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robertodr/dftd3-gradient-profile.py

Created April 7, 2021 08:18
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Example profiling script for D3 gradient with JAX
Raw
dftd3-gradient-profile.py
import cProfile
from dftd3.dftd3 import D3Configuration, D3_derivatives
def main(order, config, charges, coordinates):
_ = D3_derivatives(order, config, charges, *coordinates)
coordinates = [
4.01376695,
-0.42094027,
0.00413283,
2.37659705,
-2.06988695,
-0.07118787,
3.23930049,
2.02346393,
0.03394893,
6.09063455,
-0.5931548,
0.05363799,
1.40721479,
2.12118734,
-0.0108338,
-4.04214497,
0.34532288,
-0.03309288,
-2.55773675,
2.13450991,
-0.01370996,
-3.05560778,
-2.01961834,
0.06482139,
-6.12485749,
0.3304205,
-0.12008265,
-1.22314224,
-1.95250094,
0.14005516,
]
charges = [6, 8, 8, 1, 1, 6, 8, 8, 1, 1]
functional = "B3LYP"
damping = "zero"
#damping = "bj"
config = D3Configuration(functional=functional, damp=damping)
order = 1
cProfile.run("main(order, config, charges, coordinates)")
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Result of running the script:

>>> D3-dispersion correction with zero damping
    - Damping parameters (from database): s6 = 1.0; rs6 = 1.261; s8 = 1.703
    - 3-body term will not be calculated

WARNING:absl:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
         209116280 function calls (204923527 primitive calls) in 213.708 seconds

   Ordered by: standard name

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   111720    0.573    0.000    9.857    0.000 lax.py:1478(_device_put_raw)
     1080    0.005    0.000    0.252    0.000 lax.py:1726(full_like)
    17730    0.030    0.000    6.318    0.000 lax.py:188(exp)
   116803    0.100    0.000    0.263    0.000 lax.py:1967(<lambda>)
        3    0.000    0.000    0.000    0.000 lax.py:1968(<lambda>)
        2    0.000    0.000    0.000    0.000 lax.py:1969(<lambda>)
      542    0.000    0.000    0.000    0.000 lax.py:1973(<genexpr>)
      271    0.001    0.000    0.001    0.000 lax.py:1973(<lambda>)
   153839    1.110    0.000    9.382    0.000 lax.py:1984(standard_abstract_eval)
   425026    0.133    0.000    0.178    0.000 lax.py:1985(<genexpr>)
       24    0.000    0.000    0.001    0.000 lax.py:2025(standard_translate)
       48    0.000    0.000    0.000    0.000 lax.py:2026(<genexpr>)
    36761    0.080    0.000    0.587    0.000 lax.py:2030(unop_dtype_rule)
   110283    0.074    0.000    0.471    0.000 lax.py:2031(<genexpr>)
    36761    0.019    0.000    0.029    0.000 lax.py:2048(<lambda>)
   116806    0.799    0.000    4.516    0.000 lax.py:2051(naryop_dtype_rule)
   116806    0.053    0.000    0.053    0.000 lax.py:2052(<listcomp>)
   700836    0.350    0.000    2.241    0.000 lax.py:2054(<genexpr>)
   116806    0.094    0.000    0.165    0.000 lax.py:2074(_broadcasting_shape_rule)
   116806    0.070    0.000    0.070    0.000 lax.py:2075(<listcomp>)
       17    0.000    0.000    0.000    0.000 lax.py:2087(_standard_weak_type_rule)
       34    0.000    0.000    0.000    0.000 lax.py:2088(<genexpr>)
   153550    0.257    0.000    0.673    0.000 lax.py:2090(_naryop_weak_type_rule)
   423906    0.141    0.000    0.141    0.000 lax.py:2091(<genexpr>)
   307406    0.086    0.000    0.086    0.000 lax.py:2101(<genexpr>)
