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fix juliacall implementation #2754

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fix juliacall implementation #2754

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JacksonBurns
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  • CI updates: run CI on all platforms with and without RMS, split regression tests into separate job after that so that regression is only checked on one platform
  • installation updates: make RMG-Py actually pip-installable as reactionmechanismgenerator to avoid having to set the PYTHONPATH variable, which breaks juliacall, add a convenience script for installing RMS
  • code changes: fix some small bugs in the new optional-rms setup (one missed requires_rms and one incorrect rebase)

This PR replaces #2749

@JacksonBurns
fix juliacall incompatibilities; see extended
a7730a6 
 - CI updates: run CI on all platforms with and without RMS, split regression tests into separate job after that so that regression is only checked on one platform
- installation updates: make RMG-Py actually `pip`-installable as `reactionmechanismgenerator` to avoid having to set the `PYTHONPATH` variable, which breaks `juliacall`, add a convenience script for installing RMS
 - code changes: fix some small bugs in the new optional-rms setup (one missed `requires_rms` and one incorrect rebase)
@JacksonBurns
docker build should wait for regression test
0e33bf3
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Hmm...

Conducting simulation of reaction system 1...
2025-01-26T03:57:42.5395991Z Error: Model core reactions:
2025-01-26T03:57:42.5784866Z Error: []
2025-01-26T03:57:42.8444156Z Traceback (most recent call last):
2025-01-26T03:57:42.8444806Z   File "/home/runner/work/RMG-Py/RMG-Py/rmg.py", line 108, in <module>
2025-01-26T03:57:42.8445400Z     main()
2025-01-26T03:57:42.8445827Z   File "/home/runner/work/RMG-Py/RMG-Py/rmg.py", line 102, in main
2025-01-26T03:57:42.8446374Z     rmg.execute(**kwargs)
2025-01-26T03:57:42.8446937Z   File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/rmg/main.py", line 963, in execute
2025-01-26T03:57:42.8447576Z     ) = reaction_system.simulate(
2025-01-26T03:57:42.8448415Z   File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/rmg/reactionmechanismsimulator_reactors.py", line 436, in simulate
2025-01-26T03:57:42.8450003Z     edge_react, edge_domains, edge_interfaces, edge_p = self.generate_reactor(self.edge_phase_system)
2025-01-26T03:57:42.8451509Z   File "/home/runner/work/RMG-Py/RMG-Py/rmgpy/rmg/reactionmechanismsimulator_reactors.py", line 529, in generate_reactor
2025-01-26T03:57:42.8452530Z     domaincat, y0cat, pcat = Main.ConstantTAPhiDomain(
2025-01-26T03:57:42.8453373Z   File "/home/runner/.julia/packages/PythonCall/WMWY0/src/JlWrap/any.jl", line 262, in __call__
2025-01-26T03:57:42.8454303Z     return self._jl_callmethod($(pyjl_methodnum(pyjlany_call)), args, kwargs)
2025-01-26T03:57:42.8455482Z juliacall.JuliaError: AssertionError: CH4 not found in species list: ["vacantX", "HX", "OX", "CH3X", "HOX", "H2OX", "CO2X", "OCX", "CX", "CH2X", "CHX", "C.[Pt]"]
2025-01-26T03:57:42.8456442Z Stacktrace:
2025-01-26T03:57:42.8458712Z  [1] ConstantTAPhiDomain(; phase::IdealSurface{Tuple{Arrheniusvec{Vector{Float64}, Vector{Float64}, Vector{Float64}}}, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, ReactionMechanismSimulator.NASAvec{EmptyThermoUncertainty}, Vector{Float64}}, initialconds::Dict{String, Float64}, constantspecies::Vector{Union{}}, sparse::Bool, sensitivity::Bool, stationary::Bool)
2025-01-26T03:57:42.8461682Z    @ ReactionMechanismSimulator ~/.julia/packages/ReactionMechanismSimulator/74Olv/src/Domain.jl:677
2025-01-26T03:57:42.8462695Z  [2] pyjlany_call(self::Type{ConstantTAPhiDomain}, args_::Py, kwargs_::Py)
2025-01-26T03:57:42.8463492Z    @ PythonCall.JlWrap ~/.julia/packages/PythonCall/WMWY0/src/JlWrap/any.jl:44
2025-01-26T03:57:42.8464468Z  [3] _pyjl_callmethod(f::Any, self_::Ptr{PythonCall.C.PyObject}, args_::Ptr{PythonCall.C.PyObject}, nargs::Int64)
2025-01-26T03:57:42.8465451Z    @ PythonCall.JlWrap ~/.julia/packages/PythonCall/WMWY0/src/JlWrap/base.jl:73
2025-01-26T03:57:42.8466311Z  [4] _pyjl_callmethod(o::Ptr{PythonCall.C.PyObject}, args::Ptr{PythonCall.C.PyObject})
2025-01-26T03:57:42.8467171Z    @ PythonCall.JlWrap.Cjl ~/.julia/packages/PythonCall/WMWY0/src/JlWrap/C.jl:63
2025-01-26T03:57:47.4130995Z RMS_liquidSurface_ch4o2cat Failed to Execute

@JacksonBurns
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@jonwzheng there is one final small issue - the above regression test errors out. Can you take a look?

