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starsimhub / starsim

Starsim disease modeling framework
http://starsim.org
MIT License
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ConstantInference error #327

Closed MObrien-IDM closed 7 months ago

MObrien-IDM commented 7 months ago 
[c:\Users\michelleob\Anaconda3\lib\site-packages\pandas\core\arrays\masked.py:60](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/pandas/core/arrays/masked.py:60): UserWarning: Pandas requires version '1.3.6' or newer of 'bottleneck' (version '1.3.5' currently installed).
  from pandas.core import (
Starsim 0.2.4 (2024-02-27) — © 2023-2024 by IDM
0.2.4
Initializing sim with 5000 agents
---------------------------------------------------------------------------
ConstantInferenceError                    Traceback (most recent call last)
Cell In [1], [line 20](vscode-notebook-cell:?execution_count=1&line=20)
     [18](vscode-notebook-cell:?execution_count=1&line=18) # Make the sim, run and plot
     [19](vscode-notebook-cell:?execution_count=1&line=19) sim = ss.Sim(pars)
---> [20](vscode-notebook-cell:?execution_count=1&line=20) sim.run()
     [21](vscode-notebook-cell:?execution_count=1&line=21) sim.plot()

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\sim.py:536, in Sim.run(self, until, reset_seed, verbose)
    [534](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:534) T = sc.timer()
    [535](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:535) if not self.initialized:
--> [536](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:536)     self.initialize()
    [537](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:537)     self._orig_pars = sc.dcp(self.pars)  # Create a copy of the parameters to restore after the run
    [539](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:539) if verbose is None:

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\sim.py:113, in Sim.initialize(self, reset, **kwargs)
    [111](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:111) self.init_demographics()
    [112](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:112) self.init_networks()
--> [113](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:113) self.init_diseases()
    [114](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:114) self.init_connectors()
    [115](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:115) self.init_interventions()

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\sim.py:370, in Sim.init_diseases(self)
    [368](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:368) # Interate over diseases and initialize them
    [369](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:369) for disease in diseases:
--> [370](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:370)     disease.initialize(self)
    [372](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:372)     # Add the disease's parameters and results into the Sim's dicts
    [373](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/sim.py:373)     self.pars[disease.name] = disease.pars

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\disease.py:41, in Disease.initialize(self, sim)
     [39](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:39) self.validate_pars(sim)
     [40](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:40) self.init_results(sim)
---> [41](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:41) self.set_initial_states(sim)
     [42](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:42) return

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\disease.py:212, in Infection.set_initial_states(self, sim)
    [210](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:210) alive_uids = ss.true(sim.people.alive)  # Maybe just sim.people.uid?
    [211](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:211) initial_cases = self.pars.init_prev.filter(alive_uids)
--> [212](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:212) self.set_prognoses(sim, initial_cases)  # TODO: sentinel value to indicate seeds?
    [213](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/disease.py:213) return

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\diseases\sir.py:71, in SIR.set_prognoses(self, sim, uids, source_uids)
     [69](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/diseases/sir.py:69) d_rvs = p.dur_inf.rvs(dead_uids)
     [70](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/diseases/sir.py:70) r_rvs = p.dur_inf.rvs(rec_uids)
---> [71](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/diseases/sir.py:71) self.ti_dead[dead_uids] = sim.ti + d_rvs
     [72](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/diseases/sir.py:72) self.ti_recovered[rec_uids] = sim.ti + r_rvs
     [73](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/diseases/sir.py:73) return

File [c:\users\michelleob\onedrive](file:///C:/users/michelleob/onedrive) - bill & melinda gates foundation\documents\github\starsim\starsim\states.py:202, in UIDArray.__setitem__(self, key, value)
    [200](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/states.py:200) else:
    [201](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/states.py:201)     if isinstance(value, (np.ndarray, UIDArray)):
--> [202](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/states.py:202)         return self._set_vals_uids_multiple(self.values, key, self._uid_map.__array__(), value.__array__())
    [203](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/states.py:203)     else:
    [204](file:///C:/users/michelleob/onedrive%20-%20bill%20&%20melinda%20gates%20foundation/documents/github/starsim/starsim/states.py:204)         return self._set_vals_uids_single(self.values, key, self._uid_map.__array__(), value)

File [c:\Users\michelleob\Anaconda3\lib\site-packages\numba\core\dispatcher.py:480](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:480), in _DispatcherBase._compile_for_args(self, *args, **kws)
    [476](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:476)     error_rewrite(e, 'interpreter')
    [477](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:477) except errors.ConstantInferenceError as e:
    [478](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:478)     # this is from trying to infer something as constant when it isn't
    [479](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:479)     # or isn't supported as a constant
--> [480](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:480)     error_rewrite(e, 'constant_inference')
    [481](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:481) except Exception as e:
    [482](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:482)     if config.SHOW_HELP:

File [c:\Users\michelleob\Anaconda3\lib\site-packages\numba\core\dispatcher.py:409](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:409), in _DispatcherBase._compile_for_args.<locals>.error_rewrite(e, issue_type)
    [407](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:407)     raise e
    [408](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:408) else:
--> [409](file:///C:/Users/michelleob/Anaconda3/lib/site-packages/numba/core/dispatcher.py:409)     raise e.with_traceback(None)

ConstantInferenceError: Failed in nopython mode pipeline (step: nopython rewrites)
no single definition for 'errormsg'

File "..\..\starsim\states.py", line 130:
    def _set_vals_uids_multiple(vals, key, uid_map, value):
        <source elided>
                errormsg = f'Attempted to write to a non-existant index ({idx}) - this can happen if attempting to write to new entries that have not yet been allocated via grow()'
                raise IndexError(errormsg)
                ^

sc.metadata() #0. 'version': None #1. 'timestamp': '2024-Feb-27 11:47:04' #2. 'user': 'michelleob' #3. 'system': #0. 'platform': 'Windows-10-10.0.19045-SP0' #1. 'executable': 'C:\Users\michelleob\Anaconda3\python.exe' #2. 'version': '3.9.12 (main, Apr 4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]' #4. 'versions': #0. 'python': '3.9.12' #1. 'sciris': '3.1.3' #2. 'numpy': '1.23.5' #3. 'pandas': '2.2.1' #4. 'matplotlib': '3.5.3' #5. 'calling_info': #0. 'filename': 'N/A' #1. 'lineno': 'N/A' #6. 'git_info': #0. 'branch': 'main' #1. 'hash': '8efde4a' #2. 'date': 'Date N/A' #7. 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'3.8.0', 'zope.interface': '5.4.0', 'zstandard': '0.22.0'} #8. 'require': None #9. 'comments': None

RomeshA commented 7 months ago

Hi @MObrien-IDM as the SIR demo seems to run OK, this might be related to the input parameters somehow - do you have a script to reproduce, or otherwise a listing of the pars being passed in?

MObrien-IDM commented 7 months ago

Thanks, @RomeshA - I was attempting to run the tut_intro script during our starsim training, and @cliffckerr and I encountered this odd error.

cliffckerr commented 7 months ago

@RomeshA i think it's something related to the python version or library versions (or maybe windows??) -- will try to reproduce and if i can't will close, but just wanted to make this issue in case we came across it again!

RomeshA commented 7 months ago

Ah I see - I can reproduce this with numba==0.56.3 as per the sc.metadata() output, and running pip install --upgrade numbato install 0.59.0 appears to fix the problem for me

cliffckerr commented 7 months ago

Thanks for investigating @RomeshA ! Will close this since not a Starsim bug it seems.