   187200    0.796    0.000    3.783    0.000 lax.py:2140(_brcast)
    28125    0.023    0.000    2.622    0.000 lax.py:2177(<lambda>)
        2    0.000    0.000    0.000    0.000 lax.py:2179(_sign_translation_rule)
    15570    0.014    0.000    3.263    0.000 lax.py:2231(<lambda>)
      270    0.003    0.000    0.212    0.001 lax.py:2441(_abs_jvp_rule)
     2160    0.006    0.000    0.925    0.000 lax.py:2452(<lambda>)
      270    0.007    0.000    0.420    0.002 lax.py:2461(_pow_jvp_lhs)
       17    0.000    0.000    0.000    0.000 lax.py:2471(_integer_pow_dtype_rule)
       17    0.000    0.000    0.001    0.000 lax.py:2478(_integer_pow_translation_rule)
    33870    0.147    0.000   17.262    0.001 lax.py:2495(_integer_pow_jvp)
    44940    0.031    0.000    0.696    0.000 lax.py:2528(<lambda>)
      945    0.001    0.000    0.024    0.000 lax.py:2550(<lambda>)
    30465    0.049    0.000    3.875    0.000 lax.py:2551(<lambda>)
     4050    0.009    0.000    0.487    0.000 lax.py:2562(_div_transpose_rule)
     6000    0.010    0.000    1.425    0.000 lax.py:2568(<lambda>)
     6000    0.020    0.000    3.788    0.001 lax.py:2569(<lambda>)
        1    0.000    0.000    0.000    0.000 lax.py:2644(_convert_element_type_shape_rule)
        1    0.000    0.000    0.000    0.000 lax.py:2647(_convert_element_type_dtype_rule)
        1    0.000    0.000    0.000    0.000 lax.py:2650(_convert_element_type_weak_type_rule)
        1    0.000    0.000    0.000    0.000 lax.py:2653(_convert_element_type_translation_rule)
     1350    0.002    0.000    0.364    0.000 lax.py:299(abs)
1620/1350    0.003    0.000    0.617    0.000 lax.py:303(pow)
79440/45570    0.153    0.000   24.539    0.001 lax.py:307(integer_pow)
     5400    0.010    0.000    1.683    0.000 lax.py:311(sqrt)
     1080    0.009    0.000    0.017    0.000 lax.py:3323(_broadcast_in_dim_shape_rule)
     1080    0.000    0.000    0.000    0.000 lax.py:3340(<genexpr>)
    95850    0.138    0.000   22.020    0.000 lax.py:339(add)
    33840    0.065    0.000   12.016    0.000 lax.py:343(sub)
   236940    0.353    0.000   53.150    0.000 lax.py:347(mul)
29010/23010    0.048    0.000    9.337    0.000 lax.py:351(div)
      271    0.000    0.000    0.000    0.000 lax.py:3783(_select_shape_rule)
      271    0.001    0.000    0.005    0.000 lax.py:3793(_select_dtype_rule)
      270    0.001    0.000    0.037    0.000 lax.py:385(eq)
      270    0.001    0.000    0.038    0.000 lax.py:393(ge)
     1650    0.005    0.000    0.413    0.000 lax.py:397(gt)
   355860    1.931    0.000   39.451    0.000 lax.py:409(convert_element_type)
   117077    0.282    0.000    1.010    0.000 lax.py:6142(_check_same_dtypes)
   117077    0.213    0.000    0.706    0.000 lax.py:6152(<setcomp>)
     2160    0.002    0.000    0.003    0.000 lax.py:6227(_check_shapelike)
    36030    0.078    0.000    0.817    0.000 lax.py:6272(_const)
      270    0.001    0.000    0.008    0.000 lax.py:6287(_iscomplex)
     1080    0.005    0.000    0.038    0.000 lax.py:678(broadcast)
     1080    0.004    0.000    0.025    0.000 lax.py:696(broadcast_in_dim)
      540    0.001    0.000    0.102    0.000 lax.py:765(select)
   353700    0.529    0.000    5.381    0.000 lax_numpy.py:111(__instancecheck__)
