large water system calculation with cp2k

Phil G. phil... at aol.com
Fri Sep 9 13:27:39 CEST 2016


Dear CP2K group,

before the MD simulation of the interfacial arrangement of water molecules 
near the ferroelectric lithium niobate single crystal (here the positive 
polar surface site), I had performed the geometry optimization of the 
LiNbO3 slab (consisting of 8 unit cells) with fixing all atoms of the lower 
unit cells to get reconstructed LiNbO3 surface (Nb-O2 surface termination).
(the comparison between surface reconstruction with only the lowest atom 
layers fixed and that with all atoms of lower unit cells fixed shows no 
remarkable difference, only small energy difference of about 0.014 a.u.)

For the next step I build a large system consisting of 24 LiNbO3 unit cells 
(6x6x2) and 478 water molecules (solvated by VMD package solvate 1.5) in 
the volume cell box of size 30.888 x 26.7498 x 100.0 Angstrom^3. Like the 
geometry optimization above I set all atoms of the lower unit cells of 
LiNbO3 fixed and I want to start the geometry optimization of the large 
system (of about 3600 atoms), but short time after submitting the 
simulation files I got the error message that the required memory exceeds 
the memory size available (of a small part of super computer system at our 
institute).

After searching for the alternate way I found some interesting articles 
about new linear scaling methods:
a) J. Chem. Theory Comput. 9 (2013), 4421 
[http://pubs.acs.org/doi/abs/10.1021/ct400595k]
b) J. Chem. Theory Comput. 8 (2012), 3565 
[http://pubs.acs.org/doi/abs/10.1021/ct200897x]

Now I would like to rewrite the input code but because I am beginner and I 
don't really know how to write correct codes into the input file for 
geometry optimization and then MD simulation (one input file for geom.-opt. 
and one for MD sim.) on the basis of the linear scaling SCF method. Is it 
possible to write an efficient method for DFT calculation on a part of 
super computer system in the order of 10^2 cores?
As additional information of the energies after geometry optimization of 
the LiNbO3 slabs an additional file is attached here also.

For a better overview of the input code (this is for geometry optimization 
for LiNbO3 slab) and of the large system the files are attached here.

Kind regards,

Phil
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 Electronic density on regular grids:      -1631.9999999700        0.0000000300
  Core density on regular grids:             1631.9999999138       -0.0000000862
  Total charge density on r-space grids:       -0.0000000561
  Total charge density g-space grids:          -0.0000000561

  Overlap energy of the core charge distribution:               0.00000001896601
  Self energy of the core charge distribution:             -11259.11652246923404
  Core Hamiltonian energy:                                   2845.48164216265741
  Hartree energy:                                            3920.04473187577923
  Exchange-correlation energy:                               -931.67969460663187
  Dispersion energy:                                           -3.07256467191988
  Electronic entropic energy:                                  -0.00448116158218
  Fermi energy:                                                 0.04252472899742

  Total energy:                                             -5428.34688533529243

 ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):            -5428.352050368117489


 *** BRENT run terminated - exceeded requested execution time:  172800.000 seconds.

 *** Execution time now:   172810.448 seconds.

 *******************************************************************************
 ***                 BRENT   - NUMBER OF ENERGY EVALUATIONS :       1        ***
 *******************************************************************************

