slow to import dpdata
link89 opened this issue · 4 comments
link89 commented
I find that it would takes up to 30s to run just import dpdata on the login node of HPC. I did some investigation myself and find that it would load almost all the modules into memory when importing the dpdata module.
Here is the relative code:
https://github.com/deepmodeling/dpdata/blob/master/dpdata/__init__.py#L21-L30
Is it possible to just remove the __all__ expression? I think it is for users who like to use from dpdata import *, which is not a good practices IMO.
njzjz commented
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import time: 788 | 1136 | pandas.core.arrays.datetimelike
import time: 109 | 109 | pandas.core.arrays._ranges
import time: 226 | 226 | pandas.core.arrays.numeric
import time: 77 | 77 | pandas.core.tools
import time: 127 | 203 | pandas.core.tools.numeric
import time: 289 | 717 | pandas.core.arrays.integer
import time: 88 | 88 | pandas.tseries.offsets
import time: 458 | 2506 | pandas.core.arrays.datetimes
import time: 196 | 196 | pandas.core.arrays.floating
import time: 74 | 74 | pandas.core.indexes
import time: 370 | 370 | pandas._libs.index
import time: 335 | 335 | pandas._libs.join
import time: 314 | 314 | pandas._libs.sparse
import time: 152 | 152 | pandas.core.arrays.sparse.dtype
import time: 227 | 227 | pandas.io.formats.printing
import time: 320 | 1012 | pandas.core.arrays.sparse.array
import time: 192 | 1203 | pandas.core.arrays.sparse.accessor
import time: 87 | 1290 | pandas.core.arrays.sparse
import time: 150 | 1440 | pandas.core.dtypes.concat
import time: 106 | 106 | pandas.core.array_algos.putmask
import time: 105 | 105 | pandas.core.indexes.frozen
import time: 1726 | 4153 | pandas.core.indexes.base
import time: 793 | 4946 | pandas.core.arrays.interval
import time: 412 | 412 | pandas.core.arrays.numpy_
import time: 754 | 754 | pandas.core.arrays.period
import time: 382 | 382 | pandas.core.arrays.string_
import time: 321 | 321 | pandas.core.arrays.string_arrow
import time: 350 | 350 | pandas.core.arrays.timedeltas
import time: 183 | 74744 | pandas.core.arrays
import time: 126 | 126 | pandas.core.flags
import time: 316 | 316 | pandas._libs.reduction
import time: 317 | 317 | pandas.core.indexes.extension
import time: 339 | 656 | pandas.core.indexes.category
import time: 338 | 338 | pandas.core.indexes.numeric
import time: 114 | 114 | pandas.core.tools.timedeltas
import time: 478 | 928 | pandas.core.indexes.datetimelike
import time: 98 | 98 | pandas.core.tools.times
import time: 695 | 1719 | pandas.core.indexes.datetimes
import time: 1061 | 1061 | pandas.core.indexes.multi
import time: 176 | 176 | pandas.core.indexes.timedeltas
import time: 588 | 1824 | pandas.core.indexes.interval
import time: 324 | 324 | pandas.core.indexes.period
import time: 857 | 857 | pandas.core.indexes.range
import time: 152 | 5531 | pandas.core.indexes.api
import time: 143 | 5673 | pandas.core.aggregation
import time: 405 | 405 | pandas.core.apply
import time: 230 | 230 | pandas._libs.indexing
import time: 1093 | 1322 | pandas.core.indexing
import time: 82 | 82 | pandas.core.reshape
import time: 184 | 184 | backports_abc
import time: 487 | 670 | pandas._libs.internals
import time: 241 | 241 | pandas._libs.writers
import time: 144 | 144 | pandas.core.array_algos.quantile
import time: 158 | 158 | pandas.core.array_algos.replace
import time: 652 | 1193 | pandas.core.internals.blocks
import time: 123 | 1986 | pandas.core.internals.api
import time: 173 | 173 | pandas.core.internals.base
import time: 442 | 615 | pandas.core.internals.array_manager
import time: 252 | 252 | pandas.core.internals.ops
import time: 417 | 669 | pandas.core.internals.managers
import time: 203 | 871 | pandas.core.internals.concat
import time: 100 | 3570 | pandas.core.internals
import time: 225 | 3876 | pandas.core.reshape.concat
import time: 238 | 238 | gzip
import time: 860 | 1097 | pandas.io.common
import time: 670 | 1767 | pandas.io.formats.format
import time: 196 | 5838 | pandas.core.describe
import time: 228 | 228 | pandas.core.internals.construction
import time: 90 | 90 | pandas.core.shared_docs
import time: 73 | 73 | pandas._libs.window
import time: 330 | 403 | pandas._libs.window.aggregations