   187740    0.344    0.000    6.260    0.000 lax_numpy.py:239(_promote_shapes)
   164610    0.262    0.000    5.812    0.000 lax_numpy.py:244(<listcomp>)
   164610    0.067    0.000    0.067    0.000 lax_numpy.py:245(<listcomp>)
   147810    0.587    0.000   45.769    0.000 lax_numpy.py:269(_promote_dtypes)
   147810    0.342    0.000   33.710    0.000 lax_numpy.py:278(<listcomp>)
    41280    0.188    0.000    8.603    0.000 lax_numpy.py:280(_promote_dtypes_inexact)
    41280    0.078    0.000    6.000    0.000 lax_numpy.py:289(<listcomp>)
    41280    0.028    0.000    0.322    0.000 lax_numpy.py:291(_to_inexact_dtype)
   353700    0.175    0.000    6.115    0.000 lax_numpy.py:305(_arraylike)
   189090    0.256    0.000    6.906    0.000 lax_numpy.py:308(_check_arraylike)
   542790    0.256    0.000    6.371    0.000 lax_numpy.py:311(<genexpr>)
   187740    0.158    0.000    6.847    0.000 lax_numpy.py:317(_check_no_float0s)
   540090    0.322    0.000    6.482    0.000 lax_numpy.py:319(<genexpr>)
   147810    0.644    0.000   63.768    0.000 lax_numpy.py:329(_promote_args)
    39930    0.169    0.000   11.296    0.000 lax_numpy.py:335(_promote_args_inexact)
     1350    0.002    0.000    0.046    0.000 lax_numpy.py:343(_constant_like)
    44280    0.033    0.000    0.314    0.000 lax_numpy.py:356(issubdtype)
   109290    0.124    0.000    0.317    0.000 lax_numpy.py:360(isscalar)
    23130    0.060    0.000   13.333    0.001 lax_numpy.py:374(<lambda>)
    33570    0.189    0.000   26.089    0.001 lax_numpy.py:387(<lambda>)
   111240    0.537    0.000   93.098    0.001 lax_numpy.py:395(fn)
     1650    0.007    0.000    1.232    0.001 lax_numpy.py:457(fn)
   194130    0.430    0.000  156.868    0.001 lax_numpy.py:5253(deferring_binary_op)
    41265    0.060    0.000   30.763    0.001 lax_numpy.py:5260(<lambda>)
    16800    0.033    0.000   14.529    0.001 lax_numpy.py:536(true_divide)
    40920    0.088    0.000   25.140    0.001 lax_numpy.py:588(power)
     1350    0.024    0.000    2.436    0.002 lax_numpy.py:864(cbrt)
   880875    0.197    0.000    0.197    0.000 lazy.py:80(is_trivial)
       60    0.000    0.000    0.000    0.000 linear_util.py:103(val)
       60    0.000    0.000    0.000    0.000 linear_util.py:109(__nonzero__)
      210    0.000    0.000    0.000    0.000 linear_util.py:131(__init__)
      180    0.000    0.000    0.000    0.000 linear_util.py:141(wrap)
       30    0.063    0.002  187.646    6.255 linear_util.py:152(call_wrapped)
      120    0.000    0.000    0.000    0.000 linear_util.py:200(transformation)
       60    0.000    0.000    0.000    0.000 linear_util.py:210(transformation_with_aux)
       60    0.000    0.000    0.000    0.000 linear_util.py:214(<lambda>)
       30    0.000    0.000    0.000    0.000 linear_util.py:223(wrap_init)
       60    0.000    0.000    0.000    0.000 linear_util.py:91(__init__)
       60    0.000    0.000    0.000    0.000 linear_util.py:94(store)
       30    0.000    0.000    0.000    0.000 multiarray.py:1054(copyto)
  3630000    0.536    0.000    0.536    0.000 multiarray.py:644(result_type)
       30    0.000    0.000    0.001    0.000 numeric.py:148(ones)
  2535486    1.521    0.000    2.329    0.000 numerictypes.py:285(issubclass_)
  1267743    1.413    0.000    3.916    0.000 numerictypes.py:359(issubdtype)
