GPU for minimizing

zhangxo_o · January 14, 2024, 8:42am

Dear All,
I am trying to use GPU to accelerate my LAMMPS,but it seems to be slower.
I cant figure out the reason
Can anybody help？

THIS is my input file:

zhangxo_o:

log             log.afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89 append
units           real
atom_style      full
boundary        p p p

pair_style      lj/cut 5.000
bond_style      harmonic
angle_style     hybrid cosine/periodic fourier
dihedral_style  harmonic
improper_style  fourier

special_bonds   lj/coul 0.0 0.0 1.0
dielectric      1.0
pair_modify     tail yes mix arithmetic
box tilt        large
read_data       data.afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89

#### Atom Groupings ####
group           fram     id   1:264
#### END Atom Groupings ####

min_style       cg
print           "MinStep,CellMinStep,AtomMinStep,FinalStep,Energy,EDiff" file afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89.min.csv screen no
variable        min_eval   equal 1.00e-06
variable        prev_E     equal 50000.00
variable        iter       loop 100000
label           loop_min
min_style       cg
fix             1 all box/relax aniso 0.0 vmax 0.01
minimize        1.0e-15 1.0e-15 10000 100000
unfix           1
min_style       fire
variable        tempstp    equal $(step)
variable        CellMinStep equal ${tempstp}
minimize        1.0e-15 1.0e-15 10000 100000
variable        AtomMinStep equal $(step)
variable        temppe     equal $(pe)
variable        min_E      equal abs(${prev_E}-${temppe})
print           "${iter},${CellMinStep},${AtomMinStep},${AtomMinStep},$(pe),${min_E}" append afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89.min.csv screen no
if              "${min_E} < ${min_eval}" then "jump SELF break_min"
variable        prev_E     equal ${temppe}
next            iter
jump            SELF loop_min
label           break_min
run 0
variable        inputpe    equal $(pe)
min_style       cg
variable        tempstp    equal $(step)
minimize        1.0e-15 1.0e-15 10000 100000
variable        AtomMinStep equal $(step)
variable        relaxedpe  equal $(pe)
variable        min_E      equal abs(${inputpe}-${relaxedpe})
print           "${AtomMinStep},$(pe),${min_E}" append afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89.min.csv screen no
dump            afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89_relax all custom 1 relaxed_afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89.lammpstrj element xs ys zs
dump_modify     afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89_relax element C C C H N O S
run 0

when I use MPI only, like
mpirun -np 12 lmp -in in.afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89
it seems to be faster than
mpirun -np 12 lmp -sf gpu -pk gpu 1 -in in.afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89

akohlmey · January 14, 2024, 1:00pm

Please read this post with guidelines and suggestions for this forum to learn:

how to correctly quote inputs and outputs so that people can read them (yours are mangled and thus not readable)
which information to always provide when reporting problems with a job

Without knowing what kind of GPU hardware you have, it is not possible to make any suggestions. Please keep in mind that when using 12 MPI ranks attached to the same GPU your possible acceleration from the GPU is split between the 12 processes and thus there cannot be as much acceleration as would be possible for a single process plus the overhead of launching GPU kernels will apply to each process.

zhangxo_o · January 15, 2024, 4:48am

Thanks for your advice!
I have changed my input, and my GPU is NVIDIA GeForce RTX 3090.

zhangxo_o · January 15, 2024, 5:44am

I also have tryed less MPIs.
mpirun -np 2 lmp -in in.afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89
takes 51s.
mpirun -np 2 lmp -sf gpu -pk gpu 1 -in in.afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89 takes 3min.

zhangxo_o · January 15, 2024, 8:26am

Attached is data file for input file.