import time: 140 | 140 | pandas.core.util.numba_
import time: 91 | 91 | pandas.core.window.common
import time: 186 | 186 | pandas.core.window.doc
import time: 282 | 282 | pandas._libs.window.indexers
import time: 301 | 582 | pandas.core.window.indexers
import time: 130 | 130 | pandas.core.window.numba_
import time: 161 | 161 | pandas.core.window.online
import time: 1133 | 1133 | pandas.core.window.rolling
import time: 427 | 3249 | pandas.core.window.ewm
import time: 558 | 558 | pandas.core.window.expanding
import time: 94 | 3901 | pandas.core.window
import time: 4291 | 15669 | pandas.core.generic
import time: 88 | 88 | pandas.core.reshape.util
import time: 318 | 406 | pandas.core.reshape.melt
import time: 253 | 253 | pandas._libs.reshape
import time: 438 | 438 | pandas.core.indexes.accessors
import time: 98 | 98 | pandas.arrays
import time: 310 | 408 | pandas.core.tools.datetimes
import time: 864 | 864 | pandas.plotting._core
import time: 138 | 138 | pandas.plotting._misc
import time: 104 | 1105 | pandas.plotting
import time: 2323 | 4526 | pandas.core.series
import time: 359 | 359 | pandas.io.formats.info
import time: 14559 | 35516 | pandas.core.frame
import time: 211 | 211 | pandas.core.groupby.base
import time: 386 | 386 | pandas._libs.groupby
import time: 136 | 136 | pandas.core.groupby.numba_
import time: 82 | 82 | pandas.core.groupby.categorical
import time: 235 | 316 | pandas.core.groupby.grouper
import time: 449 | 765 | pandas.core.groupby.ops
import time: 1632 | 2918 | pandas.core.groupby.groupby
import time: 1375 | 46412 | pandas.core.groupby.generic
import time: 95 | 46506 | pandas.core.groupby
import time: 158 | 123577 | pandas.core.api
import time: 130 | 130 | pandas.tseries.api
import time: 89 | 89 | pandas.core.computation.common
import time: 154 | 243 | pandas.core.computation.align
import time: 272 | 272 | pprint
import time: 193 | 193 | pandas.compat.chainmap
import time: 270 | 734 | pandas.core.computation.scope
import time: 366 | 1100 | pandas.core.computation.ops
import time: 139 | 139 | pandas.core.computation.parsing
import time: 1032 | 2269 | pandas.core.computation.expr
import time: 243 | 2754 | pandas.core.computation.engines
import time: 150 | 2903 | pandas.core.computation.eval
import time: 93 | 2995 | pandas.core.computation.api
import time: 794 | 794 | pandas.core.reshape.merge
import time: 725 | 725 | pandas.core.reshape.pivot
import time: 305 | 305 | pandas.core.reshape.reshape
import time: 193 | 193 | pandas.core.reshape.tile
import time: 169 | 2184 | pandas.core.reshape.api
import time: 149 | 149 | pandas.api.extensions
import time: 92 | 92 | pandas.api.indexers
import time: 100 | 100 | pandas.core.dtypes.api
import time: 100 | 200 | pandas.api.types
import time: 148 | 588 | pandas.api
import time: 133 | 133 | pandas.util._print_versions
import time: 105 | 105 | pandas.io.clipboards
import time: 170 | 170 | backports_abc
import time: 564 | 733 | pandas._libs.parsers
import time: 152 | 152 | pandas.io.excel._util
import time: 145 | 145 | pandas.io.date_converters
import time: 1257 | 1401 | pandas.io.parsers.base_parser
import time: 185 | 185 | pandas.io.parsers.c_parser_wrapper
import time: 314 | 314 | pandas.io.parsers.python_parser
import time: 1118 | 3017 | pandas.io.parsers.readers
import time: 108 | 3125 | pandas.io.parsers
import time: 189 | 189 | pandas.io.excel._odfreader
import time: 308 | 308 | pandas.io.excel._openpyxl
import time: 130 | 130 | pandas.io.excel._pyxlsb
import time: 121 | 121 | pandas.io.excel._xlrd
import time: 833 | 5587 | pandas.io.excel._base
import time: 187 | 187 | pandas._libs.json
import time: 131 | 131 | pandas.io.formats._color_data
import time: 173 | 173 | pandas.io.formats.css
import time: 430 | 734 | pandas.io.formats.excel
import time: 185 | 1105 | pandas.io.excel._odswriter
import time: 183 | 183 | pandas.io.excel._xlsxwriter
import time: 135 | 135 | pandas.io.excel._xlwt
import time: 118 | 7126 | pandas.io.excel
import time: 242 | 242 | pandas.io.feather_format
import time: 109 | 109 | pandas.io.gbq
import time: 516 | 516 | pandas.io.html
import time: 495 | 495 | pandas.io.json._normalize
import time: 121 | 121 | pandas.io.json._table_schema
