Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0009515/0.0009515, allocations: 80.94 kB / 19.94 MB, free: 4.543 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.0008783/0.0008783, allocations: 177 kB / 23.36 MB, free: 1.129 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.8789/0.8789, allocations: 177.1 MB / 203.8 MB, free: 5.477 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.08474/0.08474, allocations: 17.38 MB / 277.6 MB, free: 11.52 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.052e-06/1.052e-06, allocations: 0 / 300.6 MB, free: 1.867 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 9.378e-06/1.043e-05, allocations: 6.25 kB / 300.6 MB, free: 1.859 MB / 266.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.03163/0.03164, allocations: 34.99 MB / 335.6 MB, free: 1.625 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.006994/0.03863, allocations: 6.301 MB / 341.9 MB, free: 11.3 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004278/0.03906, allocations: 19.81 kB / 341.9 MB, free: 11.28 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004529/0.03951, allocations: 190.3 kB / 342.1 MB, free: 11.09 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001409/0.04092, allocations: 0.8571 MB / 343 MB, free: 10.23 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001736/0.04266, allocations: 0.8711 MB / 343.8 MB, free: 9.352 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001496/0.04416, allocations: 1.587 MB / 345.4 MB, free: 7.758 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005352/0.04469, allocations: 0.7351 MB / 346.2 MB, free: 6.992 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0006904/0.04538, allocations: 1.072 MB / 347.2 MB, free: 5.918 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006379/0.04602, allocations: 0.7132 MB / 348 MB, free: 5.203 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001216/0.04614, allocations: 132 kB / 348.1 MB, free: 5.074 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0008462/0.04699, allocations: 0.5851 MB / 348.7 MB, free: 4.488 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002051/0.04719, allocations: 331 kB / 349 MB, free: 4.164 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003255/0.04752, allocations: 0.5028 MB / 349.5 MB, free: 3.66 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001278/0.0488, allocations: 1.716 MB / 351.2 MB, free: 1.938 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.685e-06/0.0488, allocations: 0 / 351.2 MB, free: 1.938 MB / 314.7 MB
Notification: Performance of FrontEnd: time 1.102e-06/0.0488, allocations: 0 / 351.2 MB, free: 1.938 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 8.777e-06/0.04881, allocations: 0 / 351.2 MB, free: 1.938 MB / 314.7 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 0.001533/0.05034, allocations: 1.512 MB / 352.7 MB, free: 404 kB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.015e-05/0.05037, allocations: 16.03 kB / 352.7 MB, free: 388 kB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0006486/0.05102, allocations: 430.9 kB / 353.2 MB, free: 15.95 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005308/0.05155, allocations: 0.491 MB / 353.7 MB, free: 15.44 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.732e-05/0.05163, allocations: 138.1 kB / 353.8 MB, free: 15.29 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000121/0.05175, allocations: 124.2 kB / 353.9 MB, free: 15.17 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008251/0.05257, allocations: 0.9775 MB / 354.9 MB, free: 14.14 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.748e-05/0.05259, allocations: 4.125 kB / 354.9 MB, free: 14.14 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.931e-05/0.05266, allocations: 48.12 kB / 354.9 MB, free: 14.09 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.633e-05/0.05268, allocations: 28 kB / 355 MB, free: 14.06 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008368/0.05351, allocations: 0.8457 MB / 355.8 MB, free: 13.2 MB / 330.7 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 0.00294/0.05645, allocations: 2.616 MB / 358.4 MB, free: 10.51 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002006/0.05846, allocations: 1.939 MB / 360.4 MB, free: 8.566 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002572/0.05872, allocations: 278.7 kB / 360.6 MB, free: 8.285 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002227/0.06095, allocations: 1.959 MB / 362.6 MB, free: 6.309 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.165e-05/0.06097, allocations: 35.22 kB / 362.6 MB, free: 6.266 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.194e-06/0.06097, allocations: 4 kB / 362.6 MB, free: 6.262 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.005852/0.06682, allocations: 2.711 MB / 365.3 MB, free: 3.52 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.843e-05/0.06685, allocations: 60.41 kB / 365.4 MB, free: 3.449 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002973/0.06715, allocations: 0.5308 MB / 365.9 MB, free: 2.902 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.125e-05/0.06719, allocations: 41.7 kB / 366 MB, free: 2.855 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001846/0.06737, allocations: 0.4932 MB / 366.5 MB, free: 2.352 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001712/0.06754, allocations: 353 kB / 366.8 MB, free: 2.004 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003374/0.06788, allocations: 230.7 kB / 367 MB, free: 1.773 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001039/0.06799, allocations: 398.6 kB / 367.4 MB, free: 1.375 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001715/0.06816, allocations: 157.4 kB / 367.6 MB, free: 1.219 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003332/0.06849, allocations: 0.5602 MB / 368.1 MB, free: 488 kB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000604/0.06909, allocations: 0.851 MB / 369 MB, free: 15.45 MB / 346.