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jonwzheng commented Jan 27, 2025 •
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looking into it now, just going to type out what I see so far:

  • CH4 is successfully initialized in reaction_model.core and present in the core right before kinetic simulation. But it's not present in the edge.
  • Crash is due to CH4 not found in edge reactions list. Edit: specifically for the surface phase. Currently checking out: are the edge species not being properly constructed, or the edge reactions?

The model size is identical to the (currently passing) main branch test: https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/12984841799/job/36208494954#step:12:20982 which indicates that the model generation part is fine. Not likely an issue with extending reactions in edge unless it's something specifically with surface.

julia calls are handled in ConstantTLiquidSurfaceReactor

Proximal cause:

        domainliq, y0liq, pliq = Main.ConstantTVDomain(phase=liq, initialconds=to_julia(liq_initial_cond), constantspecies=to_julia(liq_constant_species))
        domaincat, y0cat, pcat = Main.ConstantTAPhiDomain(
            phase=surf, initialconds=to_julia(liq_initial_cond), constantspecies=to_julia(cat_constant_species),
        )

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jonwzheng commented Jan 27, 2025 •
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I think this is the problem: main...feat/py39_rebase#diff-e3891a3f45a445b7ce7074350473a30915530d790d1c56025a10195281742948R555

ConstantTAPhiDomain is called using liq initial conditions, not surface initial conditions.

Pushing a patch that will fix this in a minute.

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jonwzheng commented Jan 27, 2025 •
edited
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Okay, so changing initialconds=to_julia(liq_initial_cond), to initialconds=to_julia(self.initial_conditions["surface"]) fixes this issue, but now another bug comes up. It's the same type of error: the surface initial_conditions contains a key d, which doesn't exist as a species in the phase_system.phases["Surface"] list.

initial_conditions contains both species initial conditions as well as simulation parameters like T and A. Normally these are safely handled explicitly in the RMS code, but d is not: https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl/blob/c4d543583d40ee6cbf68cae27fd44e6926edd8b9/src/Domain.jl#L668

The surface initial conditions contains d as a distance metric, added 2 months ago: 21c960f

I'm kind of confused why the code was working at all before, because it seems like this issue would've been encountered even in the old code.

@JacksonBurns
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Met in person to talk about this.

the branch of RMS used in this PR (the one that contains the new JuliaCall code) was not up to date with the for_rmg branch of RMS currently used with RMG.

We have rebased our branch onto that one, and restarted the CI.

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Regression Testing Results

WARNING:root:Initial mole fractions do not sum to one; normalizing.
WARNING:root:Initial mole fractions do not sum to one; normalizing.
WARNING:root:Initial mole fractions do not sum to one; normalizing.
⚠️ One or more regression tests failed.
Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:08
Current: Execution time (DD:HH:MM:SS): 00:00:00:50
Reference: Memory used: 2766.00 MB
Current: Memory used: 2097.96 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython aromatics Passed Core Comparison ✅

Original model has 15 species.
Test model has 15 species. ✅
Original model has 11 reactions.
Test model has 11 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython aromatics Passed Edge Comparison ✅

Original model has 106 species.
Test model has 106 species. ✅
Original model has 358 reactions.
Test model has 358 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:22
Current: Execution time (DD:HH:MM:SS): 00:00:01:55
Reference: Memory used: 2894.75 MB
Current: Memory used: 2185.24 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 241 reactions.
Test model has 241 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython liquid_oxidation Failed Edge Comparison ❌

Original model has 214 species.
Test model has 214 species. ✅
Original model has 1590 reactions.
Test model has 1590 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(CCC=O)OO(116) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(115) <=> [OH](22) + CC(=O)CCCOO(112) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CC(C[CH]COO)OO(118) <=> CC(CC[CH]OO)OO(133) origin: intra_H_migration
rxn: CC(C[CH]COO)OO(118) <=> C[C](CCCOO)OO(132) origin: intra_H_migration

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:27
Current: Execution time (DD:HH:MM:SS): 00:00:00:59
Reference: Memory used: 2890.47 MB
Current: Memory used: 2176.61 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython nitrogen Passed Core Comparison ✅

Original model has 41 species.
Test model has 41 species. ✅
Original model has 360 reactions.
Test model has 360 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython nitrogen Failed Edge Comparison ❌

Original model has 133 species.
Test model has 133 species. ✅
Original model has 983 reactions.
Test model has 983 reactions. ✅

Non-identical thermo! ❌
original: O1[C]=N1
tested: O1[C]=N1

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
141.64 58.66 12.26 12.27 12.09 11.96 12.26 12.72 12.15
116.46 53.90 11.62 12.71 13.49 13.96 14.14 13.85 13.58