import time: 675 | 1290 | pandas.io.json._json
import time: 112 | 1402 | pandas.io.json
import time: 84 | 84 | pandas.io.orc
import time: 293 | 293 | pandas.io.parquet
import time: 170 | 170 | pandas.compat.pickle_compat
import time: 234 | 404 | pandas.io.pickle
import time: 370 | 370 | pandas.core.computation.pytables
import time: 1355 | 1724 | pandas.io.pytables
import time: 145 | 145 | pandas.io.sas.sasreader
import time: 104 | 248 | pandas.io.sas
import time: 84 | 84 | pandas.io.spss
import time: 541 | 541 | pandas.io.sql
import time: 1035 | 1035 | pandas.io.stata
import time: 524 | 524 | pandas.io.xml
import time: 194 | 14623 | pandas.io.api
import time: 120 | 120 | pandas.util._tester
import time: 201 | 201 | pandas._testing._random
import time: 148 | 148 | pandas._testing.contexts
import time: 190 | 538 | pandas._testing._io
import time: 98 | 98 | pandas._testing._warnings
import time: 145 | 145 | cmath
import time: 179 | 323 | pandas._libs.testing
import time: 204 | 527 | pandas._testing.asserters
import time: 81 | 81 | pandas._testing.compat
import time: 472 | 1714 | pandas._testing
import time: 78 | 1791 | pandas.testing
import time: 76 | 76 | pandas._version
import time: 326 | 180708 | pandas
import time: 126 | 126 | backports_abc
import time: 823 | 823 | typing_extensions
import time: 117 | 117 | backports_abc
import time: 111 | 111 | backports_abc
import time: 109 | 109 | backports_abc
import time: 565 | 673 | pydantic.typing
import time: 1573 | 2356 | pydantic.errors
import time: 107 | 107 | backports_abc
import time: 101 | 101 | backports_abc
import time: 209 | 310 | pydantic.version
import time: 915 | 1331 | pydantic.utils
import time: 529 | 4332 | pydantic.class_validators
import time: 410 | 410 | pydantic.config
import time: 100 | 100 | backports_abc
import time: 853 | 853 | ipaddress
import time: 106 | 106 | backports_abc
import time: 106 | 106 | colorsys
import time: 507 | 719 | pydantic.color
import time: 106 | 106 | backports_abc
import time: 99 | 99 | backports_abc
import time: 1450 | 1450 | pydantic.datetime_parse
import time: 517 | 2065 | pydantic.validators
import time: 952 | 3123 | pydantic.networks
import time: 105 | 105 | backports_abc
import time: 1460 | 1564 | pydantic.types
import time: 241 | 6498 | pydantic.json
import time: 419 | 7015 | pydantic.error_wrappers
import time: 106 | 106 | backports_abc
import time: 620 | 725 | pydantic.fields
import time: 105 | 105 | backports_abc
import time: 262 | 262 | pydantic.parse
import time: 313 | 313 | backports_abc
import time: 610 | 922 | pydantic.schema
import time: 1503 | 2790 | pydantic.main
import time: 644 | 16860 | pydantic.dataclasses
import time: 105 | 105 | backports_abc
import time: 265 | 370 | pydantic.annotated_types
import time: 268 | 268 | pydantic.decorator
import time: 102 | 102 | backports_abc
import time: 647 | 748 | pydantic.env_settings
import time: 238 | 238 | pydantic.tools
import time: 301 | 18783 | pydantic
import time: 100 | 100 | bson
import time: 196 | 196 | ruamel.yaml.compat
import time: 348 | 544 | ruamel.yaml.error
import time: 157 | 157 | ruamel.yaml.util
import time: 175 | 331 | ruamel.yaml.reader
import time: 360 | 360 | ruamel.yaml.tokens
import time: 427 | 786 | ruamel.yaml.scanner
import time: 222 | 222 | ruamel.yaml.events
import time: 83 | 83 | ruamel.yaml.anchor
import time: 164 | 247 | ruamel.yaml.scalarstring
import time: 591 | 838 | ruamel.yaml.comments
import time: 285 | 1343 | ruamel.yaml.parser
import time: 130 | 130 | ruamel.yaml.nodes
import time: 135 | 265 | ruamel.yaml.composer
import time: 155 | 155 | ruamel.yaml.scalarint
import time: 115 | 115 | ruamel.yaml.scalarfloat
import time: 94 | 94 | ruamel.yaml.scalarbool
import time: 90 | 90 | ruamel.yaml.timestamp
import time: 436 | 888 | ruamel.yaml.constructor
import time: 898 | 898 | ruamel.yaml.emitter
import time: 158 | 158 | ruamel.yaml.serializer
import time: 303 | 303 | ruamel.yaml.representer
import time: 291 | 5803 | _ruamel_yaml
import time: 276 | 276 | ruamel.yaml.resolver
import time: 233 | 6311 | ruamel.yaml.cyaml
import time: 179 | 179 | ruamel.yaml.loader
import time: 151 | 151 | ruamel.yaml.dumper
import time: 389 | 718 | ruamel.yaml.main
import time: 253 | 7281 | ruamel.yaml
