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 0.007583/0.007583, allocations: 99.64 kB / 15.73 MB, free: 6.035 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001697/0.001697, allocations: 189.6 kB / 16.67 MB, free: 5.969 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.428/1.428, allocations: 222.9 MB / 240.4 MB, free: 4.195 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.284/0.284, allocations: 15.33 MB / 305.9 MB, free: 15.3 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001384/0.001384, allocations: 63.91 kB / 425.2 MB, free: 13.1 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.319/0.3204, allocations: 53.61 MB / 478.8 MB, free: 25.88 MB / 366.1 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 0.03506/0.3555, allocations: 25.41 MB / 0.4924 GB, free: 9.277 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01836/0.3739, allocations: 16.66 MB / 0.5087 GB, free: 8.555 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.00171/0.3757, allocations: 11.94 kB / 0.5087 GB, free: 8.543 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001864/0.3776, allocations: 341.5 kB / 0.509 GB, free: 8.207 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.008304/0.3859, allocations: 1.478 MB / 0.5104 GB, free: 6.719 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.008962/0.3949, allocations: 1.984 MB / 0.5124 GB, free: 4.719 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.003398/0.3983, allocations: 1.545 MB / 0.5139 GB, free: 3.168 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001559/0.3999, allocations: 0.8473 MB / 0.5147 GB, free: 2.297 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001553/0.4015, allocations: 0.7754 MB / 0.5155 GB, free: 1.52 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001774/0.4033, allocations: 0.8528 MB / 0.5163 GB, free: 0.6641 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0004621/0.4038, allocations: 132 kB / 0.5164 GB, free: 0.5352 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007137/0.4109, allocations: 1.783 MB / 0.5182 GB, free: 14.75 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005971/0.4116, allocations: 331 kB / 0.5185 GB, free: 14.43 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001424/0.413, allocations: 0.6845 MB / 0.5192 GB, free: 13.74 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.008625/0.4216, allocations: 3.344 MB / 0.5224 GB, free: 10.38 MB / 398.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.712e-06/0.4217, allocations: 4 kB / 0.5224 GB, free: 10.38 MB / 398.1 MB
Notification: Performance of FrontEnd: time 1.482e-06/0.4217, allocations: 0 / 0.5224 GB, free: 10.38 MB / 398.1 MB
Notification: Performance of Transformations before backend: time 6.195e-05/0.4218, allocations: 0 / 0.5224 GB, free: 10.38 MB / 398.1 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 0.003918/0.4257, allocations: 1.805 MB / 0.5242 GB, free: 8.52 MB / 398.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.719e-05/0.4257, allocations: 15.91 kB / 0.5242 GB, free: 8.504 MB / 398.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001243/0.427, allocations: 274.8 kB / 0.5245 GB, free: 8.234 MB / 398.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001176/0.4282, allocations: 0.6648 MB / 0.5251 GB, free: 7.527 MB / 398.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001167/0.4283, allocations: 112.4 kB / 0.5252 GB, free: 7.41 MB / 398.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002079/0.4285, allocations: 116.3 kB / 0.5253 GB, free: 7.297 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002195/0.4307, allocations: 1.333 MB / 0.5266 GB, free: 5.918 MB / 398.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.464e-05/0.4308, allocations: 3.984 kB / 0.5266 GB, free: 5.914 MB / 398.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001048/0.4309, allocations: 44 kB / 0.5267 GB, free: 5.871 MB / 398.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.152e-05/0.4309, allocations: 32 kB / 0.5267 GB, free: 5.84 MB / 398.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002583/0.4335, allocations: 1.695 MB / 0.5284 GB, free: 4.137 MB / 398.1 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 0.006625/0.4401, allocations: 4.283 MB / 0.5326 GB, free: 15.64 MB / 414.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003369/0.4435, allocations: 2.271 MB / 0.5348 GB, free: 13.29 MB / 414.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008223/0.4444, allocations: 0.5889 MB / 0.5353 GB, free: 12.7 MB / 414.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.007348/0.4517, allocations: 5.38 MB / 0.5406 GB, free: 6.695 MB / 414.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.487e-05/0.4518, allocations: 43.22 kB / 0.5406 GB, free: 6.645 MB / 414.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.855e-06/0.4518, allocations: 0 / 0.5406 GB, free: 6.645 MB / 414.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01472/0.4665, allocations: 3.569 MB / 0.5441 GB, free: 3.004 MB / 414.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.986e-05/0.4666, allocations: 68.34 kB / 0.5442 GB, free: 2.922 MB / 414.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007895/0.4674, allocations: 0.5861 MB / 0.5448 GB, free: 2.324 MB / 414.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.914e-05/0.4675, allocations: 45.7 kB / 0.5448 GB, free: 2.273 MB / 414.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003582/0.4679, allocations: 0.5333 MB / 0.5453 GB, free: 1.73 MB / 414.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002587/0.4681, allocations: 331.3 kB / 0.5456 GB, free: 1.402 MB / 414.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003187/0.4684, allocations: 234.7 kB / 0.5459 GB, free: 1.168 MB / 414.