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 0.0008834/0.0008834, allocations: 90.05 kB / 16.02 MB, free: 80 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0009769/0.0009769, allocations: 177.3 kB / 16.92 MB, free: 6.652 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.405/1.405, allocations: 223.3 MB / 241 MB, free: 5.266 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.1832/0.1832, allocations: 15.27 MB / 307.4 MB, free: 15.64 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003425/0.0003428, allocations: 11.98 kB / 372.8 MB, free: 3.523 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2732/0.2736, allocations: 54.62 MB / 427.4 MB, free: 40.43 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65: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:3019:6-3019:65: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 0.02647/0.3001, allocations: 25.36 MB / 452.7 MB, free: 31.96 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01689/0.317, allocations: 16.43 MB / 469.2 MB, free: 20.82 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001393/0.3184, allocations: 23.44 kB / 469.2 MB, free: 20.8 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001238/0.3197, allocations: 301.2 kB / 469.5 MB, free: 20.65 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004778/0.3245, allocations: 1.308 MB / 470.8 MB, free: 19.88 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.006009/0.3305, allocations: 1.745 MB / 472.5 MB, free: 18.85 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002551/0.3331, allocations: 1.489 MB / 474 MB, free: 18.14 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001224/0.3344, allocations: 0.6991 MB / 474.7 MB, free: 17.84 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001334/0.3357, allocations: 0.7186 MB / 475.5 MB, free: 17.64 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001526/0.3373, allocations: 0.7948 MB / 476.2 MB, free: 17.22 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002817/0.3376, allocations: 72 kB / 476.3 MB, free: 17.15 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006463/0.344, allocations: 1.729 MB / 478 MB, free: 15.6 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004215/0.3445, allocations: 266 kB / 478.3 MB, free: 15.4 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009333/0.3455, allocations: 0.6334 MB / 478.9 MB, free: 14.81 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.003342/0.3488, allocations: 2.435 MB / 481.4 MB, free: 12.95 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.39e-06/0.3488, allocations: 0 / 481.4 MB, free: 12.95 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.314e-06/0.3488, allocations: 0 / 481.4 MB, free: 12.95 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.993e-05/0.3489, allocations: 0 / 481.4 MB, free: 12.95 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
 * Number of variables: 276
Notification: Performance of Generate backend data structure: time 0.002682/0.3516, allocations: 1.527 MB / 482.9 MB, free: 11.52 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.665e-05/0.3516, allocations: 12.73 kB / 482.9 MB, free: 11.5 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001077/0.3527, allocations: 272.7 kB / 483.2 MB, free: 11.27 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0007756/0.3535, allocations: 0.6266 MB / 483.8 MB, free: 10.7 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.847e-05/0.3536, allocations: 113 kB / 483.9 MB, free: 10.58 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001806/0.3538, allocations: 113 kB / 484 MB, free: 10.47 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001922/0.3557, allocations: 1.334 MB / 485.4 MB, free: 9.359 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.469e-05/0.3557, allocations: 11.88 kB / 485.4 MB, free: 9.348 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001111/0.3559, allocations: 40 kB / 485.4 MB, free: 9.309 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.787e-05/0.3559, allocations: 28.66 kB / 485.4 MB, free: 9.281 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002346/0.3582, allocations: 1.691 MB / 487.1 MB, free: 7.82 MB / 350.1 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 0.005902/0.3641, allocations: 4.259 MB / 491.4 MB, free: 4.051 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002917/0.3671, allocations: 2.276 MB / 493.7 MB, free: 1.902 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007706/0.3679, allocations: 0.5956 MB / 494.3 MB, free: 1.355 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006604/0.3745, allocations: 5.285 MB / 499.5 MB, free: 12 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.908e-05/0.3745, allocations: 39.22 kB / 499.6 MB, free: 11.96 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.755e-06/0.3746, allocations: 0 / 499.6 MB, free: 11.96 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01688/0.3914, allocations: 3.602 MB / 0.4914 GB, free: 8.754 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.409e-05/0.3915, allocations: 68.34 kB / 0.4915 GB, free: 8.676 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0008261/0.3924, allocations: 0.586 MB / 0.492 GB, free: 8.168 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.000125/0.3925, allocations: 41.7 kB / 0.4921 GB, free: 8.121 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.000392/0.3929, allocations: 0.5379 MB / 0.4926 GB, free: 7.625 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003612/0.3933, allocations: 334.2 kB / 0.4929 GB, free: 7.324 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001649/0.3935, allocations: 101.1 kB / 0.493 GB, free: 7.234 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001867/0.3937, allocations: 390.1 kB / 0.4934 GB, free: 6.871 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0007433/0.3944, allocations: 358 kB / 0.4937 GB, free: 6.566 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009964/0.3954, allocations: 0.7561 MB / 0.4945 GB, free: 5.66 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001707/0.3971, allocations: 1.204 MB / 0.4956 GB, free: 4.281 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.668e-06/0.3972, allocations: 4 kB / 0.4956 GB, free: 4.277 MB / 366.