import time: 389 | 208011 | monty.json
import time: 190 | 190 | monty.io
import time: 80 | 80 | monty.msgpack
import time: 96 | 96 | msgpack._version
import time: 147 | 147 | msgpack.exceptions
import time: 204 | 204 | msgpack.ext
import time: 187 | 187 | msgpack._cmsgpack
import time: 146 | 777 | msgpack
import time: 116 | 1162 | monty.serialization
import time: 123 | 123 | dpdata.md.pbc
import time: 462 | 462 | importlib.metadata
import time: 75 | 75 | dpdata.siesta
import time: 120 | 195 | dpdata.siesta.aiMD_output
import time: 80 | 80 | dpdata.siesta.output
import time: 82 | 82 | dpdata.plugin
import time: 134 | 216 | dpdata.format
import time: 68 | 68 | dpdata.xyz
import time: 141 | 208 | dpdata.xyz.quip_gap_xyz
import time: 98 | 98 | dpdata.xyz.xyz
import time: 68 | 68 | dpdata.pwmat
import time: 938 | 938 | dpdata.periodic_table
import time: 130 | 1135 | dpdata.pwmat.atomconfig
import time: 131 | 131 | dpdata.pwmat.movement
import time: 86 | 86 | dpdata.pymatgen
import time: 146 | 146 | pymatgen
import time: 97 | 97 | monty.fractions
import time: 256 | 256 | scipy._lib._testutils
import time: 214 | 470 | scipy._lib
import time: 186 | 656 | scipy._lib.deprecation
import time: 155 | 155 | scipy.__config__
import time: 88 | 88 | scipy.version
import time: 76 | 76 | scipy._distributor_init
import time: 370 | 370 | scipy._lib._pep440
import time: 375 | 375 | scipy._lib._ccallback_c
import time: 199 | 573 | scipy._lib._ccallback
import time: 2843 | 4757 | scipy
import time: 3630 | 3630 | scipy.constants.codata
import time: 200 | 200 | scipy.constants.constants
import time: 723 | 9309 | scipy.constants
import time: 595 | 9903 | pymatgen.core.units
import time: 106 | 106 | pymatgen.util
import time: 632 | 632 | fractions
import time: 203 | 940 | pymatgen.util.string
import time: 12333 | 23176 | pymatgen.core.periodic_table
import time: 526 | 23798 | pymatgen.core.composition
import time: 243 | 243 | multiprocessing.process
import time: 208 | 208 | multiprocessing.reduction
import time: 429 | 879 | multiprocessing.context
import time: 159 | 1037 | multiprocessing
import time: 171 | 1208 | monty.dev
import time: 69 | 69 | pymatgen.util.numpy
import time: 388 | 456 | pymatgen.util.coord_cython
import time: 208 | 664 | pymatgen.util.coord
import time: 110 | 110 | pymatgen.util.num
import time: 189 | 189 | numpy.typing._nested_sequence
import time: 74 | 74 | numpy.typing._nbit
import time: 687 | 687 | numpy.typing._char_codes
import time: 217 | 217 | numpy.typing._scalars
import time: 100 | 100 | numpy.typing._shape
import time: 189 | 189 | numpy.typing._generic_alias
import time: 1111 | 1299 | numpy.typing._dtype_like
import time: 1218 | 1218 | numpy.typing._array_like
import time: 390 | 390 | numpy.typing._add_docstring
import time: 319 | 4489 | numpy.typing
import time: 246 | 4734 | pymatgen.util.typing
import time: 460 | 7175 | pymatgen.core.lattice
import time: 84 | 84 | pymatgen.electronic_structure
import time: 463 | 546 | pymatgen.electronic_structure.core
import time: 308 | 854 | pymatgen.core.operations
import time: 248 | 248 | pymatgen.core.sites
import time: 167 | 167 | wcwidth.table_wide
import time: 157 | 157 | wcwidth.table_zero
import time: 70 | 70 | wcwidth.unicode_versions
import time: 165 | 557 | wcwidth.wcwidth
import time: 119 | 675 | wcwidth
import time: 623 | 623 | html.entities
import time: 315 | 937 | html
import time: 1428 | 3039 | tabulate
import time: 300 | 300 | pymatgen.core.bonds
import time: 97 | 97 | pymatgen.symmetry
import time: 446 | 446 | _sqlite3
import time: 244 | 690 | sqlite3.dbapi2
import time: 102 | 791 | sqlite3
import time: 130 | 130 | monty.design_patterns
import time: 12118 | 12118 | pymatgen.symmetry.groups
import time: 175 | 175 | pymatgen.symmetry.settings
import time: 315 | 13622 | pymatgen.symmetry.maggroups
import time: 3270 | 20231 | pymatgen.core.structure
import time: 483 | 52932 | pymatgen.core
import time: 149 | 53166 | dpdata.pymatgen.molecule
import time: 285 | 285 | lmp
import time: 295 | 579 | dpdata.lammps.dump
import time: 113 | 113 | dpdata.lammps.lmp
import time: 873 | 873 | dpdata.driver
import time: 146 | 146 | ase.data.vdw
import time: 285 | 430 | ase.data