        3    0.000    0.000    0.000    0.000 os.py:670(__getitem__)
        3    0.000    0.000    0.000    0.000 os.py:748(encode)
        3    0.000    0.000    0.000    0.000 os.py:766(getenv)
   117420    0.304    0.000    0.907    0.000 partial_eval.py:100(new_const)
   117060    0.350    0.000    8.153    0.000 partial_eval.py:105(new_instantiated_literal)
       60    0.000    0.000    0.000    0.000 partial_eval.py:111(new_arg)
   369285    0.434    0.000    9.151    0.000 partial_eval.py:118(instantiate_const)
   203175    0.290    0.000   27.494    0.000 partial_eval.py:136(process_primitive)
   203175    1.854    0.000   27.204    0.000 partial_eval.py:142(default_process_primitive)
   203175    0.229    0.000    0.320    0.000 partial_eval.py:145(<listcomp>)
   407730    0.166    0.000    0.166    0.000 partial_eval.py:146(<genexpr>)
   202875    0.219    0.000    0.628    0.000 partial_eval.py:149(<listcomp>)
   437385    0.563    0.000    0.760    0.000 partial_eval.py:423(__init__)
   795825    0.442    0.000    1.064    0.000 partial_eval.py:437(aval)
   734445    0.268    0.000    0.350    0.000 partial_eval.py:441(parents)
   202905    0.137    0.000    0.190    0.000 partial_eval.py:448(full_lower)
       30    0.117    0.004  187.764    6.259 partial_eval.py:459(trace_to_jaxpr)
   437415    0.326    0.000    0.623    0.000 partial_eval.py:50(__new__)
       90    0.011    0.000    6.911    0.077 partial_eval.py:513(trace_to_subjaxpr)
       30    0.000    0.000    0.000    0.000 partial_eval.py:516(<listcomp>)
       90    0.000    0.000    0.001    0.000 partial_eval.py:522(<genexpr>)
       30    0.000    0.000    0.000    0.000 partial_eval.py:528(<listcomp>)
       60    0.000    0.000    0.000    0.000 partial_eval.py:532(instantiate_const_at)
   202875    0.483    0.000    1.713    0.000 partial_eval.py:550(new_eqn_recipe)
   155715    0.323    0.000    4.725    0.000 partial_eval.py:576(recipe_to_eqn)
   155715    0.062    0.000    0.062    0.000 partial_eval.py:579(<listcomp>)
   155715    0.097    0.000    0.340    0.000 partial_eval.py:580(<listcomp>)
   155715    0.143    0.000    3.809    0.000 partial_eval.py:581(<listcomp>)
       30    0.367    0.012    6.898    0.230 partial_eval.py:585(tracers_to_jaxpr)
   439140    0.451    0.000    3.887    0.000 partial_eval.py:602(getvar)
   117450    0.108    0.000    0.369    0.000 partial_eval.py:61(known)
       90    0.000    0.000    0.000    0.000 partial_eval.py:627(<genexpr>)
   319965    0.316    0.000    0.677    0.000 partial_eval.py:65(unknown)
   155805    0.033    0.000    0.033    0.000 partial_eval.py:69(is_known)
  1893705    0.412    0.000    0.412    0.000 partial_eval.py:72(get_known)
   951570    0.442    0.000    0.709    0.000 partial_eval.py:76(get_aval)
   117390    0.072    0.000    0.979    0.000 partial_eval.py:91(pure)
        1    0.000    0.000    0.000    0.000 posixpath.py:117(splitext)
        1    0.000    0.000    0.000    0.000 posixpath.py:140(basename)
        1    0.000    0.000    0.000    0.000 posixpath.py:41(_get_sep)
      327    0.000    0.000    0.000    0.000 pprint_util.py:25(__init__)
       73    0.000    0.000    0.000    0.000 pprint_util.py:28(indent)
       73    0.000    0.000    0.000    0.000 pprint_util.py:29(<listcomp>)