Created on Mon Dec 25 20:41:06 2023 

         264 atoms
         306 bonds
         528 angles
         840 dihedrals
         432 impropers

           7 atom types
          14 bond types
          26 angle types
           7 dihedral types
           1 improper types
           0.000000  32.553000 xlo xhi
           0.000000  28.191725 ylo yhi
           0.000000  29.284400 zlo zhi
         -16.276500   0.000000   0.000000 xy xz yz

Masses

    1    12.010700000 # C_3
    2    12.010700000 # C_2
    3    12.010700000 # C_R
    4     1.007940000 # H_
    5    14.006700000 # N_R
    6    15.999400000 # O_R
    7    32.065000000 # S_R

Bond Coeffs

    1      367.712375        1.489000  # C_3 C_2
    2      369.943935        1.486000  # C_3 C_R
    3      331.069389        1.109401  # C_3 H_
    4      517.346067        1.328833  # C_2 C_2
    5      354.483902        1.084416  # C_2 H_
    6      462.655054        1.379256  # C_R C_R
    7      389.261715        1.461000  # C_R C_2
    8      561.491352        1.422196  # C_R N_R
    9      391.669513        1.458000  # C_R C_R
   10      663.718927        1.345073  # C_R N_R
   11      646.680887        1.311940  # C_R O_R
   12      357.440381        1.081418  # C_R H_
   13      348.470281        1.701355  # C_R S_R
   14      529.459447        1.043423  # H_ N_R

Angle Coeffs

    1                      fourier      225.865192        0.343737        0.374972        0.281246 # C_2 C_3 C_R
    2                      fourier      121.290688        0.343737        0.374972        0.281246 # C_2 C_3 H_
    3                      fourier      121.777217        0.343737        0.374972        0.281246 # C_R C_3 H_
    4                      fourier       75.498766        0.343737        0.374972        0.281246 # H_ C_3 H_
    5              cosine/periodic      103.977836              -1               3 # C_3 C_2 C_2
    6              cosine/periodic       49.433937              -1               3 # C_3 C_2 H_
    7              cosine/periodic       61.080982              -1               3 # C_2 C_2 H_
    8              cosine/periodic      111.297508              -1               3 # C_R C_R C_R
    9              cosine/periodic      101.852144              -1               3 # C_R C_R C_2
   10              cosine/periodic      107.277537              -1               3 # C_R C_2 C_2
   11              cosine/periodic       51.271325              -1               3 # C_R C_2 H_
   12              cosine/periodic      141.337441              -1               3 # C_R C_R N_R
   13              cosine/periodic      140.838129              -1               3 # C_R C_R N_R
   14              cosine/periodic      131.755710              -1               3 # C_R C_R O_R
   15              cosine/periodic      199.301576              -1               3 # N_R C_R O_R
   16              cosine/periodic       57.289016              -1               3 # C_R C_R H_
   17              cosine/periodic      153.699352              -1               3 # C_R C_R N_R
   18              cosine/periodic      111.374904              -1               3 # C_R C_R S_R
   19              cosine/periodic      103.925969              -1               3 # C_R C_R S_R
   20              cosine/periodic      152.688210              -1               3 # N_R C_R S_R
   21              cosine/periodic       99.137149              -1               3 # C_R C_R C_3
   22              cosine/periodic      110.133094              -1               3 # C_R N_R C_R
   23              cosine/periodic       56.286932              -1               3 # C_R N_R H_
   24              cosine/periodic       62.535612              -1               3 # C_R N_R H_
   25              cosine/periodic      120.000516              -1               3 # C_R N_R C_R
   26              cosine/periodic      121.961124              -1               3 # C_R S_R C_R

Dihedral Coeffs

    1        0.166667               1               3 # C_R C_3 C_2 C_2
    2        0.833333              -1               2 # C_2 C_3 C_R C_R
    3        4.871694              -1               2 # C_3 C_2 C_2 C_R
    4        3.368555              -1               2 # C_R C_R C_R C_2
    5        1.250000              -1               2 # C_R C_R C_2 C_2
    6        6.737110              -1               2 # C_R C_R N_R C_R
    7        5.326153              -1               2 # C_R C_R S_R C_R

Improper Coeffs

    1        2.000000        1.000000       -1.000000        0.000000               0 # C_3 C_2 C_2 H_

Pair Coeffs

    1        0.105000        3.430851 # C_3 C_3
    2        0.105000        3.430851 # C_2 C_2
    3        0.105000        3.430851 # C_R C_R
    4        0.044000        2.571134 # H_ H_
    5        0.069000        3.260689 # N_R N_R
    6        0.060000        3.118146 # O_R O_R
    7        0.274000        3.594776 # S_R S_R

