulz 2 11.0 0.023 0.426 389.123 389.457
make_m2s 1474 14.0 7.055 7.820 283.134 324.396
mp_alltoall_i22 569 14.7 236.860 323.813 236.860 323.813
make_images 1474 15.0 36.912 39.536 268.811 310.928
ls_scf_post 2 9.0 0.009 0.087 274.798 279.184
mp_sum_l 2322 13.8 207.665 270.645 207.665 270.645
density_matrix_trs4 1 10.0 0.015 0.042 248.757 249.218
qs_ks_update_qs_env 50 11.0 0.000 0.000 208.761 218.124
make_images_data 1474 16.0 0.081 0.122 152.463 205.226
hybrid_alltoall_any 1525 16.9 0.731 22.546 142.014 199.699
matrix_ls_to_qs 51 11.0 0.001 0.001 183.276 198.338
mp_sum_d 2810 12.6 148.925 197.472 148.925 197.472
rebuild_ks_matrix 52 11.9 0.042 0.061 194.777 195.286
build_xtb_ks_matrix 52 12.9 5.507 6.598 194.735 195.237
dbcsr_complete_redistribute 101 12.5 89.804 93.327 171.256 191.421
post_scf_homo_lumo 2 10.0 0.000 0.001 186.075 186.911
matrix_decluster 51 12.0 0.095 0.238 147.731 168.361
dbcsr_finalize 3365 14.5 2.293 2.770 140.479 155.280
dbcsr_frobenius_norm 712 13.0 34.195 35.252 114.124 139.443
mp_sum_dm 430 9.1 131.588 135.181 131.588 135.181
mp_allgather_i34 737 15.0 71.689 130.243 71.689 130.243
dbcsr_merge_all 2761 15.5 72.120 75.581 118.675 123.148
qs_energies_init_hamiltonians 2 8.0 0.007 0.082 119.151 119.333
dbcsr_add_d 1749 13.0 0.006 0.008 100.754 111.917
dbcsr_add_anytype 1749 14.0 25.357 28.939 100.748 111.910
build_xtb_matrices 4 8.0 64.662 80.037 110.824 111.490
make_images_sizes 1474 16.0 0.006 0.036 37.330 106.622
mp_alltoall_i44 1474 17.0 37.324 106.617 37.324 106.617
dbcsr_dot_sd 345 13.0 13.894 14.777 73.443 101.347
arnoldi_extremal 9 11.2 0.089 0.533 98.396 100.332
arnoldi_normal_ev 9 12.2 0.343 0.839 98.307 100.124
build_xtb_coulomb 52 13.9 18.489 19.417 99.082 99.771
calculate_dispersion_pairpot 2 9.0 57.454 70.439 92.449 92.457
ao_charges_kp_2 52 13.9 2.220 2.512 89.914 91.795
mp_alltoall_d11v 1707 14.8 89.032 90.724 89.032 90.724
ao_charges_2 52 14.9 4.520 4.815 87.694 89.634
build_subspace 39 13.3 0.645 1.234 87.475 88.719
mp_shift_i 8184 9.0 46.858 66.427 46.858 66.427
setup_rec_index_2d 1474 15.0 59.164 65.956 59.164 65.956
dbcsr_matrix_vector_mult 884 14.0 0.068 1.905 61.132 64.708
dbcsr_data_release 70614 16.3 31.961 59.053 32.162 59.250
mp_sum_iv 744 14.9 42.010 51.567 42.010 51.567
mp_sum_dv 5097 15.6 44.088 50.582 44.088 50.582
ls_scf_initial_guess 2 10.0 0.000 0.015 47.606 48.384
calculate_w_matrix 2 10.0 0.000 0.000 44.894 45.647
dbcsr_copy_into_existing 51 12.0 35.076 44.774 35.077 44.775
dbcsr_matrix_vector_mult_local 884 15.0 38.363 44.350 38.371 44.359
dbcsr_multiply_generic_mpsum_f 60 12.7 0.000 0.000 28.968 43.956
ls_scf_store_result 2 10.0 0.020 0.206 42.334 42.976
