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 0.001553/0.001553, allocations: 110.6 kB / 16.41 MB, free: 6.496 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001272/0.001272, allocations: 187 kB / 17.34 MB, free: 5.762 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.362/1.362, allocations: 222.9 MB / 241 MB, free: 15.16 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08663/0.08663, allocations: 15.31 MB / 306.5 MB, free: 15.42 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001256/0.001256, allocations: 67.89 kB / 425.9 MB, free: 11.46 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1096/0.1109, allocations: 53.61 MB / 479.5 MB, free: 5.797 MB / 350.1 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 0.03602/0.147, allocations: 25.4 MB / 0.493 GB, free: 12.48 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2763/0.4233, allocations: 16.66 MB / 0.5093 GB, free: 18.21 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007008/0.4241, allocations: 11.69 kB / 0.5093 GB, free: 18.21 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009841/0.425, allocations: 331.6 kB / 0.5096 GB, free: 18.21 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004649/0.4297, allocations: 1.487 MB / 0.5111 GB, free: 18.19 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00615/0.4359, allocations: 1.983 MB / 0.513 GB, free: 17.57 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002594/0.4385, allocations: 1.541 MB / 0.5145 GB, free: 17.27 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001292/0.4398, allocations: 0.8509 MB / 0.5154 GB, free: 17.21 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001159/0.441, allocations: 0.7686 MB / 0.5161 GB, free: 17.13 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001328/0.4423, allocations: 0.8522 MB / 0.5169 GB, free: 17 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002497/0.4426, allocations: 134.5 kB / 0.5171 GB, free: 17 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006881/0.4495, allocations: 1.785 MB / 0.5188 GB, free: 16.83 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004705/0.45, allocations: 325.1 kB / 0.5191 GB, free: 16.64 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001054/0.451, allocations: 0.6853 MB / 0.5198 GB, free: 16.25 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.009596/0.4606, allocations: 3.341 MB / 0.5231 GB, free: 15.02 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.674e-06/0.4607, allocations: 1.781 kB / 0.5231 GB, free: 15.02 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.745e-06/0.4607, allocations: 1.156 kB / 0.5231 GB, free: 15.02 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 2.555e-05/0.4607, allocations: 0 / 0.5231 GB, free: 15.02 MB / 382.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 276
 * Number of variables: 276
Notification: Performance of Generate backend data structure: time 0.003821/0.4645, allocations: 1.8 MB / 0.5248 GB, free: 13.94 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.905e-05/0.4646, allocations: 12.06 kB / 0.5248 GB, free: 13.94 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001288/0.4659, allocations: 271.7 kB / 0.5251 GB, free: 13.86 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001072/0.467, allocations: 0.6774 MB / 0.5257 GB, free: 13.42 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001032/0.4671, allocations: 110.9 kB / 0.5259 GB, free: 13.35 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001841/0.4673, allocations: 109.6 kB / 0.526 GB, free: 13.31 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002188/0.4695, allocations: 1.337 MB / 0.5273 GB, free: 12.77 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.474e-05/0.4695, allocations: 1.188 kB / 0.5273 GB, free: 12.77 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001117/0.4696, allocations: 45.34 kB / 0.5273 GB, free: 12.73 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.422e-05/0.4696, allocations: 25.56 kB / 0.5273 GB, free: 12.73 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002537/0.4722, allocations: 1.698 MB / 0.529 GB, free: 12.23 MB / 382.1 MB
Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.006413/0.4786, allocations: 4.293 MB / 0.5332 GB, free: 9.273 MB / 382.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003029/0.4817, allocations: 2.277 MB / 0.5354 GB, free: 8.082 MB / 382.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007411/0.4824, allocations: 0.5917 MB / 0.536 GB, free: 7.781 MB / 382.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006056/0.4885, allocations: 5.383 MB / 0.5412 GB, free: 2.906 MB / 382.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.104e-05/0.4885, allocations: 41.81 kB / 0.5413 GB, free: 2.859 MB / 382.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.575e-06/0.4886, allocations: 0 / 0.5413 GB, free: 2.859 MB / 382.1 MB
Notification: Performance of matching and sorting (n=95): time 0.0136/0.5022, allocations: 3.576 MB / 0.5448 GB, free: 15.26 MB / 398.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.399e-05/0.5022, allocations: 64.34 kB / 0.5448 GB, free: 15.18 MB / 398.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007268/0.503, allocations: 0.5822 MB / 0.5454 GB, free: 14.59 MB / 398.1 MB