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001738/0.4686, allocations: 394.7 kB / 0.5462 GB, free: 0.7734 MB / 414.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000589/0.4692, allocations: 354.5 kB / 0.5466 GB, free: 436 kB / 414.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008838/0.4701, allocations: 0.748 MB / 0.5473 GB, free: 15.5 MB / 430.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001582/0.4717, allocations: 1.204 MB / 0.5485 GB, free: 14.12 MB / 430.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.372e-06/0.4717, allocations: 4 kB / 0.5485 GB, free: 14.12 MB / 430.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003938/0.4757, allocations: 1.47 MB / 0.5499 GB, free: 12.63 MB / 430.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.604e-05/0.4757, allocations: 15.98 kB / 0.5499 GB, free: 12.62 MB / 430.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.768e-05/0.4757, allocations: 12.84 kB / 0.55 GB, free: 12.61 MB / 430.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001974/0.4777, allocations: 237.5 kB / 0.5502 GB, free: 12.37 MB / 430.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00143/0.4792, allocations: 331.5 kB / 0.5505 GB, free: 12.04 MB / 430.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005407/0.4846, allocations: 3.873 MB / 0.5543 GB, free: 7.898 MB / 430.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001019/0.4856, allocations: 43.94 kB / 0.5543 GB, free: 7.855 MB / 430.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001229/0.4858, allocations: 63.98 kB / 0.5544 GB, free: 7.793 MB / 430.1 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 0.0005128/0.4863, allocations: 277.3 kB / 0.5547 GB, free: 7.512 MB / 430.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002367/0.4865, allocations: 82.97 kB / 0.5547 GB, free: 7.43 MB / 430.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004067/0.4906, allocations: 1.332 MB / 0.556 GB, free: 6.074 MB / 430.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.201e-05/0.4906, allocations: 15.88 kB / 0.556 GB, free: 6.059 MB / 430.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.777e-06/0.4907, allocations: 4 kB / 0.556 GB, free: 6.055 MB / 430.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.265e-05/0.4907, allocations: 7.922 kB / 0.5561 GB, free: 6.047 MB / 430.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001519/0.4922, allocations: 1.077 MB / 0.5571 GB, free: 4.902 MB / 430.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.169e-06/0.4922, allocations: 0 / 0.5571 GB, free: 4.902 MB / 430.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001223/0.4934, allocations: 219.9 kB / 0.5573 GB, free: 4.688 MB / 430.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001865/0.4953, allocations: 233.4 kB / 0.5575 GB, free: 4.453 MB / 430.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.536e-05/0.4954, allocations: 35.92 kB / 0.5576 GB, free: 4.418 MB / 430.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005131/0.5006, allocations: 3.768 MB / 0.5613 GB, free: 380 kB / 430.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.564e-06/0.5006, allocations: 0 / 0.5613 GB, free: 380 kB / 430.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004363/0.505, allocations: 1.744 MB / 0.563 GB, free: 14.59 MB / 446.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003061/0.5053, allocations: 152 kB / 0.5631 GB, free: 14.42 MB / 446.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001034/0.5054, allocations: 20.06 kB / 0.5631 GB, free: 14.4 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005108/0.5059, allocations: 24 kB / 0.5631 GB, free: 14.38 MB / 446.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002182/0.5062, allocations: 80.89 kB / 0.5632 GB, free: 14.3 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.663e-05/0.5062, allocations: 43.92 kB / 0.5633 GB, free: 14.26 MB / 446.1 MB
Notification: Performance of sorting global known variables: time 0.0005635/0.5068, allocations: 387.1 kB / 0.5636 GB, free: 13.89 MB / 446.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.5068, allocations: 0 / 0.5636 GB, free: 13.89 MB / 446.1 MB
Notification: Performance of remove unused functions: time 0.002343/0.5092, allocations: 0.6675 MB / 0.5643 GB, free: 13.22 MB / 446.1 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 0.001657/0.5108, allocations: 0.8066 MB / 0.5651 GB, free: 12.4 MB / 446.1 MB
Notification: Performance of simCode: created initialization part: time 0.002373/0.5132, allocations: 1.262 MB / 0.5663 GB, free: 11.11 MB / 446.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.157e-05/0.5133, allocations: 0 / 0.5663 GB, free: 11.11 MB / 446.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001113/0.5144, allocations: 0.7456 MB / 0.567 GB, free: 10.35 MB / 446.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.00109/0.5155, allocations: 205.1 kB / 0.5672 GB, free: 10.14 MB / 446.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003646/0.5191, allocations: 1.971 MB / 0.5692 GB, free: 8.137 MB / 446.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005821/0.5197, allocations: 1.038 MB / 0.5702 GB, free: 7.074 MB / 446.1 MB
Notification: Performance of simCode: alias equations: time 0.0007564/0.5205, allocations: 239.2 kB / 0.5704 GB, free: 6.836 MB / 446.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000332/0.5208, allocations: 149.5 kB / 0.5705 GB, free: 6.691 MB / 446.1 MB
Notification: Performance of SimCode: time 4.21e-07/0.5209, allocations: 0 / 0.5705 GB, free: 6.691 MB / 446.1 MB
Notification: Performance of Templates: time 0.03915/0.56, allocations: 24.01 MB / 0.594 GB, free: 14.77 MB / 478.1 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)