 *** GEO run terminated - exceeded requested execution time:  172800.000 seconds.

 *** Execution time now:   172810.454 seconds.

 -------------------------------------------------------------------------------
 -                                                                             -
 -                                DBCSR STATISTICS                             -
 -                                                                             -
 -------------------------------------------------------------------------------
 COUNTER                                      CPU                  ACC      ACC%
 number of processed stacks             388044753                    0       0.0
 matmuls inhomo. stacks                 392765078                    0       0.0
 matmuls total                        17075438864                    0       0.0
 flops   6 x   24 x    6              11481937920                    0       0.0
 flops  26 x   24 x    6              49461235200                    0       0.0
 flops   6 x   24 x   26              49461235200                    0       0.0
 flops   6 x   24 x   17              89189898336                    0       0.0
 flops  17 x   24 x    6              89189898336                    0       0.0
 flops  26 x   24 x   26             210512240640                    0       0.0
 flops  26 x   24 x   17             391582035936                    0       0.0
 flops  17 x   24 x   26             391582035936                    0       0.0
 flops   6 x    6 x   64             579242926080                    0       0.0
 flops  17 x   24 x   17             669807023040                    0       0.0
 flops   6 x   32 x    6             857318031360                    0       0.0
 flops   6 x    6 x   96            1737728778240                    0       0.0
 flops   6 x   26 x   64            2432820289536                    0       0.0
 flops  26 x    6 x   64            2442474338304                    0       0.0
 flops  26 x   32 x    6            3693105561600                    0       0.0
 flops   6 x   32 x   26            3693105561600                    0       0.0
 flops  17 x    6 x   64            4391449208832                    0       0.0
 flops   6 x   17 x   64            4399647071232                    0       0.0
 flops   6 x   32 x   17            6659512409088                    0       0.0
 flops  17 x   32 x    6            6659512409088                    0       0.0
 flops   6 x   26 x   96            7298460868608                    0       0.0
 flops  26 x    6 x   96            7327423014912                    0       0.0
 flops  26 x   26 x   64           10625889677312                    0       0.0
 flops  17 x    6 x   96           13174347626496                    0       0.0
 flops   6 x   17 x   96           13198941213696                    0       0.0
 flops  26 x   32 x   26           15718247301120                    0       0.0
 flops  17 x   26 x   64           19234507918080                    0       0.0
 flops  26 x   17 x   64           19366021828608                    0       0.0
 flops  26 x   32 x   17           29238125349888                    0       0.0
 flops  17 x   32 x   26           29238125349888                    0       0.0
 flops  26 x   26 x   96           31877669031936                    0       0.0
 flops  17 x   17 x   64           33332691987840                    0       0.0
 flops  17 x   32 x   17           50012257720320                    0       0.0
 flops  17 x   26 x   96           57703523754240                    0       0.0
 flops  26 x   17 x   96           58098065485824                    0       0.0
 flops  17 x   17 x   96           99998075963520                    0       0.0
 flops total                      585918323221568                    0       0.0
 marketing flops                  646631550908928
 -------------------------------------------------------------------------------
 Warning: using a non-square number of MPI ranks might lead to poor performance.
          used ranks: 96
          suggested : 100 196
 -------------------------------------------------------------------------------

 -------------------------------------------------------------------------------
 -                                                                             -
 -                         MESSAGE PASSING PERFORMANCE                         -
 -                                                                             -
 -------------------------------------------------------------------------------

 ROUTINE             CALLS  TOT TIME [s]  AVE VOLUME [Bytes]  PERFORMANCE [MB/s]
 MP_Group                6         0.000
 MP_Bcast            33698         1.067              30001.              947.54
 MP_Allreduce       410497       707.285                469.                0.27
 MP_Gather            2628         1.430               1920.                3.53
 MP_Sync             16945        63.365
 MP_Alltoall        943370     12506.668            4261539.              321.45
 MP_ISendRecv      9562320        76.272              39456.             4946.63
 MP_Wait          14174504      5734.873
 MP_comm_split       16940        73.824
 MP_ISend          4926060      1676.555             296941.              872.47
 MP_IRecv          4898066        56.286             291419.            25359.35
 MP_Recv             60984        42.633            1019904.             1458.91
 MP_Memory         1697910         8.566
 -------------------------------------------------------------------------------

