Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false)
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001339/0.001339, allocations: 107 kB / 16.42 MB, free: 6.512 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001431/0.001431, allocations: 189.5 kB / 17.35 MB, free: 5.754 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.32/1.32, allocations: 222.9 MB / 241.1 MB, free: 15.13 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.0869/0.0869, allocations: 15.31 MB / 306.5 MB, free: 15.41 MB / 254.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.967e-05/1.968e-05, allocations: 5.594 kB / 425.8 MB, free: 11.52 MB / 302.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66:writable] Notification: The diagnostics message for the missing inner is: 
Your model is using an outer "system" component but
an inner "system" component is not defined.
For simulation drag Modelica.Fluid.System into your model
to specify system properties.
Notification: Performance of NFInst.instantiate(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.04526/0.04528, allocations: 25.4 MB / 451.2 MB, free: 2.23 MB / 318.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02193/0.06723, allocations: 16.68 MB / 467.9 MB, free: 1.477 MB / 334.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001103/0.06839, allocations: 11.94 kB / 467.9 MB, free: 1.465 MB / 334.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009922/0.0694, allocations: 337.6 kB / 468.2 MB, free: 1.133 MB / 334.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004391/0.0738, allocations: 1.482 MB / 469.7 MB, free: 15.64 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005588/0.0794, allocations: 1.988 MB / 471.7 MB, free: 13.64 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002569/0.08199, allocations: 1.701 MB / 473.4 MB, free: 11.93 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001087/0.08309, allocations: 0.8674 MB / 474.3 MB, free: 11.05 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009478/0.08405, allocations: 0.7988 MB / 475.1 MB, free: 10.25 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0009899/0.08505, allocations: 0.8333 MB / 475.9 MB, free: 9.414 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.000176/0.08523, allocations: 132 kB / 476 MB, free: 9.285 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005829/0.09107, allocations: 1.779 MB / 477.8 MB, free: 7.504 MB / 350.1 MB
Notification: Performance of combineBinaries: time 0.001694/0.09278, allocations: 2.085 MB / 479.9 MB, free: 5.398 MB / 350.1 MB
Notification: Performance of replaceArrayConstructors: time 0.0007041/0.0935, allocations: 1.17 MB / 481.1 MB, free: 4.215 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000321/0.09383, allocations: 211.4 kB / 481.3 MB, free: 4.008 MB / 350.1 MB
Notification: Performance of FrontEnd: time 0.0003042/0.09414, allocations: 51.92 kB / 481.3 MB, free: 3.957 MB / 350.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 276 (272)
 * Number of variables: 276 (270)
Notification: Performance of Bindings: time 0.005338/0.09949, allocations: 6.11 MB / 487.4 MB, free: 13.6 MB / 366.1 MB
Notification: Performance of FunctionAlias: time 0.0008919/0.1004, allocations: 0.8594 MB / 488.3 MB, free: 12.71 MB / 366.1 MB
Notification: Performance of Early Inline: time 0.005591/0.106, allocations: 5.276 MB / 493.6 MB, free: 7.371 MB / 366.1 MB
Notification: Performance of simplify1: time 0.0004238/0.1064, allocations: 351.6 kB / 493.9 MB, free: 7.027 MB / 366.1 MB
Notification: Performance of Alias: time 0.007452/0.1139, allocations: 6.077 MB / 500 MB, free: 456 kB / 366.1 MB
Notification: Performance of simplify2: time 0.000506/0.1144, allocations: 299.7 kB / 0.4885 GB, free: 156 kB / 366.1 MB
Notification: Performance of Events: time 0.000299/0.1147, allocations: 247.7 kB / 0.4888 GB, free: 15.9 MB / 382.1 MB
Notification: Performance of Detect States: time 0.0008411/0.1156, allocations: 0.7644 MB / 0.4895 GB, free: 15.11 MB / 382.1 MB
Notification: Performance of Partitioning: time 0.001058/0.1167, allocations: 0.8843 MB / 0.4904 GB, free: 14.17 MB / 382.1 MB
Error: Internal error NBSlice.resolveDependency (single dependency) failed because list of scalar variables(2) {reaction.substrates[1].u, reaction.substrates[2].u}, does not fit the equation size 1.
Error: Internal error NBSlice.resolveDependency failed for: reaction.substrates.u.
Error: Internal error NBAdjacency.Matrix.upgradeRow failed for:
[SCAL] (1) reaction.du = reaction.p * reaction.products.u - reaction.s * reaction.substrates.u ($RES_SIM_52)