import time: 224 | 654 | ase.atom
import time: 176 | 176 | ase.units
import time: 497 | 497 | ase.formula
import time: 373 | 870 | ase.utils
import time: 179 | 1048 | ase.utils.arraywrapper
import time: 738 | 1786 | ase.cell
import time: 121 | 121 | ase.stress
import time: 125 | 125 | ase.geometry.cell
import time: 126 | 126 | ase.geometry.minkowski_reduction
import time: 133 | 259 | ase.geometry.geometry
import time: 74 | 74 | ase.geometry.distance
import time: 102 | 558 | ase.geometry
import time: 199 | 199 | ase.symbols
import time: 597 | 3436 | ase.atoms
import time: 176 | 176 | ase.parallel
import time: 159 | 4424 | ase
import time: 71 | 71 | ase.calculators
import time: 306 | 306 | ase.outputs
import time: 151 | 151 | ase.calculators.abc
import time: 496 | 952 | ase.calculators.calculator
import time: 204 | 1226 | ase.calculators.singlepoint
import time: 379 | 379 | scipy.linalg._fblas
import time: 72 | 72 | scipy.linalg._cblas
import time: 30 | 30 | scipy.linalg._fblas_64
import time: 208 | 689 | scipy.linalg.blas
import time: 608 | 608 | scipy.linalg._flapack
import time: 52 | 52 | scipy.linalg._clapack
import time: 30 | 30 | scipy.linalg._flapack_64
import time: 347 | 347 | scipy._lib._util
import time: 973 | 2007 | scipy.linalg.lapack
import time: 166 | 2860 | scipy.linalg.misc
import time: 152 | 152 | scipy.linalg._flinalg
import time: 137 | 289 | scipy.linalg.flinalg
import time: 217 | 217 | scipy.linalg.decomp
import time: 107 | 107 | scipy.linalg.decomp_svd
import time: 197 | 197 | scipy.linalg._solve_toeplitz
import time: 285 | 1093 | scipy.linalg.basic
import time: 100 | 100 | scipy.linalg.decomp_lu
import time: 95 | 95 | scipy.linalg._decomp_ldl
import time: 87 | 87 | scipy.linalg.decomp_cholesky
import time: 98 | 98 | scipy.linalg.decomp_qr
import time: 98 | 98 | scipy.linalg._decomp_qz
import time: 198 | 198 | scipy.linalg.decomp_schur
import time: 85 | 85 | scipy.linalg._decomp_polar
import time: 149 | 149 | scipy.linalg.special_matrices
import time: 99 | 99 | scipy.linalg._expm_frechet
import time: 194 | 194 | scipy.linalg._matfuncs_sqrtm_triu
import time: 110 | 304 | scipy.linalg._matfuncs_sqrtm
import time: 223 | 773 | scipy.linalg.matfuncs
import time: 145 | 145 | scipy.linalg._solvers
import time: 69 | 69 | scipy.linalg._procrustes
import time: 281 | 281 | scipy.linalg.cython_blas
import time: 906 | 906 | scipy.linalg.cython_lapack
import time: 219 | 1405 | scipy.linalg._decomp_update
import time: 133 | 133 | scipy.sparse.sputils
import time: 378 | 510 | scipy.sparse.base
import time: 853 | 853 | scipy.sparse._sparsetools
import time: 198 | 198 | scipy.sparse.data
import time: 148 | 148 | scipy.sparse.dia
import time: 119 | 119 | scipy.sparse._index
import time: 454 | 917 | scipy.sparse.compressed
import time: 151 | 1920 | scipy.sparse.csr
import time: 118 | 118 | scipy.sparse.csc
import time: 477 | 477 | scipy.sparse._csparsetools
import time: 652 | 1129 | scipy.sparse.lil
import time: 212 | 212 | scipy.sparse.dok
import time: 164 | 164 | scipy.sparse.coo
import time: 245 | 245 | scipy.sparse.bsr
import time: 156 | 156 | scipy.sparse.construct
import time: 78 | 78 | scipy.sparse.extract
import time: 78 | 78 | scipy.sparse._matrix_io
import time: 117 | 117 | scipy.sparse.csgraph._laplacian
import time: 157 | 157 | scipy.sparse.csgraph._tools
import time: 108 | 265 | scipy.sparse.csgraph._validation
import time: 242 | 507 | scipy.sparse.csgraph._shortest_path
import time: 150 | 150 | scipy.sparse.csgraph._traversal
import time: 189 | 189 | scipy.sparse.csgraph._min_spanning_tree
import time: 261 | 261 | scipy.sparse.csgraph._flow
import time: 197 | 197 | scipy.sparse.csgraph._matching
import time: 188 | 188 | scipy.sparse.csgraph._reordering
import time: 143 | 1749 | scipy.sparse.csgraph
import time: 293 | 6645 | scipy.sparse
import time: 102 | 6746 | scipy.linalg._sketches
import time: 126 | 126 | scipy.linalg._decomp_cossin
import time: 246 | 14218 | scipy.linalg
import time: 121 | 121 | ase.utils.parsemath
import time: 818 | 15155 | ase.constraints
import time: 208 | 208 | ase.io.jsonio
import time: 186 | 186 | ase.io.pickletrajectory
import time: 281 | 17055 | ase.io.trajectory
import time: 275 | 275 | ase.io.ulm
