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ARC conda environment is too stiff to be created #707

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wangdu817 opened this issue Oct 17, 2023 · 2 comments
Open

ARC conda environment is too stiff to be created #707

wangdu817 opened this issue Oct 17, 2023 · 2 comments
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Type: Question Good for newcomers

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@wangdu817
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I tried to install dependencies of ARC through "conda env create -f environment.yml" , but the dependency is too stiff to be solved, I can not create it correctly. Conda will get stuck in "Solving environment", is there any alternative way to install the dependencies?
@wangdu817 wangdu817 added the Type: Question Good for newcomers label Oct 17, 2023
@wangdu817 wangdu817 changed the title ARC conda environment is too stiff to create ARC conda environment is too stiff to be created Oct 17, 2023
@calvinp0
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calvinp0 commented Oct 17, 2023 •
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Hi @wangdu817, we suggest you either change the solver for Conda to libmamba, as described here or you can utilize mamabaforge

@wangdu817
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wangdu817 commented Oct 18, 2023 •
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Hi @calvinp0 ,thank you so much, it works! But after I installed the dependencies, ARC could not run, and gave the following information, do you have any ideal how to fix it?

ERROR:root:Unable to find specified property fr_Al_COO
ERROR:root:Unable to find specified property fr_Al_OH
ERROR:root:Unable to find specified property fr_Al_OH_noTert
ERROR:root:Unable to find specified property fr_ArN
ERROR:root:Unable to find specified property fr_Ar_COO
ERROR:root:Unable to find specified property fr_Ar_N
ERROR:root:Unable to find specified property fr_Ar_NH
ERROR:root:Unable to find specified property fr_Ar_OH
ERROR:root:Unable to find specified property fr_COO
ERROR:root:Unable to find specified property fr_COO2
ERROR:root:Unable to find specified property fr_C_O
ERROR:root:Unable to find specified property fr_C_O_noCOO
ERROR:root:Unable to find specified property fr_C_S
ERROR:root:Unable to find specified property fr_HOCCN
ERROR:root:Unable to find specified property fr_Imine
ERROR:root:Unable to find specified property fr_NH0
ERROR:root:Unable to find specified property fr_NH1
ERROR:root:Unable to find specified property fr_NH2
ERROR:root:Unable to find specified property fr_N_O
ERROR:root:Unable to find specified property fr_Ndealkylation1
ERROR:root:Unable to find specified property fr_Ndealkylation2
ERROR:root:Unable to find specified property fr_Nhpyrrole
ERROR:root:Unable to find specified property fr_SH
ERROR:root:Unable to find specified property fr_aldehyde
ERROR:root:Unable to find specified property fr_alkyl_carbamate
ERROR:root:Unable to find specified property fr_alkyl_halide
ERROR:root:Unable to find specified property fr_allylic_oxid
ERROR:root:Unable to find specified property fr_amide
ERROR:root:Unable to find specified property fr_amidine
ERROR:root:Unable to find specified property fr_aniline
ERROR:root:Unable to find specified property fr_aryl_methyl
ERROR:root:Unable to find specified property fr_azide
ERROR:root:Unable to find specified property fr_azo
ERROR:root:Unable to find specified property fr_barbitur
ERROR:root:Unable to find specified property fr_benzene
ERROR:root:Unable to find specified property fr_benzodiazepine
ERROR:root:Unable to find specified property fr_bicyclic
ERROR:root:Unable to find specified property fr_diazo
ERROR:root:Unable to find specified property fr_dihydropyridine
ERROR:root:Unable to find specified property fr_epoxide
ERROR:root:Unable to find specified property fr_ester
ERROR:root:Unable to find specified property fr_ether
ERROR:root:Unable to find specified property fr_furan
ERROR:root:Unable to find specified property fr_guanido
ERROR:root:Unable to find specified property fr_halogen
ERROR:root:Unable to find specified property fr_hdrzine
ERROR:root:Unable to find specified property fr_hdrzone
ERROR:root:Unable to find specified property fr_imidazole
ERROR:root:Unable to find specified property fr_imide
ERROR:root:Unable to find specified property fr_isocyan
ERROR:root:Unable to find specified property fr_isothiocyan
ERROR:root:Unable to find specified property fr_ketone
ERROR:root:Unable to find specified property fr_ketone_Topliss
ERROR:root:Unable to find specified property fr_lactam
ERROR:root:Unable to find specified property fr_lactone
ERROR:root:Unable to find specified property fr_methoxy
ERROR:root:Unable to find specified property fr_morpholine
ERROR:root:Unable to find specified property fr_nitrile
ERROR:root:Unable to find specified property fr_nitro
ERROR:root:Unable to find specified property fr_nitro_arom