matrix_qs_to_ls 50 10.0 0.001 0.021 35.255 37.254
matrix_cluster 50 11.0 0.115 0.300 35.254 37.254
and DBCSR statistics
COUNTER TOTAL BLAS SMM ACC
flops 2 x 2 x 2 36142856249008 0.0% 100.0% 0.0%
flops 2 x 2 x 8 39213980112512 0.0% 100.0% 0.0%
flops 8 x 2 x 2 43804007223424 0.0% 100.0% 0.0%
flops 2 x 8 x 2 44584775765312 0.0% 100.0% 0.0%
flops 4 x 2 x 2 90117651537184 0.0% 100.0% 0.0%
flops 2 x 4 x 2 90294481986400 0.0% 100.0% 0.0%
flops 2 x 2 x 4 97540850606240 0.0% 100.0% 0.0%
flops 8 x 8 x 2 97563507289344 0.0% 100.0% 0.0%
flops 2 x 4 x 8 107600053992192 0.0% 100.0% 0.0%
flops 4 x 2 x 8 107835358956416 0.0% 100.0% 0.0%
flops 8 x 4 x 2 117969022215680 0.0% 100.0% 0.0%
flops 4 x 8 x 2 119092012799616 0.0% 100.0% 0.0%
flops 8 x 2 x 4 130156579707520 0.0% 100.0% 0.0%
flops 2 x 8 x 4 130528054439040 0.0% 100.0% 0.0%
flops 8 x 2 x 8 161502281254912 0.0% 100.0% 0.0%
flops 2 x 8 x 8 166307689803776 0.0% 100.0% 0.0%
flops 4 x 4 x 2 229852669562368 0.0% 100.0% 0.0%
flops 2 x 4 x 4 247224891759168 0.0% 100.0% 0.0%
flops 4 x 2 x 4 249694810664896 0.0% 100.0% 0.0%
flops 8 x 8 x 4 305672038397440 0.0% 100.0% 0.0%
flops 4 x 4 x 8 308761351253760 0.0% 100.0% 0.0%
flops 8 x 4 x 4 362908283625472 0.0% 100.0% 0.0%
flops 4 x 8 x 4 365532741502720 0.0% 100.0% 0.0%
flops 8 x 4 x 8 455052334568448 0.0% 100.0% 0.0%
flops 4 x 8 x 8 465166240374272 0.0% 100.0% 0.0%
flops 4 x 4 x 4 648336487473152 0.0% 100.0% 0.0%
flops 8 x 8 x 8 10568517651483648 0.0% 100.0% 0.0%
flops inhomo. stacks 2554975071623610 100.0% 0.0% 0.0%
flops total 18.341948E+15 13.9% 86.1% 0.0%
flops max/rank 18.975286E+12 15.8% 84.2% 0.0%
matmuls inhomo. stacks 1752383451045 100.0% 0.0% 0.0%
matmuls total 55112132774528 3.2% 96.8% 0.0%
number of processed stacks 61576905441 3.4% 96.6% 0.0%
average stack size 830.2 897.3 0.0
marketing flops 36.676667E+21
-------------------------------------------------------------------------------
# multiplications 737
max memory usage/rank 7.564362E+09
# max total images/rank 1
# max 3D layers 1
# MPI messages exchanged 46790656
MPI messages size (bytes):
total size 4.348855E+15
min size 0.000000E+00
max size 202.967424E+06
average size 92.942816E+06
MPI breakdown and total messages size (bytes):
size <= 128 153760 0
128 < size <= 8192 83948 332481200
8192 < size <= 32768 54994 1018984136
32768 < size <= 131072 468286 34129603760
131072 < size <= 4194304 1278316 958318296392
4194304 < size <= 16777216 630819 5065558052384
16777216 < size 44120533 4342797468343176
-------------------------------------------------------------------------------
- -
- DBCSR MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS AVE VOLUME [Bytes]
MP_Group 1
MP_Bcast 28 12.