import time: 250 | 525 | ase.io.bundletrajectory
import time: 246 | 246 | ase.io.netcdftrajectory
import time: 673 | 673 | ase.io.formats
import time: 132 | 23052 | ase.io
import time: 79 | 79 | dpdata.cp2k
import time: 197 | 197 | dpdata.unit
import time: 83 | 83 | dpdata.cp2k.cell
import time: 401 | 759 | dpdata.cp2k.output
import time: 72 | 72 | dpdata.gaussian
import time: 176 | 176 | swig_runtime_data4
import time: 8634 | 8810 | openbabel.openbabel
import time: 196 | 9006 | openbabel
import time: 233 | 9309 | dpdata.gaussian.gjf
import time: 192 | 192 | dpdata.gaussian.log
import time: 1198 | 1198 | h5py._errors
import time: 569 | 569 | h5py.defs
import time: 209 | 209 | h5py._objects
import time: 116 | 116 | h5py.h5py_warnings
import time: 225 | 1118 | h5py.h5
import time: 263 | 1381 | h5py.version
import time: 167 | 167 | h5py.h5r
import time: 126 | 126 | h5py.utils
import time: 265 | 391 | h5py.h5s
import time: 121 | 121 | h5py.h5ac
import time: 623 | 1134 | h5py.h5p
import time: 899 | 2033 | h5py.h5t
import time: 275 | 2474 | h5py._conv
import time: 186 | 186 | h5py.h5z
import time: 132 | 132 | h5py._proxy
import time: 259 | 391 | h5py.h5a
import time: 370 | 370 | h5py.h5d
import time: 190 | 190 | h5py.h5ds
import time: 312 | 312 | h5py.h5g
import time: 163 | 163 | h5py.h5i
import time: 298 | 772 | h5py.h5f
import time: 218 | 218 | h5py.h5fd
import time: 131 | 131 | h5py.h5pl
import time: 98 | 98 | h5py._hl
import time: 82 | 82 | h5py._hl.compat
import time: 284 | 366 | h5py._hl.filters
import time: 475 | 475 | h5py._hl.base
import time: 252 | 252 | h5py.h5o
import time: 219 | 219 | h5py.h5l
import time: 160 | 160 | backports_abc
import time: 388 | 547 | h5py._selector
import time: 201 | 201 | h5py._hl.selections
import time: 99 | 99 | h5py._hl.selections2
import time: 100 | 100 | h5py._hl.datatype
import time: 235 | 235 | h5py._hl.vds
import time: 430 | 1610 | h5py._hl.dataset
import time: 410 | 2489 | h5py._hl.group
import time: 278 | 2767 | h5py._hl.files
import time: 176 | 176 | h5py._hl.attrs
import time: 429 | 11614 | h5py
import time: 101 | 101 | dpdata.deepmd
import time: 84 | 84 | dpdata.deepmd.raw
import time: 175 | 359 | dpdata.deepmd.comp
import time: 553 | 553 | wcmatch.__meta__
import time: 113 | 666 | wcmatch
import time: 380 | 380 | bracex.__meta__
import time: 700 | 1079 | bracex
import time: 791 | 791 | wcmatch.util
import time: 109 | 109 | wcmatch.posix
import time: 938 | 938 | wcmatch._wcmatch
import time: 5316 | 7153 | wcmatch._wcparse
import time: 1273 | 10169 | wcmatch.glob
import time: 151 | 10320 | dpdata.deepmd.hdf5
import time: 242 | 242 | dpdata.deepmd.mixed
import time: 102 | 102 | dpdata.fhi_aims
import time: 183 | 284 | dpdata.fhi_aims.output
import time: 2559 | 2559 | rdkit.rdBase
import time: 228 | 2787 | rdkit
import time: 98 | 98 | rdkit.RDPaths
import time: 160 | 160 | pyPgSQL
import time: 194 | 451 | rdkit.RDConfig
import time: 4763 | 4763 | rdkit.DataStructs.cDataStructs
import time: 160 | 4923 | rdkit.DataStructs
import time: 1427 | 1427 | rdkit.Geometry.rdGeometry
import time: 159 | 1585 | rdkit.Geometry
import time: 8377 | 8377 | rdkit.Chem.rdchem
import time: 6005 | 6005 | rdkit.Chem.rdmolfiles
import time: 6171 | 6171 | rdkit.Chem.rdmolops
import time: 573 | 573 | rdkit.Chem.rdCIPLabeler
import time: 1347 | 1347 | rdkit.Chem.rdinchi
import time: 193 | 193 | rdkit.RDLogger
import time: 277 | 1815 | rdkit.Chem.inchi
import time: 764 | 764 | rdkit.Chem.rdMolInterchange
import time: 703 | 703 | rdkit.Chem.rdCoordGen
import time: 396 | 34545 | rdkit.Chem
import time: 122 | 122 | dpdata.rdkit
import time: 187 | 309 | dpdata.rdkit.utils
import time: 79 | 79 | dpdata.amber
import time: 106 | 106 | scipy._lib.doccer
import time: 82 | 82 | scipy.io.matlab.byteordercodes
import time: 268 | 455 | scipy.io.matlab.miobase
import time: 164 | 164 | scipy.io.matlab.mio_utils
import time: 303 | 467 | scipy.io.matlab.mio4
import time: 193 | 193 | scipy.io.matlab.streams
import time: 306 | 306 | scipy.io.matlab.mio5_params
import time: 314 | 811 | scipy.io.matlab.mio5_utils
import time: 510 | 1321 | scipy.io.matlab.mio5
import time: 324 | 2565 | scipy.io.matlab.mio
import time: 129 | 2694 | scipy.io.matlab