ERROR:root:Unable to find specified property fr_nitro_arom_nonortho
ERROR:root:Unable to find specified property fr_nitroso
ERROR:root:Unable to find specified property fr_oxazole
ERROR:root:Unable to find specified property fr_oxime
ERROR:root:Unable to find specified property fr_para_hydroxylation
ERROR:root:Unable to find specified property fr_phenol
ERROR:root:Unable to find specified property fr_phenol_noOrthoHbond
ERROR:root:Unable to find specified property fr_phos_acid
ERROR:root:Unable to find specified property fr_phos_ester
ERROR:root:Unable to find specified property fr_piperdine
ERROR:root:Unable to find specified property fr_piperzine
ERROR:root:Unable to find specified property fr_priamide
ERROR:root:Unable to find specified property fr_prisulfonamd
ERROR:root:Unable to find specified property fr_pyridine
ERROR:root:Unable to find specified property fr_quatN
ERROR:root:Unable to find specified property fr_sulfide
ERROR:root:Unable to find specified property fr_sulfonamd
ERROR:root:Unable to find specified property fr_sulfone
ERROR:root:Unable to find specified property fr_term_acetylene
ERROR:root:Unable to find specified property fr_tetrazole
ERROR:root:Unable to find specified property fr_thiazole
ERROR:root:Unable to find specified property fr_thiocyan
ERROR:root:Unable to find specified property fr_thiophene
ERROR:root:Unable to find specified property fr_unbrch_alkane
ERROR:root:Unable to find specified property fr_urea
ERROR:root:Unable to make new descriptors, descriptor generator not installed
ERROR:root:Unable to find specified property fr_Al_COO
ERROR:root:Unable to find specified property fr_Al_OH
ERROR:root:Unable to find specified property fr_Al_OH_noTert
ERROR:root:Unable to find specified property fr_ArN
ERROR:root:Unable to find specified property fr_Ar_COO
ERROR:root:Unable to find specified property fr_Ar_N
ERROR:root:Unable to find specified property fr_Ar_NH
ERROR:root:Unable to find specified property fr_Ar_OH
ERROR:root:Unable to find specified property fr_COO
ERROR:root:Unable to find specified property fr_COO2
ERROR:root:Unable to find specified property fr_C_O
ERROR:root:Unable to find specified property fr_C_O_noCOO
ERROR:root:Unable to find specified property fr_C_S
ERROR:root:Unable to find specified property fr_HOCCN
ERROR:root:Unable to find specified property fr_Imine
ERROR:root:Unable to find specified property fr_NH0
ERROR:root:Unable to find specified property fr_NH1
ERROR:root:Unable to find specified property fr_NH2
ERROR:root:Unable to find specified property fr_N_O
ERROR:root:Unable to find specified property fr_Ndealkylation1
ERROR:root:Unable to find specified property fr_Ndealkylation2
ERROR:root:Unable to find specified property fr_Nhpyrrole
ERROR:root:Unable to find specified property fr_SH
ERROR:root:Unable to find specified property fr_aldehyde
ERROR:root:Unable to find specified property fr_alkyl_carbamate
ERROR:root:Unable to find specified property fr_alkyl_halide
ERROR:root:Unable to find specified property fr_allylic_oxid
ERROR:root:Unable to find specified property fr_amide
ERROR:root:Unable to find specified property fr_amidine
ERROR:root:Unable to find specified property fr_aniline
ERROR:root:Unable to find specified property fr_aryl_methyl
ERROR:root:Unable to find specified property fr_azide
ERROR:root:Unable to find specified property fr_azo
ERROR:root:Unable to find specified property fr_barbitur
ERROR:root:Unable to find specified property fr_benzene
ERROR:root:Unable to find specified property fr_benzodiazepine
ERROR:root:Unable to find specified property fr_bicyclic
ERROR:root:Unable to find specified property fr_diazo
ERROR:root:Unable to find specified property fr_dihydropyridine
ERROR:root:Unable to find specified property fr_epoxide
ERROR:root:Unable to find specified property fr_ester
ERROR:root:Unable to find specified property fr_ether
ERROR:root:Unable to find specified property fr_furan
ERROR:root:Unable to find specified property fr_guanido
ERROR:root:Unable to find specified property fr_halogen
ERROR:root:Unable to find specified property fr_hdrzine
ERROR:root:Unable to find specified property fr_hdrzone
ERROR:root:Unable to find specified property fr_imidazole
ERROR:root:Unable to find specified property fr_imide
ERROR:root:Unable to find specified property fr_isocyan
ERROR:root:Unable to find specified property fr_isothiocyan
ERROR:root:Unable to find specified property fr_ketone
ERROR:root:Unable to find specified property fr_ketone_Topliss
ERROR:root:Unable to find specified property fr_lactam
ERROR:root:Unable to find specified property fr_lactone
ERROR:root:Unable to find specified property fr_methoxy
ERROR:root:Unable to find specified property fr_morpholine
ERROR:root:Unable to find specified property fr_nitrile
ERROR:root:Unable to find specified property fr_nitro
ERROR:root:Unable to find specified property fr_nitro_arom
ERROR:root:Unable to find specified property fr_nitro_arom_nonortho
