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) [Timeout 90]
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001383/0.001383, allocations: 107.6 kB / 18.19 MB, free: 3.879 MB / 14.72 MB
[Timeout remaining time 90]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 90]
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001578/0.001578, allocations: 189.9 kB / 21.34 MB, free: 0.7383 MB / 14.72 MB
[Timeout remaining time 90]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 90]
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.415/1.415, allocations: 225.6 MB / 249.9 MB, free: 13.43 MB / 206.1 MB
[Timeout remaining time 88]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false) [Timeout 90]
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08373/0.08373, allocations: 15.54 MB / 320.6 MB, free: 9.531 MB / 254.1 MB
[Timeout remaining time 90]
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=500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
Notification: Performance of FrontEnd - loaded program: time 0.002005/0.002005, allocations: 71.89 kB / 448.6 MB, free: 11.1 MB / 318.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1166/0.1186, allocations: 56.54 MB / 0.4933 GB, free: 2.441 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 0.4256/0.5442, allocations: 26.26 MB / 0.519 GB, free: 6.363 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01775/0.562, allocations: 16.73 MB / 0.5353 GB, free: 13.79 MB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001103/0.5631, allocations: 12.78 kB / 0.5353 GB, free: 13.79 MB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001258/0.5643, allocations: 336.6 kB / 0.5357 GB, free: 13.61 MB / 398.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005749/0.5701, allocations: 1.489 MB / 0.5371 GB, free: 12.8 MB / 398.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.007645/0.5777, allocations: 2.006 MB / 0.5391 GB, free: 11.64 MB / 398.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002945/0.5807, allocations: 1.544 MB / 0.5406 GB, free: 10.89 MB / 398.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001379/0.582, allocations: 0.7105 MB / 0.5413 GB, free: 10.54 MB / 398.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001371/0.5834, allocations: 0.7688 MB / 0.542 GB, free: 10.27 MB / 398.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001636/0.585, allocations: 0.8633 MB / 0.5429 GB, free: 9.922 MB / 398.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002968/0.5853, allocations: 134.4 kB / 0.543 GB, free: 9.922 MB / 398.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.008729/0.5941, allocations: 1.801 MB / 0.5448 GB, free: 9.469 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0008956/0.595, allocations: 334.5 kB / 0.5451 GB, free: 9.262 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0015/0.5965, allocations: 0.682 MB / 0.5457 GB, free: 8.863 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01107/0.6075, allocations: 3.354 MB / 0.549 GB, free: 7.082 MB / 398.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.482e-06/0.6075, allocations: 0 / 0.549 GB, free: 7.082 MB / 398.1 MB
Notification: Performance of FrontEnd: time 1.723e-06/0.6075, allocations: 1.375 kB / 0.549 GB, free: 7.082 MB / 398.1 MB
Notification: Performance of Transformations before backend: time 3.335e-05/0.6076, allocations: 4 kB / 0.549 GB, free: 7.078 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 0.004186/0.6118, allocations: 1.848 MB / 0.5508 GB, free: 5.75 MB / 398.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.412e-05/0.6118, allocations: 11.38 kB / 0.5508 GB, free: 5.75 MB / 398.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001298/0.6131, allocations: 272.3 kB / 0.5511 GB, free: 5.629 MB / 398.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001212/0.6143, allocations: 0.6779 MB / 0.5518 GB, free: 5.074 MB / 398.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001275/0.6144, allocations: 111.3 kB / 0.5519 GB, free: 5.004 MB / 398.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001992/0.6146, allocations: 111.5 kB / 0.552 GB, free: 4.965 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002213/0.6169, allocations: 1.339 MB / 0.5533 GB, free: 4.145 MB / 398.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.363e-05/0.6169, allocations: 0 / 0.5533 GB, free: 4.145 MB / 398.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001173/0.617, allocations: 46.75 kB / 0.5533 GB, free: 4.109 MB / 398.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.731e-05/0.617, allocations: 25.19 kB / 0.5533 GB, free: 4.109 MB / 398.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002565/0.6196, allocations: 1.691 MB / 0.555 GB, free: 3.379 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 0.007511/0.6271, allocations: 4.299 MB / 0.5592 GB, free: 72 kB / 398.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003473/0.6306, allocations: 2.207 MB / 0.5614 GB, free: 14.9 MB / 414.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008391/0.6314, allocations: 0.5305 MB / 0.5619 GB, free: 14.63 MB / 414.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00828/0.6397, allocations: 5.395 MB / 0.5671 GB, free: 9.77 MB / 414.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.931e-05/0.6397, allocations: 42.91 kB / 0.5672 GB, free: 9.723 MB / 414.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.504e-06/0.6397, allocations: 0 / 0.5672 GB, free: 9.723 MB / 414.1 MB
Notification: Performance of matching and sorting (n=95): time 0.0156/0.6553, allocations: 3.582 MB / 0.5707 GB, free: 7.738 MB / 414.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.608e-05/0.6554, allocations: 67.44 kB / 0.5707 GB, free: 7.664 MB / 414.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007962/0.6562, allocations: 0.5898 MB / 0.5713 GB, free: 7.305 MB / 414.1 MB