Notification: Performance of collectPreVariables (initialization): time 8.674e-05/0.5031, allocations: 48.36 kB / 0.5454 GB, free: 14.54 MB / 398.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003104/0.5034, allocations: 0.5272 MB / 0.546 GB, free: 14 MB / 398.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002625/0.5036, allocations: 338.6 kB / 0.5463 GB, free: 13.68 MB / 398.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003063/0.504, allocations: 230.8 kB / 0.5465 GB, free: 13.45 MB / 398.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001563/0.5041, allocations: 390.8 kB / 0.5469 GB, free: 13.05 MB / 398.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005754/0.5047, allocations: 354.5 kB / 0.5472 GB, free: 12.71 MB / 398.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008207/0.5055, allocations: 0.7583 MB / 0.548 GB, free: 11.79 MB / 398.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001503/0.507, allocations: 1.198 MB / 0.5491 GB, free: 10.45 MB / 398.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.925e-06/0.5071, allocations: 7.938 kB / 0.5491 GB, free: 10.44 MB / 398.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003814/0.5109, allocations: 1.473 MB / 0.5506 GB, free: 8.969 MB / 398.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.738e-05/0.5109, allocations: 12 kB / 0.5506 GB, free: 8.957 MB / 398.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.191e-05/0.511, allocations: 15.98 kB / 0.5506 GB, free: 8.941 MB / 398.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001846/0.5128, allocations: 249.1 kB / 0.5508 GB, free: 8.703 MB / 398.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001413/0.5142, allocations: 322.2 kB / 0.5511 GB, free: 8.391 MB / 398.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005373/0.5196, allocations: 3.863 MB / 0.5549 GB, free: 4.277 MB / 398.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001048/0.5207, allocations: 42.62 kB / 0.555 GB, free: 4.238 MB / 398.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001108/0.5208, allocations: 67.98 kB / 0.555 GB, free: 4.172 MB / 398.1 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 58
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (152):
 * Single equations (assignments): 150
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.0005046/0.5213, allocations: 276 kB / 0.5553 GB, free: 3.895 MB / 398.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001857/0.5215, allocations: 86.88 kB / 0.5554 GB, free: 3.809 MB / 398.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003756/0.5253, allocations: 1.331 MB / 0.5567 GB, free: 2.496 MB / 398.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.466e-05/0.5253, allocations: 18.59 kB / 0.5567 GB, free: 2.48 MB / 398.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.881e-06/0.5253, allocations: 0 / 0.5567 GB, free: 2.48 MB / 398.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.466e-05/0.5253, allocations: 3.984 kB / 0.5567 GB, free: 2.477 MB / 398.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001477/0.5268, allocations: 1.072 MB / 0.5577 GB, free: 1.371 MB / 398.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.303e-06/0.5268, allocations: 4 kB / 0.5577 GB, free: 1.367 MB / 398.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001188/0.528, allocations: 211.8 kB / 0.5579 GB, free: 1.16 MB / 398.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001816/0.5299, allocations: 230.8 kB / 0.5582 GB, free: 0.9375 MB / 398.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.469e-05/0.53, allocations: 35.98 kB / 0.5582 GB, free: 0.9023 MB / 398.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004686/0.5347, allocations: 3.768 MB / 0.5619 GB, free: 12.88 MB / 414.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.697e-06/0.5347, allocations: 3.938 kB / 0.5619 GB, free: 12.88 MB / 414.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004173/0.5389, allocations: 1.739 MB / 0.5636 GB, free: 11.11 MB / 414.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.000303/0.5392, allocations: 156 kB / 0.5637 GB, free: 10.94 MB / 414.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001208/0.5393, allocations: 20 kB / 0.5637 GB, free: 10.92 MB / 414.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005011/0.5398, allocations: 20 kB / 0.5638 GB, free: 10.9 MB / 414.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002011/0.54, allocations: 83.48 kB / 0.5638 GB, free: 10.82 MB / 414.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.101e-05/0.5401, allocations: 39.98 kB / 0.5639 GB, free: 10.78 MB / 414.1 MB
Notification: Performance of sorting global known variables: time 0.0004453/0.5406, allocations: 395 kB / 0.5643 GB, free: 10.4 MB / 414.1 MB
Notification: Performance of sort global known variables: time 1.3e-07/0.5406, allocations: 0 / 0.5643 GB, free: 10.4 MB / 414.1 MB
Notification: Performance of remove unused functions: time 0.002355/0.5429, allocations: 0.6714 MB / 0.5649 GB, free: 9.73 MB / 414.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 5
 * Number of states: 5 (solution.temperature,CH4.logn,CO2.logn,H2O.logn,H2.logn)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (98):
 * Single equations (assignments): 96
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001575/0.5445, allocations: 0.8036 MB / 0.5657 GB, free: 9.055 MB / 414.1 MB
Notification: Performance of simCode: created initialization part: time 0.002122/0.5467, allocations: 1.259 MB / 0.5669 GB, free: 7.777 MB / 414.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.526e-06/0.5467, allocations: 0 / 0.5669 GB, free: 7.777 MB / 414.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001015/0.5477, allocations: 0.7503 MB / 0.5677 GB, free: 7.012 MB / 414.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001112/0.5488, allocations: 204.6 kB / 0.5679 GB, free: 6.84 MB / 414.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003216/0.552, allocations: 2.004 MB / 0.5698 GB, free: 4.836 MB / 414.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00053/0.5526, allocations: 1.031 MB / 0.5708 GB, free: 3.793 MB / 414.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004847/0.5531, allocations: 205.8 kB / 0.571 GB, free: 3.598 MB / 414.1 MB
Notification: Performance of SimCode: time 1.102e-06/0.5531, allocations: 0 / 0.571 GB, free: 3.598 MB / 414.1 MB
Notification: Performance of Templates: time 0.03175/0.5849, allocations: 26.26 MB / 0.5967 GB, free: 9.941 MB / 446.1 MB
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
(rm -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)