Atoms

       1      444        1     0.00000   -8.02431   14.87565    3.87843
       2      444        1     0.00000    6.84948   12.93324    4.17976
       3      444        2     0.00000    5.55615   13.66960    4.40115
       4      444        2     0.00000   23.34311   14.01354    3.53521
       5      444        3     0.00000   15.77437    0.38256    7.60838
       6      444        3     0.00000   15.61698    1.75973    7.34394
       7      444        2     0.00000   14.83098    2.59900    8.28339
       8      444        2     0.00000   14.20857    2.06392    9.33967
       9      444        3     0.00000   16.25876    2.33287    6.22557
      10      444        3     0.00000   17.21338    4.55071    5.84312
      11      444        3     0.00000   17.03238    1.53025    5.37808
      12      444        3     0.00000   17.20947    0.17084    5.64369
      13      444        3     0.00000   15.99361    7.96529    5.56667
      14      444        3     0.00000   14.95680    8.90520    5.52802
      15      444        3     0.00000   12.99288   10.34749    5.56609
      16      444        3     0.00000   11.64877   10.93952    5.63900
      17      444        3     0.00000   15.22569   10.27419    5.58249
      18      444        3     0.00000   17.04801    6.00258    5.70197
      19      444        3     0.00000   16.55662   10.70242    5.66917
      20      444        3     0.00000   17.59929    9.77943    5.70607
      21      444        3     0.00000   17.30794    8.41664    5.64603
      22      444        3     0.00000   -6.73001   14.69578    8.01748
      23      444        3     0.00000   -7.89345   13.99832    7.62507
      24      444        3     0.00000   -6.01189   15.43102    7.05461
      25      444        3     0.00000   -6.44777   15.47444    5.72861
      26      444        3     0.00000   -7.59103   14.77810    5.32449
      27      444        1     0.00000   -6.25278   14.68000    9.45945
      28      444        3     0.00000   -3.62006   15.63880    7.49681
      29      444        3     0.00000   -2.45352   16.47637    7.80576
      30      444        2     0.00000    5.34292   14.45051    5.46623
      31      444        3     0.00000    6.15235   15.48205    7.61687
      32      444        3     0.00000    7.17191   15.69574    8.55368
      33      444        3     0.00000    8.43774   15.12993    8.37856
      34      444        2     0.00000   10.70473   14.83392    9.25885
      35      444        3     0.00000    9.97733   13.74600    7.07482
      36      444        3     0.00000    8.69865   14.32168    7.25638
      37      444        3     0.00000   10.20537   12.89771    5.97050
      38      444        3     0.00000    9.18092   12.66598    5.04453
      39      444        3     0.00000    7.91868   13.24701    5.20208
      40      444        3     0.00000    7.66639   14.07641    6.31489
      41      444        3     0.00000    6.39520   14.66449    6.49147
      42      444        2     0.00000    9.48432   15.36111    9.39414
      43      444        1     0.00000   11.10253   14.01636    8.05907
      44      444        3     0.00000   18.78503   11.65164    5.96172
      45      444        3     0.00000   19.97810   12.47033    6.21239
      46      444        2     0.00000   22.66438   13.32059    4.45621
      47      444        3     0.00000   22.33543   12.61439    6.85021
      48      444        3     0.00000   22.77668   12.56956    8.17503
      49      444        3     0.00000   23.92515   13.25913    8.57037
      50      444        3     0.00000   24.22676   14.03807    6.27389
      51      444        3     0.00000   23.06836   13.33412    5.88411
      52      444        3     0.00000   -1.32426   18.35394    8.23038
      53      444        3     0.00000   -1.07262   19.71447    8.41897
      54      444        3     0.00000   -0.88056   22.13389    8.57242
      55      444        3     0.00000   -0.25180   17.46787    8.15073
      56      444        3     0.00000    0.23031   20.19740    8.51034
      57      444        3     0.00000    1.29610   19.29301    8.43156
      58      444        3     0.00000    3.30071   17.92571    8.20520
      59      444        3     0.00000    4.65931   17.38302    8.05585
      60      444        3     0.00000    1.06725   17.92853    8.24912
      61      444        3     0.00000   -1.08076   23.58858    8.52498
      62      444        3     0.00000   -0.16097   25.82954    8.15014
      63      444        3     0.00000   -0.96617   26.62314    8.97655
      64      444        3     0.00000   -1.14180   27.98621    8.71914
      65      444        2     0.00000    1.76356   27.54811    4.73499
      66      444        2     0.00000    1.95888   26.24621    4.96253