Notification: Performance of collectPreVariables (initialization): time 8.067e-05/0.6563, allocations: 41.33 kB / 0.5714 GB, free: 7.262 MB / 414.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004092/0.6567, allocations: 0.5435 MB / 0.5719 GB, free: 6.77 MB / 414.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0004684/0.6571, allocations: 356.6 kB / 0.5722 GB, free: 6.457 MB / 414.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003011/0.6574, allocations: 231.7 kB / 0.5725 GB, free: 6.324 MB / 414.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002094/0.6577, allocations: 393.1 kB / 0.5728 GB, free: 5.949 MB / 414.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006091/0.6583, allocations: 359.2 kB / 0.5732 GB, free: 5.777 MB / 414.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009284/0.6592, allocations: 0.7498 MB / 0.5739 GB, free: 5.074 MB / 414.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001811/0.661, allocations: 1.209 MB / 0.5751 GB, free: 4.098 MB / 414.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.135e-06/0.661, allocations: 4 kB / 0.5751 GB, free: 4.094 MB / 414.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004499/0.6655, allocations: 1.467 MB / 0.5765 GB, free: 2.613 MB / 414.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.048e-05/0.6655, allocations: 12.19 kB / 0.5765 GB, free: 2.602 MB / 414.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.281e-05/0.6656, allocations: 23.98 kB / 0.5766 GB, free: 2.578 MB / 414.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002119/0.6677, allocations: 245.4 kB / 0.5768 GB, free: 2.332 MB / 414.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001666/0.6693, allocations: 327.5 kB / 0.5771 GB, free: 2.012 MB / 414.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.006532/0.6759, allocations: 3.859 MB / 0.5809 GB, free: 13.88 MB / 430.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001124/0.677, allocations: 40 kB / 0.5809 GB, free: 13.84 MB / 430.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001355/0.6771, allocations: 67.98 kB / 0.581 GB, free: 13.78 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 0.0005424/0.6777, allocations: 277.4 kB / 0.5812 GB, free: 13.5 MB / 430.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002175/0.6779, allocations: 91.5 kB / 0.5813 GB, free: 13.41 MB / 430.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004462/0.6824, allocations: 1.336 MB / 0.5826 GB, free: 12.05 MB / 430.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.252e-05/0.6824, allocations: 11.94 kB / 0.5826 GB, free: 12.04 MB / 430.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.2e-06/0.6824, allocations: 0 / 0.5826 GB, free: 12.04 MB / 430.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.202e-05/0.6824, allocations: 3.984 kB / 0.5826 GB, free: 12.03 MB / 430.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001735/0.6841, allocations: 1.077 MB / 0.5837 GB, free: 10.89 MB / 430.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.769e-06/0.6841, allocations: 0 / 0.5837 GB, free: 10.89 MB / 430.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001248/0.6854, allocations: 223.7 kB / 0.5839 GB, free: 10.67 MB / 430.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002104/0.6875, allocations: 225.6 kB / 0.5841 GB, free: 10.44 MB / 430.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001042/0.6876, allocations: 39.97 kB / 0.5842 GB, free: 10.4 MB / 430.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005744/0.6933, allocations: 3.764 MB / 0.5878 GB, free: 6.359 MB / 430.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.789e-06/0.6933, allocations: 4.031 kB / 0.5878 GB, free: 6.355 MB / 430.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004903/0.6982, allocations: 1.74 MB / 0.5895 GB, free: 4.578 MB / 430.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003098/0.6985, allocations: 156.6 kB / 0.5897 GB, free: 4.406 MB / 430.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001164/0.6987, allocations: 24 kB / 0.5897 GB, free: 4.383 MB / 430.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005334/0.6992, allocations: 16 kB / 0.5897 GB, free: 4.367 MB / 430.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002031/0.6994, allocations: 80.89 kB / 0.5898 GB, free: 4.289 MB / 430.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.426e-05/0.6995, allocations: 39.92 kB / 0.5898 GB, free: 4.25 MB / 430.1 MB
Notification: Performance of sorting global known variables: time 0.0005047/0.7, allocations: 391.1 kB / 0.5902 GB, free: 3.875 MB / 430.1 MB
Notification: Performance of sort global known variables: time 9e-08/0.7, allocations: 0 / 0.5902 GB, free: 3.875 MB / 430.1 MB
Notification: Performance of remove unused functions: time 0.002267/0.7023, allocations: 0.6895 MB / 0.5909 GB, free: 3.184 MB / 430.1 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 0.001603/0.7039, allocations: 0.8206 MB / 0.5917 GB, free: 2.348 MB / 430.1 MB
Notification: Performance of simCode: created initialization part: time 0.002483/0.7063, allocations: 1.192 MB / 0.5929 GB, free: 1.133 MB / 430.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.286e-06/0.7063, allocations: 0 / 0.5929 GB, free: 1.133 MB / 430.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001143/0.7075, allocations: 0.6983 MB / 0.5935 GB, free: 424 kB / 430.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001073/0.7086, allocations: 187.4 kB / 0.5937 GB, free: 232 kB / 430.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003737/0.7123, allocations: 2.053 MB / 0.5957 GB, free: 14.12 MB / 446.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007539/0.7131, allocations: 1.034 MB / 0.5967 GB, free: 13.07 MB / 446.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005588/0.7136, allocations: 204.9 kB / 0.5969 GB, free: 12.87 MB / 446.1 MB
Notification: Performance of SimCode: time 1.102e-06/0.7136, allocations: 0 / 0.5969 GB, free: 12.87 MB / 446.1 MB
Notification: Performance of Templates: time 0.03718/0.7508, allocations: 26.33 MB / 0.6226 GB, free: 2.562 MB / 462.1 MB
[Timeout remaining time 659]
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(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) [Timeout 480]