       19    0.000    0.000    0.000    0.000 pprint_util.py:36(__add__)
       99    0.000    0.000    0.000    0.000 pprint_util.py:39(__rshift__)
       44    0.000    0.000    0.000    0.000 pprint_util.py:52(__str__)
       89    0.000    0.000    0.000    0.000 pprint_util.py:53(<genexpr>)
      162    0.000    0.000    0.000    0.000 pprint_util.py:56(pp)
      162    0.000    0.000    0.000    0.000 pprint_util.py:57(<listcomp>)
       18    0.000    0.000    0.000    0.000 pprint_util.py:62(vcat)
   202875    0.267    0.000    1.013    0.000 source_info_util.py:64(current)
   311430    0.226    0.000    0.226    0.000 source_info_util.py:67(user_context)
        1    0.000    0.000    0.000    0.000 threading.py:1031(name)
        1    0.000    0.000    0.000    0.000 threading.py:1306(current_thread)
        1    0.000    0.000    0.000    0.000 threading.py:81(RLock)
       90    0.000    0.000    0.000    0.000 traceback_util.py:107(filtered_tracebacks_supported)
       90    0.000    0.000    0.001    0.000 traceback_util.py:110(api_boundary)
    60/30    0.553    0.009  213.853    7.128 traceback_util.py:136(reraise_with_filtered_traceback)
       60    0.000    0.000    0.005    0.000 tree_util.py:168(tree_map)
      210    0.000    0.000    0.001    0.000 tree_util.py:54(tree_flatten)
      150    0.001    0.000    0.001    0.000 tree_util.py:71(tree_unflatten)
   155715    0.023    0.000    0.023    0.000 typing.py:1149(cast)
       30    0.560    0.019    1.657    0.055 util.py:122(toposort)
       30    0.000    0.000    0.000    0.000 util.py:139(<listcomp>)
       30    0.247    0.008    0.658    0.022 util.py:153(check_toposort)
   528120    0.111    0.000    0.139    0.000 util.py:156(<genexpr>)
       30    0.000    0.000    0.000    0.000 util.py:159(_remove_duplicates)
    88/44    0.000    0.000    0.223    0.005 util.py:189(cached)
471389/471345    1.821    0.000    4.805    0.000 util.py:193(wrapper)
        6    0.000    0.000    0.000    0.000 util.py:206(memoized)
  5599188    5.715    0.000   10.641    0.000 util.py:210(wrapper)
       60    0.000    0.000    0.000    0.000 util.py:227(__init__)
      870    0.000    0.000    0.000    0.000 util.py:239(__init__)
   190154    0.665    0.000    0.734    0.000 util.py:30(safe_zip)
      180    0.001    0.000    0.002    0.000 util.py:301(wraps)
5349253/4935133   14.188    0.000   37.191    0.000 util.py:36(safe_map)
   192074    0.488    0.000    0.769    0.000 util.py:43(unzip2)
     1920    0.005    0.000    0.005    0.000 util.py:99(__get__)
     1350    0.004    0.000    0.006    0.000 utils.py:120(lin)
     1650    0.724    0.000  130.796    0.079 utils.py:130(getc6)
       30    0.000    0.000    0.000    0.000 utils.py:172(check_inputs)
       30    0.122    0.004   12.750    0.425 utils.py:78(ncoord)
       30    0.000    0.000    0.109    0.004 utils.py:95(<listcomp>)
     1920    0.003    0.000    0.032    0.000 xla.py:1019(_forward_method)
   583065    0.691    0.000    1.985    0.000 xla.py:1033(make_device_array)
  1345200    2.633    0.000    2.633    0.000 xla.py:1075(__init__)
       44    0.000    0.000    0.001    0.000 xla.py:108(aval_to_result_handler)
   118770    0.041    0.000    0.041    0.000 xla.py:1101(_check_if_deleted)
   118770    1.292    0.000    1.452    0.000 xla.py:1118(_value)