      67      444        1     0.00000    1.37699   25.53888    6.15705
      68      444        3     0.00000    0.49904   26.40606    7.04436
      69      444        3     0.00000    0.31462   27.77872    6.76470
      70      444        1     0.00000   14.21101    0.58526    9.61817
      71      444        2     0.00000   -7.10534   13.86131   10.39303
      72      444        2     0.00000   24.35746   13.20670    9.98129
      73      444        1     0.00000   -8.02431   14.87565   19.22462
      74      444        1     0.00000    6.84948   12.93324   19.52567
      75      444        2     0.00000    5.55615   13.66960   19.74735
      76      444        2     0.00000   23.34311   14.01354   18.88141
      77      444        3     0.00000   15.77437    0.38256   22.95458
      78      444        3     0.00000   15.61698    1.75973   22.68985
      79      444        2     0.00000   14.83098    2.59900   23.62958
      80      444        2     0.00000   14.20857    2.06392   24.68558
      81      444        3     0.00000   16.25876    2.33287   21.57147
      82      444        3     0.00000   17.03238    1.53025   20.72428
      83      444        3     0.00000   17.20947    0.17084   20.98959
      84      444        3     0.00000   17.21338    4.55071   21.18931
      85      444        3     0.00000   15.99361    7.96529   20.91258
      86      444        3     0.00000   14.95680    8.90520   20.87392
      87      444        3     0.00000   12.99288   10.34749   20.91228
      88      444        3     0.00000   11.64877   10.93952   20.98520
      89      444        3     0.00000   15.22569   10.27419   20.92839
      90      444        3     0.00000   17.04801    6.00258   21.04816
      91      444        3     0.00000   16.55662   10.70242   21.01536
      92      444        3     0.00000   17.59929    9.77943   21.05226
      93      444        3     0.00000   17.30794    8.41664   20.99194
      94      444        3     0.00000   -6.01189   15.43102   22.40052
      95      444        3     0.00000   -6.44777   15.47444   21.07452
      96      444        3     0.00000   -7.59103   14.77810   20.67039
      97      444        3     0.00000   -6.73001   14.69578   23.36339
      98      444        3     0.00000   -7.89345   13.99832   22.97127
      99      444        1     0.00000   -6.25278   14.68000   24.80535
     100      444        3     0.00000   -3.62006   15.63880   22.84300
     101      444        3     0.00000   -2.45352   16.47637   23.15166
     102      444        2     0.00000    5.34292   14.45051   20.81213
     103      444        3     0.00000   10.20537   12.89771   21.31670
     104      444        3     0.00000    9.18092   12.66598   20.39043
     105      444        3     0.00000    7.91868   13.24701   20.54798
     106      444        3     0.00000    7.66639   14.07641   21.66108
     107      444        3     0.00000    6.39520   14.66449   21.83738
     108      444        3     0.00000    6.15235   15.48205   22.96307
     109      444        3     0.00000    7.17191   15.69574   23.89958
     110      444        3     0.00000    8.43774   15.12993   23.72446
     111      444        2     0.00000   10.70473   14.83392   24.60475
     112      444        3     0.00000    9.97733   13.74600   22.42072
     113      444        3     0.00000    8.69865   14.32168   22.60229
     114      444        2     0.00000    9.48432   15.36111   24.74034
     115      444        1     0.00000   11.10253   14.01636   23.40497
     116      444        3     0.00000   18.78503   11.65164   21.30762
     117      444        3     0.00000   19.97810   12.47033   21.55859
     118      444        2     0.00000   22.66438   13.32059   19.80240
     119      444        3     0.00000   24.22676   14.03807   21.61979
     120      444        3     0.00000   23.06836   13.33412   21.23002
     121      444        3     0.00000   22.33543   12.61439   22.19611
     122      444        3     0.00000   22.77668   12.56956   23.52094
     123      444        3     0.00000   23.92515   13.25913   23.91628
     124      444        3     0.00000   -1.32426   18.35394   23.57658
     125      444        3     0.00000   -1.07262   19.71447   23.76488
     126      444        3     0.00000   -0.88056   22.13389   23.91862
     127      444        3     0.00000   -0.25180   17.46787   23.49663
     128      444        3     0.00000    0.23031   20.19740   23.85654
     129      444        3     0.00000    1.29610   19.29301   23.77747
     130      444        3     0.00000    3.30071   17.92571   23.55110
     131      444        3     0.00000    4.65931   17.38302   23.40204
     132      444        3     0.00000    1.06725   17.92853   23.59532