ERROR:root:Unable to find specified property fr_nitroso
ERROR:root:Unable to find specified property fr_oxazole
ERROR:root:Unable to find specified property fr_oxime
ERROR:root:Unable to find specified property fr_para_hydroxylation
ERROR:root:Unable to find specified property fr_phenol
ERROR:root:Unable to find specified property fr_phenol_noOrthoHbond
ERROR:root:Unable to find specified property fr_phos_acid
ERROR:root:Unable to find specified property fr_phos_ester
ERROR:root:Unable to find specified property fr_piperdine
ERROR:root:Unable to find specified property fr_piperzine
ERROR:root:Unable to find specified property fr_priamide
ERROR:root:Unable to find specified property fr_prisulfonamd
ERROR:root:Unable to find specified property fr_pyridine
ERROR:root:Unable to find specified property fr_quatN
ERROR:root:Unable to find specified property fr_sulfide
ERROR:root:Unable to find specified property fr_sulfonamd
ERROR:root:Unable to find specified property fr_sulfone
ERROR:root:Unable to find specified property fr_term_acetylene
ERROR:root:Unable to find specified property fr_tetrazole
ERROR:root:Unable to find specified property fr_thiazole
ERROR:root:Unable to find specified property fr_thiocyan
ERROR:root:Unable to find specified property fr_thiophene
ERROR:root:Unable to find specified property fr_unbrch_alkane
ERROR:root:Unable to find specified property fr_urea
Traceback (most recent call last):
File "/home/test/ARC_NEW/ARC.py", line 12, in
from arc.common import read_yaml_file
File "/home/test/ARC_NEW/arc/init.py", line 2, in
import arc.main
File "/home/test/ARC_NEW/arc/main.py", line 21, in
from arkane.encorr.corr import assign_frequency_scale_factor
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/arkane/i nit.py", line 34, in
from arkane.common import ArkaneSpecies
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/arkane/com mon.py", line 62, in
from arkane.pdep import PressureDependenceJob
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/arkane/pde p.py", line 43, in
from rmgpy.chemkin import write_kinetics_entry
File "rmgpy/chemkin.pyx", line 52, in init rmgpy.chemkin
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/rmg/ pdep.py", line 48, in
from rmgpy.rmg.react import react_species
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/rmg/ react.py", line 36, in
from rmgpy.data.rmg import get_db
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/data /rmg.py", line 42, in
from rmgpy.data.thermo import ThermoDatabase
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/data /thermo.py", line 47, in
from rmgpy.ml.estimator import MLEstimator
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/rmgpy/ml/e stimator.py", line 36, in
import chemprop
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/init.py", line 1, in
# -- coding: utf-8 --
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/data/init.py", line 1, in
# -- coding: utf-8 --
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/data/data.py", line 10, in
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/features/init.py", line 1, in
# -- coding: utf-8 --
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/chemprop-0 .0.1-py3.7.egg/chemprop/features/features_generators.py", line 95, in
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/descriptas torus-2.0.0.32-py3.7.egg/descriptastorus/descriptors/init.py", line 3, in
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 668, in _load_unlocked
File "", line 638, in _load_backward_compatible
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/descriptas torus-2.0.0.32-py3.7.egg/descriptastorus/descriptors/rdDescriptors.py", line 278 , in
File "/home/test/anaconda3/envs/arc_env/lib/python3.7/site-packages/descriptas torus-2.0.0.32-py3.7.egg/descriptastorus/descriptors/rdDescriptors.py", line 271 , in init
ValueError: RDKit2D: Failed to initialize: unable to find specified properties:
fr_Al_COO
fr_Al_OH
fr_Al_OH_noTert
fr_ArN
fr_Ar_COO
fr_Ar_N
fr_Ar_NH
fr_Ar_OH
fr_COO
fr_COO2
fr_C_O
fr_C_O_noCOO
fr_C_S
fr_HOCCN
fr_Imine
fr_NH0
fr_NH1
fr_NH2
fr_N_O
fr_Ndealkylation1
fr_Ndealkylation2
fr_Nhpyrrole
fr_SH
fr_aldehyde
fr_alkyl_carbamate
fr_alkyl_halide
fr_allylic_oxid
fr_amide
fr_amidine
fr_aniline
fr_aryl_methyl
fr_azide
fr_azo
fr_barbitur
fr_benzene
fr_benzodiazepine
fr_bicyclic
fr_diazo
fr_dihydropyridine
fr_epoxide
fr_ester
fr_ether
fr_furan
fr_guanido
fr_halogen
fr_hdrzine
fr_hdrzone
fr_imidazole
fr_imide
fr_isocyan
fr_isothiocyan
fr_ketone
fr_ketone_Topliss
fr_lactam
fr_lactone
fr_methoxy
fr_morpholine
fr_nitrile
fr_nitro
fr_nitro_arom
fr_nitro_arom_nonortho
fr_nitroso
fr_oxazole
fr_oxime
fr_para_hydroxylation
fr_phenol
fr_phenol_noOrthoHbond
fr_phos_acid
fr_phos_ester
fr_piperdine
fr_piperzine
fr_priamide
fr_prisulfonamd
fr_pyridine
fr_quatN
fr_sulfide
fr_sulfonamd
fr_sulfone
fr_term_acetylene
fr_tetrazole
fr_thiazole
fr_thiocyan
fr_thiophene
fr_unbrch_alkane
fr_urea

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@wangdu817 @calvinp0