  2998260    0.919    0.000    0.919    0.000 xla.py:1126(shape)
  3065160    0.784    0.000    0.784    0.000 xla.py:1130(dtype)
     3510    0.002    0.000    0.002    0.000 xla.py:1138(ndim)
   111764    0.163    0.000    1.414    0.000 xla.py:114(array_result_handler)
   117060    0.404    0.000    3.346    0.000 xla.py:1192(item)
       30    0.000    0.000    0.000    0.000 xla.py:1239(__array__)
   116820    0.178    0.000    1.602    0.000 xla.py:1247(<lambda>)
   913185    1.354    0.000   14.181    0.000 xla.py:126(device_put)
   117060    0.089    0.000    0.089    0.000 xla.py:1265(__hash__)
   762135    0.669    0.000    7.071    0.000 xla.py:1296(_device_put_device_array)
   762135    3.169    0.000    5.740    0.000 xla.py:1302(_copy_device_array_to_device)
   880875    0.584    0.000    0.781    0.000 xla.py:1323(_force)
   151050    1.862    0.000    2.022    0.000 xla.py:133(_device_put_array)
   913185    0.804    0.000    3.734    0.000 xla.py:149(canonicalize_dtype)
   150180    0.305    0.000    2.634    0.000 xla.py:160(_canonicalize_ndarray_dtype)
      870    0.002    0.000    0.007    0.000 xla.py:163(_canonicalize_python_scalar_dtype)
   801525    0.609    0.000    2.063    0.000 xla.py:173(abstractify)
      930    0.002    0.000    0.013    0.000 xla.py:184(_make_abstract_python_scalar)
       19    0.000    0.000    0.000    0.000 xla.py:210(_param_uses_outfeed)
       44    0.000    0.000    0.000    0.000 xla.py:219(primitive_uses_outfeed)
   801465    0.536    0.000    2.597    0.000 xla.py:232(arg_spec)
   471345    1.911    0.000   45.355    0.000 xla.py:239(apply_primitive)
       44    0.001    0.000    0.223    0.005 xla.py:253(xla_primitive_callable)
       44    0.000    0.000    0.000    0.000 xla.py:297(_device_from_arg_devices)
       44    0.000    0.000    0.000    0.000 xla.py:308(<setcomp>)
       44    0.002    0.000    0.008    0.000 xla.py:314(primitive_computation)
       44    0.209    0.005    0.209    0.005 xla.py:352(backend_compile)
   471345   19.647    0.000   36.042    0.000 xla.py:357(_execute_compiled_primitive)
  1272810    0.658    0.000   11.171    0.000 xla.py:359(<genexpr>)
   471345    1.883    0.000    3.547    0.000 xla.py:375(check_special)
   762135    0.126    0.000    0.126    0.000 xla.py:75(identity)
       44    0.000    0.000    0.003    0.000 xla.py:788(_xla_callable_args)
       44    0.000    0.000    0.002    0.000 xla.py:806(<listcomp>)
       62    0.000    0.000    0.001    0.000 xla.py:834(_xla_param)
       62    0.000    0.000    0.001    0.000 xla.py:86(_make_array_shape)
       62    0.000    0.000    0.001    0.000 xla.py:96(aval_to_xla_shapes)
        2    0.000    0.000    0.015    0.008 xla_bridge.py:126(_get_local_backend)
        3    0.000    0.000    0.015    0.005 xla_bridge.py:166(get_backend)
   913229    1.376    0.000    1.392    0.000 xla_bridge.py:181(get_device_backend)
       44    0.000    0.000    0.000    0.000 xla_bridge.py:187(device_count)
       62    0.000    0.000    0.001    0.000 xla_bridge.py:316(parameter)
       44    0.001    0.000    0.001    0.000 xla_bridge.py:407(make_computation_builder)
       44    0.001    0.000    0.001    0.000 xla_bridge.py:66(get_compile_options)
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