     133      444        3     0.00000   -1.08076   23.58858   23.87089
     134      444        3     0.00000   -0.16097   25.82954   23.49634
     135      444        3     0.00000   -0.96617   26.62314   24.32274
     136      444        3     0.00000   -1.14180   27.98621   24.06533
     137      444        2     0.00000    1.76356   27.54811   20.08119
     138      444        2     0.00000    1.95888   26.24621   20.30844
     139      444        1     0.00000    1.37699   25.53888   21.50324
     140      444        3     0.00000    0.49904   26.40606   22.39056
     141      444        3     0.00000    0.31462   27.77872   22.11089
     142      444        1     0.00000   14.21101    0.58526   24.96407
     143      444        2     0.00000   -7.10534   13.86131   25.73894
     144      444        2     0.00000   24.35746   13.20670   25.32720
     145      444        4     0.00000   -8.28344   15.93171    3.65001
     146      444        4     0.00000   -7.17810   14.57766    3.22333
     147      444        4     0.00000    4.76088   13.54387    3.67256
     148      444        4     0.00000    6.63788   11.84278    4.20202
     149      444        4     0.00000    9.37266   12.03336    4.18533
     150      444        4     0.00000    7.22677   13.19147    3.16682
     151      444        4     0.00000   21.81767   12.72687    4.12705
     152      444        4     0.00000   23.01774   13.97266    2.50001
     153      444        4     0.00000    2.22386   28.00481    3.86291
     154      444        4     0.00000    2.57576   25.67674    4.27377
     155      444        4     0.00000   15.16888    4.14108    5.90754
     156      444        4     0.00000   14.76718    3.67366    8.14721
     157      444        4     0.00000   13.17452    0.20580    9.49049
     158      444        4     0.00000   17.50196    1.97370    4.50745
     159      444        4     0.00000   21.21935   10.83182    6.59104
     160      444        4     0.00000   -5.88981   16.05970    5.00617
     161      444        4     0.00000   -5.21597   14.28475    9.49664
     162      444        4     0.00000    4.02811   15.41467    7.78526
     163      444        4     0.00000    4.37984   14.94359    5.54764
     164      444        4     0.00000    6.96943   16.29454    9.43456
     165      444        4     0.00000   12.33498   12.89659    5.83697
     166      444        4     0.00000   11.52572   13.05051    8.40960
     167      444        4     0.00000   11.91863   14.55257    7.52990
     168      444        4     0.00000   22.21140   11.99642    8.90129
     169      444        4     0.00000   -4.99396   17.21612    7.58144
     170      444        4     0.00000    0.95120   24.03119    8.43332
     171      444        4     0.00000    2.21686   25.13856    6.76323
     172      444        4     0.00000    0.79039   24.66438    5.80241
     173      444        4     0.00000   13.64882    2.71317   10.00619
     174      444        4     0.00000   14.50790    0.43133   10.67797
     175      444        4     0.00000   -6.81790   13.80154   11.43849
     176      444        4     0.00000   -6.20948   15.72309    9.83868
     177      444        4     0.00000    9.26442   15.95905   10.27472
     178      444        4     0.00000   11.44938   15.02140   10.02669
     179      444        4     0.00000   23.78436   12.63130   10.70374
     180      444        4     0.00000   -1.45886   26.17404    9.83136
     181      444        4     0.00000   -8.28344   15.93171   18.99620
     182      444        4     0.00000   -7.17810   14.57766   18.56924
     183      444        4     0.00000    4.76088   13.54387   19.01846
     184      444        4     0.00000    9.37266   12.03336   19.53123
     185      444        4     0.00000    7.22677   13.19147   18.51272
     186      444        4     0.00000    6.63788   11.84278   19.54822
     187      444        4     0.00000   21.81767   12.72687   19.47295
     188      444        4     0.00000   23.01774   13.97266   17.84591
     189      444        4     0.00000    2.22386   28.00481   19.20910
     190      444        4     0.00000    2.57576   25.67674   19.61996
     191      444        4     0.00000   15.16888    4.14108   21.25345
     192      444        4     0.00000   14.76718    3.67366   23.49341
     193      444        4     0.00000   13.17452    0.20580   24.83639
     194      444        4     0.00000   17.50196    1.97370   19.85336
     195      444        4     0.00000   21.21935   10.83182   21.93694
     196      444        4     0.00000   -5.88981   16.05970   20.35237
     197      444        4     0.00000   -5.21597   14.28475   24.84254
     198      444        4     0.00000    4.37984   14.94359   20.89383