MP_Allreduce 4230 325415.
MP_Alltoall 5355 22325841.
MP_Wait 200464
MP_ISend 94336 47211041.
MP_IRecv 94336 47206344.
MP_Memory 19172
-------------------------------------------------------------------------------
MEMORY| Estimated peak process memory [MiB] 6402
SCF cycles output looks like
------------------------------ Linear scaling SCF -----------------------------
SCF 1 -2019286.740626037 -2019286.740626037 257.119279
SCF 2 -2022372.558790133 -3085.818164097 283.782252
SCF 3 -2024495.728609510 -5208.987983474 72.828389
SCF 4 -2026488.297578288 -7201.556952252 117.651759
SCF 5 -2029048.217573609 -2559.919995321 229.818745
SCF 6 -2030970.001095107 -4481.703516819 73.634025
SCF 7 -2032985.476104558 -6497.178526270 114.296279
SCF 8 -2033540.457572915 -554.981468357 234.732257
SCF 9 -2033521.016724448 -535.540619890 74.614194
SCF 10 -2033612.235695642 -626.759591084 112.382977
SCF 11 -2033854.276528493 -242.040832851 237.561626
SCF 12 -2033982.666816269 -370.431120626 66.611201
SCF 13 -2034003.081946934 -390.846251292 74.652012
SCF 14 -2034069.478891714 -66.396944780 264.631421
SCF 15 -2033892.868982235 110.212964699 74.861617
SCF 16 -2034077.572747632 -74.490800698 108.504719
SCF 17 -2034120.056681868 -42.483934236 281.836313
SCF 18 -2034151.889439356 -74.316691724 66.644064
SCF 19 -2034184.719602434 -107.146854802 74.555730
SCF 20 -2034205.581420024 -20.861817590 260.906525
SCF 21 -2034080.981126470 103.738475963 75.491708
SCF 22 -2034213.969040957 -29.249438523 106.544563
SCF 23 -2034217.910995587 -3.941954630 318.571562
SCF 24 -2034219.786293399 -5.817252442 73.672705
SCF 25 -2034219.952455441 -5.983414485 104.098476
SCF 26 -2034224.105341386 -4.152885945 295.732344
SCF 27 -2034225.354788742 -5.402333301 74.348011
SCF 28 -2034225.361724817 -5.409269375 106.903410
SCF 29 -2034226.617073632 -1.255348816 312.159937
SCF 30 -2034226.664080255 -1.302355439 74.832404
SCF not converged!
SCF 1 -2034504.114579430 -102.226643770 294.428820
SCF 2 -2034582.030317720 -180.142382059 59.509095
SCF 3 -2034669.633673732 -267.745738071 67.661870
SCF 4 -2034686.756534706 -17.122860974 240.952248
SCF 5 -2034383.864712474 285.768961258 70.071076
SCF 6 -2034726.751386791 -57.117713059 97.803430
SCF 7 -2034732.385823286 -5.634436496 286.235458
SCF 8 -2034737.205264020 -10.453877229 61.265636
SCF 9 -2034749.118323179 -22.366936388 69.003241
SCF 10 -2034748.012737155 1.105586024 305.655801
SCF 11 -2034751.398910127 -2.280586948 63.232803
SCF 12 -2034751.430011003 -2.311687824 62.608883
SCF 13 -2034751.818950539 -0.388939536 333.393301
SCF 14 -2034752.073886994 -0.643875991 62.769221
SCF 15 -2034752.205481594 -0.775470591 63.329253
SCF 16 -2034752.282033039 -0.076551445 351.013058
SCF 17 -2034752.318892021 -0.113410427 63.425647
SCF 18 -2034752.322544992 -0.117063398 63.808013