import time: 287 | 287 | scipy.io.netcdf
import time: 159 | 159 | scipy.io._fortran
import time: 283 | 283 | scipy.io.mmio
import time: 234 | 234 | scipy.io.idl
import time: 163 | 163 | scipy.io.harwell_boeing._fortran_format_parser
import time: 229 | 392 | scipy.io.harwell_boeing.hb
import time: 96 | 488 | scipy.io.harwell_boeing
import time: 146 | 4288 | scipy.io
import time: 107 | 107 | parmed._version
import time: 403 | 403 | parmed.exceptions
import time: 172 | 172 | parmed.periodic_table
import time: 263 | 263 | parmed.residue
import time: 130 | 130 | openmm
import time: 13 | 143 | openmm.unit
import time: 149 | 149 | parmed.unit.mymatrix
import time: 147 | 147 | parmed.unit.baseunit
import time: 85 | 85 | parmed.unit.basedimension
import time: 86 | 171 | parmed.unit.standard_dimensions
import time: 226 | 690 | parmed.unit.unit
import time: 171 | 171 | parmed.unit.quantity
import time: 81 | 81 | parmed.unit.unit_operators
import time: 119 | 119 | parmed.unit.prefix
import time: 29379 | 29578 | parmed.unit.unit_definitions
import time: 297 | 29874 | parmed.unit.unit_math
import time: 647 | 647 | parmed.unit.constants
import time: 1005 | 32528 | parmed.unit
import time: 139 | 139 | parmed.utils.pairlist
import time: 449 | 449 | parmed.constants
import time: 135 | 135 | openmm
import time: 72 | 207 | openmm.vec3
import time: 208 | 414 | parmed.vec3
import time: 158 | 572 | parmed.geometry
import time: 1831 | 2850 | parmed.topologyobjects
import time: 235 | 3223 | parmed.utils
import time: 127 | 127 | openmm
import time: 193 | 319 | parmed.utils.decorators
import time: 163 | 163 | parmed.rdkit.rdkit
import time: 95 | 258 | parmed.rdkit
import time: 104 | 104 | openmm
import time: 871 | 1550 | parmed.structure
import time: 144 | 144 | urllib.response
import time: 205 | 348 | urllib.error
import time: 720 | 720 | http
import time: 1098 | 1098 | _ssl
import time: 3540 | 4637 | ssl
import time: 853 | 6209 | http.client
import time: 1170 | 7379 | urllib.request
import time: 161 | 7887 | parmed.utils.io
import time: 142 | 8029 | parmed.formats.registry
import time: 357 | 357 | parmed.modeller.residue
import time: 2703 | 2703 | parmed.amber.offlib
import time: 14092 | 14092 | parmed.modeller.standardtemplates
import time: 171 | 17321 | parmed.modeller
import time: 25 | 17346 | parmed.modeller.residue
import time: 366 | 17711 | parmed.formats.mol2
import time: 427 | 427 | ftplib
import time: 320 | 320 | parmed.formats.pdbx.PdbxContainers
import time: 315 | 635 | parmed.formats.pdbx.PdbxReader
import time: 144 | 144 | parmed.formats.pdbx.PdbxWriter
import time: 155 | 933 | parmed.formats.pdbx
import time: 102 | 102 | parmed.symmetry
import time: 1005 | 2465 | parmed.formats.pdb
import time: 220 | 220 | parmed.formats.pqr
import time: 586 | 586 | parmed.charmm.psf
import time: 175 | 175 | parmed.parameters
import time: 141 | 141 | parmed.charmm._charmmfile
import time: 496 | 812 | parmed.charmm.parameters
import time: 211 | 211 | parmed.charmm.charmmcrds
import time: 132 | 1740 | parmed.charmm
import time: 19 | 1759 | parmed.charmm.psf
import time: 190 | 1948 | parmed.formats.psf
import time: 123 | 123 | parmed.formats.sdf
import time: 140 | 30632 | parmed.formats
import time: 17 | 30648 | parmed.formats.registry
import time: 195 | 195 | cmd
import time: 285 | 285 | bdb
import time: 149 | 149 | codeop
import time: 174 | 322 | code
import time: 613 | 1413 | pdb
import time: 105 | 105 | parmed.utils.fortranformat._exceptions
import time: 457 | 561 | parmed.utils.fortranformat._edit_descriptors
import time: 122 | 122 | parmed.utils.fortranformat._misc
import time: 131 | 131 | parmed.utils.fortranformat.config
import time: 191 | 2416 | parmed.utils.fortranformat._input
import time: 153 | 153 | parmed.utils.fortranformat._lexer
import time: 171 | 324 | parmed.utils.fortranformat._parser
import time: 169 | 2908 | parmed.utils.fortranformat.FortranRecordReader
import time: 177 | 177 | parmed.utils.fortranformat._output
import time: 128 | 305 | parmed.utils.fortranformat.FortranRecordWriter
import time: 114 | 3326 | parmed.utils.fortranformat
import time: 792 | 34765 | parmed.amber.amberformat
import time: 434 | 434 | parmed.amber.asciicrd
import time: 277 | 277 | parmed.amber.mask