     199      444        4     0.00000    4.02811   15.41467   23.13145
     200      444        4     0.00000    6.96943   16.29454   24.78075
     201      444        4     0.00000   11.91863   14.55257   22.87609
     202      444        4     0.00000   12.33498   12.89659   21.18287
     203      444        4     0.00000   11.52572   13.05051   23.75551
     204      444        4     0.00000   22.21140   11.99642   24.24748
     205      444        4     0.00000   -4.99396   17.21612   22.92764
     206      444        4     0.00000    0.79039   24.66438   21.14861
     207      444        4     0.00000    0.95120   24.03119   23.77952
     208      444        4     0.00000    2.21686   25.13856   22.10943
     209      444        4     0.00000   13.64882    2.71317   25.35238
     210      444        4     0.00000   14.50790    0.43133   26.02387
     211      444        4     0.00000   -6.81790   13.80154   26.78439
     212      444        4     0.00000   -6.20948   15.72309   25.18488
     213      444        4     0.00000    9.26442   15.95905   25.62092
     214      444        4     0.00000   11.44938   15.02140   25.37288
     215      444        4     0.00000   23.78436   12.63130   26.04965
     216      444        4     0.00000   -1.45886   26.17404   25.17756
     217      444        5     0.00000   16.13148    3.73512    5.94590
     218      444        5     0.00000   15.84110    6.61857    5.60298
     219      444        5     0.00000   14.13565   11.07963    5.60855
     220      444        5     0.00000   18.83549   10.30069    5.87269
     221      444        5     0.00000   -4.85854   16.19164    7.42506
     222      444        5     0.00000    4.85300   16.05406    7.84119
     223      444        5     0.00000   11.49072   12.28342    5.77928
     224      444        5     0.00000   21.16466   11.87154    6.49792
     225      444        5     0.00000   -2.54744   17.80899    8.03623
     226      444        5     0.00000    0.34376   21.54581    8.58941
     227      444        5     0.00000    2.17926   17.16510    8.11939
     228      444        5     0.00000   -0.01530   24.42757    8.43010
     229      444        5     0.00000   16.13148    3.73512   21.29181
     230      444        5     0.00000   15.84110    6.61857   20.94918
     231      444        5     0.00000   14.13565   11.07963   20.95445
     232      444        5     0.00000   18.83549   10.30069   21.21889
     233      444        5     0.00000   -4.85854   16.19164   22.77126
     234      444        5     0.00000    4.85300   16.05406   23.18710
     235      444        5     0.00000   11.49072   12.28342   21.12518
     236      444        5     0.00000   21.16466   11.87154   21.84382
     237      444        5     0.00000   -2.54744   17.80899   23.38242
     238      444        5     0.00000    0.34376   21.54581   23.93531
     239      444        5     0.00000    2.17926   17.16510   23.46530
     240      444        5     0.00000   -0.01530   24.42757   23.77600
     241      444        6     0.00000   18.42890    4.06186    5.97080
     242      444        6     0.00000   10.60219   10.14113    5.65365
     243      444        6     0.00000   -3.44932   14.35692    7.25433
     244      444        6     0.00000   19.87686   13.78237    6.20800
     245      444        6     0.00000    5.68099   18.21270    8.06258
     246      444        6     0.00000   -2.30801   24.05713    8.44064
     247      444        6     0.00000   18.42890    4.06186   21.31670
     248      444        6     0.00000   10.60219   10.14113   20.99955
     249      444        6     0.00000   -3.44932   14.35692   22.60024
     250      444        6     0.00000   19.87686   13.78237   21.55390
     251      444        6     0.00000    5.68099   18.21270   23.40849
     252      444        6     0.00000   -2.30801   24.05713   23.78684
     253      444        7     0.00000   13.29660    8.67685    5.50664
     254      444        7     0.00000   18.33792    7.10291    5.75819
     255      444        7     0.00000   -0.84361   15.92973    7.82801
     256      444        7     0.00000   17.19645   12.24705    5.84194
     257      444        7     0.00000   -2.14069   21.00396    8.44621
     258      444        7     0.00000    2.94930   19.57239    8.43244
     259      444        7     0.00000   13.29660    8.67685   20.85254
     260      444        7     0.00000   18.33792    7.10291   21.10439
     261      444        7     0.00000   -0.84361   15.92973   23.17392
     262      444        7     0.00000   17.19645   12.24705   21.18785
     263      444        7     0.00000   -2.14069   21.00396   23.79240
     264      444        7     0.00000    2.94930   19.57239   23.77835