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004422/0.4016, allocations: 1.486 MB / 0.4971 GB, free: 2.773 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.633e-05/0.4016, allocations: 12 kB / 0.4971 GB, free: 2.762 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.261e-05/0.4017, allocations: 12 kB / 0.4971 GB, free: 2.75 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002265/0.4039, allocations: 266 kB / 0.4974 GB, free: 2.484 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001604/0.4056, allocations: 327.5 kB / 0.4977 GB, free: 2.164 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005953/0.4115, allocations: 3.509 MB / 0.5011 GB, free: 14.39 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001087/0.4127, allocations: 79.88 kB / 0.5012 GB, free: 14.31 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002013/0.4129, allocations: 67.98 kB / 0.5013 GB, free: 14.25 MB / 382.1 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 0.0005915/0.4135, allocations: 285.3 kB / 0.5015 GB, free: 13.96 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000213/0.4137, allocations: 83.16 kB / 0.5016 GB, free: 13.88 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004664/0.4184, allocations: 1.34 MB / 0.5029 GB, free: 12.52 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.787e-05/0.4184, allocations: 15.98 kB / 0.5029 GB, free: 12.5 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.053e-06/0.4184, allocations: 3.938 kB / 0.5029 GB, free: 12.5 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.476e-05/0.4184, allocations: 3.984 kB / 0.5029 GB, free: 12.5 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00172/0.4202, allocations: 1.081 MB / 0.504 GB, free: 11.34 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.969e-06/0.4202, allocations: 0 / 0.504 GB, free: 11.34 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001274/0.4215, allocations: 211.7 kB / 0.5042 GB, free: 11.14 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002365/0.4239, allocations: 253.5 kB / 0.5044 GB, free: 10.88 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001218/0.424, allocations: 35.98 kB / 0.5045 GB, free: 10.85 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005257/0.4293, allocations: 3.413 MB / 0.5078 GB, free: 7.164 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.997e-06/0.4293, allocations: 32 / 0.5078 GB, free: 7.164 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00483/0.4342, allocations: 1.748 MB / 0.5095 GB, free: 5.379 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002805/0.4345, allocations: 156 kB / 0.5097 GB, free: 5.207 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001625/0.4346, allocations: 16 kB / 0.5097 GB, free: 5.191 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0006353/0.4353, allocations: 35.98 kB / 0.5097 GB, free: 5.156 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002209/0.4355, allocations: 88.81 kB / 0.5098 GB, free: 5.066 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.744e-05/0.4356, allocations: 39.98 kB / 0.5098 GB, free: 5.027 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0004687/0.4361, allocations: 387.1 kB / 0.5102 GB, free: 4.656 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.3e-07/0.4361, allocations: 0 / 0.5102 GB, free: 4.656 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.002018/0.4381, allocations: 0.6675 MB / 0.5109 GB, free: 3.988 MB / 382.1 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 0.001675/0.4398, allocations: 0.8009 MB / 0.5116 GB, free: 3.18 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002303/0.4421, allocations: 1.251 MB / 0.5129 GB, free: 1.906 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.697e-06/0.4422, allocations: 0 / 0.5129 GB, free: 1.906 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001163/0.4433, allocations: 0.7449 MB / 0.5136 GB, free: 1.137 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.00136/0.4447, allocations: 200.3 kB / 0.5138 GB, free: 0.9453 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003876/0.4486, allocations: 2.551 MB / 0.5163 GB, free: 14.34 MB / 398.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006441/0.4493, allocations: 1.045 MB / 0.5173 GB, free: 13.27 MB / 398.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005682/0.4499, allocations: 202.3 kB / 0.5175 GB, free: 13.08 MB / 398.1 MB
Notification: Performance of SimCode: time 1.452e-06/0.4499, allocations: 3.938 kB / 0.5175 GB, free: 13.07 MB / 398.1 MB
Notification: Performance of Templates: time 0.03439/0.4843, allocations: 26.08 MB / 0.543 GB, free: 3.016 MB / 414.1 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)