 
 -------------------------------------------------------------------------------
 -                                                                             -
 -                                T I M I N G                                  -
 -                                                                             -
 -------------------------------------------------------------------------------
 SUBROUTINE                       CALLS  ASD         SELF TIME        TOTAL TIME
                                MAXIMUM       AVERAGE  MAXIMUM  AVERAGE  MAXIMUM
 CP2K                                 1  1.0      0.1      0.1 172810.5 172810.5
 cp_geo_opt                           1  2.0      0.0      0.0 172808.2 172808.2
 geoopt_cg                            1  3.0      0.0      0.0 172808.1 172808.2
 cp_cg_main                           1  4.0      0.0      0.2 172808.1 172808.2
 cp_eval_at                         657  8.4      0.0      0.2 172806.7 172806.8
 qs_energies_scf                    657  9.9      0.1      0.1 170190.2 170191.5
 scf_env_do_scf                     657 10.9      0.1      0.4 165744.3 166157.0
 scf_env_do_scf_inner_loop        16284 12.0      1.1      4.7 165739.8 166152.2
 cg_linmin                           97  5.0      0.0      0.0 148550.8 148550.8
 linmin_gold                         97  6.0      0.0      0.0 148550.8 148550.8
 qs_forces                          327  8.8      2.2      3.9  93387.0  93387.1
 eigensolver                      16284 13.0      0.3      0.4  93314.5  93327.3
 cp_fm_syevd                      16940 14.1  27286.0  87048.8  87025.4  87048.8
 cp_fm_syevd_base                 16940 15.0  59712.9  85201.0  59712.9  85201.0
 cg_mnbrak                           97  7.0      0.0      0.0  79419.6  79419.6
 cg_eval1d                          330  8.0      0.0      0.0  79419.6  79419.6
 cg_dbrent                           97  7.0      0.0      0.0  69131.2  69131.2
 cg_deval1d                         230  8.0      0.0      0.0  69130.1  69130.1
 rebuild_ks_matrix                16611 13.9      0.1      0.1  41848.0  41910.4
 qs_ks_build_kohn_sham_matrix     16611 14.9      4.4      6.7  41847.9  41910.3
 qs_ks_update_qs_env              16284 13.0      0.2      0.2  40866.0  40928.7
 sum_up_and_integrate             16611 15.9     81.8     87.2  27163.1  27226.0
 integrate_v_rspace               16611 16.9  20159.3  21832.4  27081.3  27169.7
 qs_rho_update_rho                16941 13.0      0.1      0.2  26126.3  26147.3
 calculate_rho_elec               16941 14.0  18098.9  19559.9  26126.2  26147.2
 fft_wrap_pw1pw2                 350484 17.4      5.3      6.5  15488.9  16204.0
 fft_wrap_pw1pw2_400             216276 18.4   1112.6   1250.7  14797.5  15473.3
 fft3d_ps                        350484 19.4   4861.0   5297.8  12769.9  13948.5
 qs_vxc_create                    16611 15.9      0.3      0.4  11627.9  11656.3
 xc_vxc_pw_create                 16611 16.9    197.1    333.1  11627.6  11655.8
 rs_pw_transfer                  168744 17.4      2.2      2.4   6983.5   8488.9
 density_rs2pw                    16941 15.0      0.8      0.9   6592.6   8138.8
 cp_fm_cholesky_restore           48852 14.0   6673.3   6745.5   6673.3   6745.5
 xc_rho_set_and_dset_create       16611 17.9    188.9    199.5   6335.1   6549.8
 yz_to_x                         100983 20.4   3093.4   5149.4   3093.4   5149.4
 x_to_yz                         148845 20.4   4603.3   5127.8   4603.3   5127.8
 rs_distribute_matrix             33879 16.4   3528.7   5043.4   3560.7   5054.9
 rs_pw_transfer_RS2PW_400         17598 16.9   2981.6   4514.0   2981.6   4514.0
 potential_pw2rs                  16611 17.9      7.3     11.0   4426.1   4456.0
 -------------------------------------------------------------------------------


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