Bonds

       1        1        1        4
       2        2        1       26
       3        3        1      145
       4        3        1      146
       5        1        2        3
       6        2        2       39
       7        3        2      148
       8        3        2      150
       9        4        3       30
      10        5        3      147
      11        4        4       46
      12        5        4      152
      13        6        5        6
      14        6        5       64
      15        6        5       69
      16        7        6        7
      17        6        6        9
      18        4        7        8
      19        5        7      156
      20        1        8       70
      21        5        8      173
      22        6        9       11
      23        8        9      217
      24        9       10       18
      25       10       10      217
      26       11       10      241
      27        6       11       12
      28       12       11      158
      29        7       12       65
      30        6       12       69
      31        6       13       14
      32        6       13       21
      33       10       13      218
      34        6       14       17
      35       13       14      253
      36        9       15       16
      37       10       15      219
      38       13       15      253
      39       10       16      223
      40       11       16      242
      41        6       17       19
      42       10       17      219
      43       10       18      218
      44       13       18      254
      45        6       19       20
      46       13       19      256
      47        6       20       21
      48       10       20      220
      49       13       21      254
      50        6       22       23
      51        6       22       24
      52        2       22       27
      53        6       23       49
      54        6       23       50
      55        6       24       25
      56        8       24      221
      57        6       25       26
      58       12       25      160
      59        6       26       50
      60        1       27       71
      61        3       27      161
      62        3       27      176
      63        9       28       29
      64       10       28      221
      65       11       28      243
      66       10       29      225
      67       13       29      255
      68        7       30       41
      69        5       30      163
      70        6       31       32
      71        6       31       41
      72        8       31      222
      73        6       32       33
      74       12       32      164
      75        6       33       36
      76        7       33       42
      77        4       34       42
      78        1       34       43
      79        5       34      178
      80        6       35       36
      81        6       35       37
      82        2       35       43
      83        6       36       40
      84        6       37       38
      85        8       37      223
      86        6       38       39
      87       12       38      149
      88        6       39       40
      89        6       40       41
      90        5       42      177
      91        3       43      166
      92        3       43      167
      93        9       44       45
      94       10       44      220
      95       13       44      256
      96       10       45      224
      97       11       45      244
      98        7       46       51
      99        5       46      151
     100        6       47       48
     101        6       47       51
     102        8       47      224
     103        6       48       49
     104       12       48      168
     105        7       49       72
     106        6       50       51
     107        6       52       53
     108        6       52       55
     109       10       52      225
     110        6       53       56
     111       13       53      257
     112        9       54       61
     113       10       54      226
     114       13       54      257
     115        6       55       60
     116       13       55      255
     117        6       56       57
     118       10       56      226
     119        6       57       60
     120       13       57      258
     121        9       58       59
     122       10       58      227
     123       13       58      258