import time: 254 | 254 | backports_abc
import time: 852 | 852 | netCDF4.utils
import time: 109 | 109 | netCDF4.sys
import time: 42 | 42 | netCDF4.posixpath
import time: 38 | 38 | netCDF4.cftime
import time: 2545 | 2545 | cftime._cftime
import time: 351 | 2895 | cftime
import time: 91 | 91 | netCDF4.numpy
import time: 50 | 50 | netCDF4.weakref
import time: 48 | 48 | netCDF4.warnings
import time: 47 | 47 | netCDF4.subprocess
import time: 45 | 45 | netCDF4.pathlib
import time: 44 | 44 | netCDF4.glob
import time: 44 | 44 | netCDF4.numpy
import time: 5043 | 9596 | netCDF4._netCDF4
import time: 266 | 9861 | netCDF4
import time: 501 | 501 | parmed.utils.netcdf
import time: 338 | 10700 | parmed.amber.netcdffiles
import time: 3139 | 3139 | parmed.amber.parameters
import time: 255 | 255 | openmm
import time: 631 | 885 | parmed.amber._amberparm
import time: 246 | 246 | parmed.amber._chamberparm
import time: 371 | 371 | parmed.amber._tinkerparm
import time: 206 | 1708 | parmed.amber.readparm
import time: 743 | 743 | parmed.amber.titratable_residues
import time: 224 | 51986 | parmed.amber
import time: 754 | 754 | parmed.gromacs._cpp
import time: 187 | 941 | parmed.gromacs._gromacsfile
import time: 959 | 1900 | parmed.gromacs.gromacstop
import time: 242 | 242 | parmed.gromacs.gromacsgro
import time: 78553 | 80694 | parmed.gromacs
import time: 212 | 212 | parmed.dlpoly.dlpolyfield
import time: 130 | 130 | parmed.dlpoly.dlpolyconfig
import time: 112 | 452 | parmed.dlpoly
import time: 180 | 180 | parmed.namd.namdbinfiles
import time: 95 | 274 | parmed.namd
import time: 579 | 579 | parmed.openmm.reporters
import time: 124 | 124 | lxml
import time: 169 | 169 | backports_abc
import time: 131 | 131 | backports_abc
import time: 638 | 769 | lxml._elementpath
import time: 117 | 117 | rnc2rng
import time: 3598 | 4651 | lxml.etree
import time: 409 | 5184 | parmed.openmm.parameters
import time: 203 | 203 | parmed.openmm.topsystem
import time: 111 | 111 | parmed.openmm.utils
import time: 192 | 192 | parmed.openmm.xmlfile
import time: 120 | 6386 | parmed.openmm
import time: 105 | 105 | pyrosetta
import time: 135 | 239 | parmed.rosetta.pose
import time: 86 | 325 | parmed.rosetta
import time: 180 | 180 | parmed.tinker.tinkerfiles
import time: 80 | 259 | parmed.tinker
import time: 195 | 195 | sierra
import time: 70 | 264 | parmed.entos.imports
import time: 213 | 477 | parmed.entos.converters
import time: 84 | 560 | parmed.entos
import time: 451 | 451 | parmed.tools.exceptions
import time: 240 | 691 | parmed.tools.argumentlist
import time: 105 | 105 | parmed.tools.parmlist
import time: 1289 | 2084 | parmed.tools.actions
import time: 120 | 2204 | parmed.tools
import time: 771 | 182151 | parmed
import time: 99 | 182249 | dpdata.amber.mask
import time: 172 | 186787 | dpdata.amber.md
import time: 160 | 160 | dpdata.amber.sqm
import time: 95 | 95 | dpdata.psi4
import time: 186 | 281 | dpdata.psi4.output
import time: 92 | 92 | dpdata.qe
import time: 167 | 258 | dpdata.qe.scf
import time: 173 | 173 | dpdata.qe.traj
import time: 84 | 84 | dpdata.gromacs
import time: 159 | 243 | dpdata.gromacs.gro
import time: 140 | 140 | dpdata.vasp.outcar
import time: 101 | 101 | dpdata.vasp.poscar
import time: 112 | 112 | xml
import time: 756 | 867 | xml.etree
import time: 434 | 434 | xml.etree.ElementPath
import time: 343 | 343 | pyexpat
import time: 499 | 842 | _elementtree
import time: 586 | 2728 | xml.etree.ElementTree
import time: 111 | 2838 | dpdata.vasp.xml
import time: 131 | 131 | dpdata.utils
import time: 81 | 81 | dpdata.abacus
import time: 150 | 150 | dpdata.abacus.scf
import time: 164 | 394 | dpdata.abacus.md
import time: 102 | 102 | dpdata.abacus.relax
import time: 275 | 275 | encodings.cp437
import time: 314 | 314 | dpdata.data_type
import time: 18046 | 358465 | dpdata.plugins
import time: 1260 | 651936 | dpdata.system
import time: 113 | 113 | dpdata._version
import time: 346 | 346 | dpdata.rdkit.sanitize
import time: 200 | 546 | dpdata.bond_order_system
import time: 264 | 653120 | dpdata
njzjz commented
@link89 it will be helpful if you show the output of python -X importtime -c 'import dpdata' to let us know which module takes the longest time.
njzjz commented