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.819e-06/0.0691, allocations: 4 kB / 369 MB, free: 15.45 MB / 346.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001343/0.07044, allocations: 0.9288 MB / 369.9 MB, free: 14.5 MB / 346.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.598e-05/0.07046, allocations: 12 kB / 369.9 MB, free: 14.49 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.101e-05/0.07047, allocations: 12 kB / 370 MB, free: 14.48 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001091/0.07156, allocations: 342 kB / 370.3 MB, free: 14.14 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006365/0.0722, allocations: 319.5 kB / 370.6 MB, free: 13.82 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002138/0.07433, allocations: 2.998 MB / 373.6 MB, free: 10.65 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003032/0.07464, allocations: 43.98 kB / 373.6 MB, free: 10.61 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.928e-05/0.0747, allocations: 55.98 kB / 373.7 MB, free: 10.55 MB / 346.7 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 0.0003306/0.07503, allocations: 192.3 kB / 373.9 MB, free: 10.36 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.71e-05/0.07512, allocations: 79.88 kB / 374 MB, free: 10.28 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001394/0.07652, allocations: 0.8724 MB / 374.8 MB, free: 9.395 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.889e-06/0.07652, allocations: 8 kB / 374.8 MB, free: 9.387 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.32e-06/0.07653, allocations: 7.984 kB / 374.8 MB, free: 9.379 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.843e-06/0.07654, allocations: 3.984 kB / 374.8 MB, free: 9.375 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006193/0.07716, allocations: 0.661 MB / 375.5 MB, free: 8.668 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.356e-06/0.07716, allocations: 12.06 kB / 375.5 MB, free: 8.656 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005149/0.07767, allocations: 207.8 kB / 375.7 MB, free: 8.453 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001077/0.07875, allocations: 325.4 kB / 376 MB, free: 8.129 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.861e-05/0.07879, allocations: 31.92 kB / 376.1 MB, free: 8.098 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001919/0.08071, allocations: 2.914 MB / 379 MB, free: 5.016 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.515e-06/0.08071, allocations: 4 kB / 379 MB, free: 5.012 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001434/0.08215, allocations: 1.054 MB / 380 MB, free: 3.926 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.91e-05/0.0822, allocations: 67.44 kB / 380.1 MB, free: 3.859 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.704e-05/0.08227, allocations: 23.94 kB / 380.1 MB, free: 3.836 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002018/0.08247, allocations: 20 kB / 380.2 MB, free: 3.816 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 9.535e-05/0.08257, allocations: 80.84 kB / 380.2 MB, free: 3.734 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.796e-05/0.08261, allocations: 31.98 kB / 380.3 MB, free: 3.703 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001409/0.08275, allocations: 228.6 kB / 380.5 MB, free: 3.48 MB / 346.7 MB
Notification: Performance of sort global known variables: time 2e-08/0.08275, allocations: 0 / 380.5 MB, free: 3.48 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.0008221/0.08357, allocations: 403.5 kB / 380.9 MB, free: 3.086 MB / 346.7 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 0.0005217/0.08409, allocations: 319.5 kB / 381.2 MB, free: 2.762 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.0007676/0.08486, allocations: 0.8796 MB / 382.1 MB, free: 1.859 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.368e-05/0.08487, allocations: 8.5 kB / 382.1 MB, free: 1.852 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004052/0.08528, allocations: 0.5562 MB / 382.6 MB, free: 1.27 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004979/0.08578, allocations: 231.6 kB / 382.9 MB, free: 1.043 MB / 346.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002098/0.08787, allocations: 1.805 MB / 384.7 MB, free: 15.18 MB / 362.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001165/0.08799, allocations: 201 kB / 384.9 MB, free: 14.97 MB / 362.7 MB
Notification: Performance of simCode: alias equations: time 0.0004254/0.08842, allocations: 214.5 kB / 385.1 MB, free: 14.76 MB / 362.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004399/0.08886, allocations: 334.6 kB / 385.4 MB, free: 14.44 MB / 362.7 MB
Notification: Performance of SimCode: time 5.01e-07/0.08886, allocations: 0 / 385.4 MB, free: 14.44 MB / 362.7 MB
Notification: Performance of Templates: time 0.02054/0.1094, allocations: 19.29 MB / 404.7 MB, free: 11.33 MB / 378.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.1783518502488732]