     124       10       59      222
     125       11       59      245
     126       10       60      227
     127       10       61      228
     128       11       61      246
     129        6       62       63
     130        6       62       68
     131        8       62      228
     132        6       63       64
     133       12       63      180
     134        2       64       70
     135        4       65       66
     136        5       65      153
     137        1       66       67
     138        5       66      154
     139        2       67       68
     140        3       67      171
     141        3       67      172
     142        6       68       69
     143        3       70      157
     144        3       70      174
     145        4       71       72
     146        5       71      175
     147        5       72      179
     148        1       73       76
     149        2       73       96
     150        3       73      181
     151        3       73      182
     152        1       74       75
     153        2       74      105
     154        3       74      185
     155        3       74      186
     156        4       75      102
     157        5       75      183
     158        4       76      118
     159        5       76      188
     160        6       77       78
     161        6       77      136
     162        6       77      141
     163        7       78       79
     164        6       78       81
     165        4       79       80
     166        5       79      192
     167        1       80      142
     168        5       80      209
     169        6       81       82
     170        8       81      229
     171        6       82       83
     172       12       82      194
     173        7       83      137
     174        6       83      141
     175        9       84       90
     176       10       84      229
     177       11       84      247
     178        6       85       86
     179        6       85       93
     180       10       85      230
     181        6       86       89
     182       13       86      259
     183        9       87       88
     184       10       87      231
     185       13       87      259
     186       10       88      235
     187       11       88      248
     188        6       89       91
     189       10       89      231
     190       10       90      230
     191       13       90      260
     192        6       91       92
     193       13       91      262
     194        6       92       93
     195       10       92      232
     196       13       93      260
     197        6       94       95
     198        6       94       97
     199        8       94      233
     200        6       95       96

 ...

zhangxo_o · January 15, 2024, 8:37am

It’s not complete because of the words limit.
The complete data file is followed by Angles,Dihedrals,Impropers.
Both the input file and the data file is generated by lammps-interface,
lammps-interface afterfirstIC1=CC2=C3C[=C[I]C=C4C=CCC1=C43]C=CC2_framework_89.cif -ff UFF --minimize --relax --lammpstrj 10 --cutoff 5

akohlmey · January 15, 2024, 1:28pm

Your system is tiny. There is no chance for GPU acceleration. The possible speed up is overcompensated by the overhead of running on the GPU. Even for MPI parallelization you may reach the limit of scaling with fewer than 12 processes.

zhangxo_o · January 15, 2024, 1:55pm

Thanks for your response! This problem has bothered me for a long time. I used to worry that there was something wrong with my use of lammps, but now I understand.Thank you again!

akohlmey · January 15, 2024, 2:10pm

Here are some new problems to worry about:

due to having a system with so few atoms, there are significant finite size effects
it is not clear why you need to run a tilted box. This just adds numerical noise and makes post processing more complicated
your cutoff for lj/cut is extremely short with 5 angstrom. Typical molecular force fields for these kinds of systems use 12-14 angstrom. Very old parameter sets may use 9 Angstrom to trade off better performance and thus better statistics against a larger error. The correct value should be given where you have picked up the other force field parameters
typical all-atom force fields for these kinds of system use partial charges. Those are missing in your case, which can render the results unphysical