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)

Non-identical kinetics! ❌
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic

k(1bar) 300K 400K 500K 600K 800K 1000K 1500K 2000K
k(T): -66.25 -46.19 -34.19 -26.21 -16.28 -10.36 -2.54 1.31
k(T): -49.54 -33.65 -24.16 -17.85 -10.01 -5.35 0.80 3.82

kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:27
Current: Execution time (DD:HH:MM:SS): 00:00:01:33
Reference: Memory used: 2757.09 MB
Current: Memory used: 2075.50 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython oxidation Passed Core Comparison ✅

Original model has 59 species.
Test model has 59 species. ✅
Original model has 694 reactions.
Test model has 694 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython oxidation Passed Edge Comparison ✅

Original model has 230 species.
Test model has 230 species. ✅
Original model has 1526 reactions.
Test model has 1526 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:55
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 2867.92 MB
Current: Memory used: 2173.80 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython sulfur Passed Core Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 74 reactions.
Test model has 74 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython sulfur Failed Edge Comparison ❌

Original model has 89 species.
Test model has 89 species. ✅
Original model has 227 reactions.
Test model has 227 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary
The tested model has 1 reactions that the original model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: SO2 Comparison

The following observables did not match:

❌ Observable species O=S=O varied by more than 0.100 on average between old model SO2(15) and new model SO2(15) in condition 1.

⚠️ The following reaction conditions had some discrepancies:
Condition 1:
Reactor Type: IdealGasReactor
Reaction Time: 0.01 s
T0: 900 K
P0: 30 bar
Initial Mole Fractions: {'S': 0.000756, '[O][O]': 0.00129, 'N#N': 0.997954}

sulfur Failed Observable Testing ❌

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:35
Current: Execution time (DD:HH:MM:SS): 00:00:00:26
Reference: Memory used: 2945.81 MB
Current: Memory used: 2304.51 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython superminimal Failed Edge Comparison ❌

Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅

Non-identical thermo! ❌
original: [O]OOO
tested: [O]OOO

Hf(300K) S(300K) Cp(300K) Cp(400K) Cp(500K) Cp(600K) Cp(800K) Cp(1000K) Cp(1500K)
20.55 73.45 16.83 18.19 18.99 19.52 20.44 21.47 23.15
20.55 74.76 16.83 18.19 18.99 19.52 20.44 21.47 23.15

Identical thermo comments:
thermo: QM MopacMolPM3 calculation attempt 1 + radical(ROOJ)

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:24
Current: Execution time (DD:HH:MM:SS): 00:00:02:33
Reference: Memory used: 3483.39 MB
Current: Memory used: 2791.58 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:06:14
Current: Execution time (DD:HH:MM:SS): 00:00:04:29
Reference: Memory used: 3450.51 MB
Current: Memory used: 2757.85 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython RMS_CSTR_liquid_oxidation Passed Core Comparison ✅

Original model has 37 species.
Test model has 37 species. ✅
Original model has 202 reactions.
Test model has 202 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython RMS_CSTR_liquid_oxidation Passed Edge Comparison ✅

Original model has 248 species.
Test model has 248 species. ✅
Original model has 2057 reactions.
Test model has 2057 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

Regression test fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:42
Current: Execution time (DD:HH:MM:SS): 00:00:00:32
Reference: Memory used: 2692.96 MB
Current: Memory used: 2038.24 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython fragment Passed Edge Comparison ✅

Original model has 33 species.
Test model has 33 species. ✅
Original model has 47 reactions.
Test model has 47 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: fragment Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

fragment Passed Observable Testing ✅

Regression test RMS_constantVIdealGasReactor_fragment:

Reference: Execution time (DD:HH:MM:SS): 00:00:03:04
Current: Execution time (DD:HH:MM:SS): 00:00:03:09
Reference: Memory used: 3637.77 MB
Current: Memory used: 2952.93 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅

Original model has 10 species.
Test model has 10 species. ✅
Original model has 2 reactions.
Test model has 2 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 24 reactions.
Test model has 24 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅

Regression test minimal_surface:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:44
Current: Execution time (DD:HH:MM:SS): 00:00:00:32
Reference: Memory used: 2868.77 MB
Current: Memory used: 2186.56 MB

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython minimal_surface Passed Core Comparison ✅

Original model has 11 species.
Test model has 11 species. ✅
Original model has 3 reactions.
Test model has 3 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython minimal_surface Passed Edge Comparison ✅

Original model has 38 species.
Test model has 38 species. ✅
Original model has 38 reactions.
Test model has 38 reactions. ✅

Detected IPython. Loading juliacall extension. See https://juliapy.github.io/PythonCall.jl/stable/compat/#IPython Observables Test Case: minimal_surface Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

minimal_surface Passed Observable Testing ✅

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@JacksonBurns @jonwzheng