Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_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 0.00121/0.00121, 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 0.001179/0.001179, allocations: 177 kB / 23.35 MB, free: 1.133 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 0.9621/0.9621, 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 master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo): time 0.1306/0.1306, allocations: 17.46 MB / 277.7 MB, free: 11.43 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/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_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.172e-06/1.172e-06, allocations: 0 / 300.8 MB, free: 1.746 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.138e-05/1.255e-05, allocations: 7.406 kB / 300.8 MB, free: 1.738 MB / 266.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66: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 master/Obsolete.mo:14335:7-14335:66: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 0.02727/0.02729, allocations: 35.04 MB / 335.8 MB, free: 1.285 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.006526/0.03381, allocations: 6.303 MB / 342.1 MB, free: 10.96 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000332/0.03414, allocations: 27.75 kB / 342.2 MB, free: 10.94 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003953/0.03454, allocations: 190.2 kB / 342.3 MB, free: 10.75 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001118/0.03566, allocations: 0.8493 MB / 343.2 MB, free: 9.895 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001137/0.03679, allocations: 0.8478 MB / 344 MB, free: 9.043 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.000978/0.03777, allocations: 1.599 MB / 345.6 MB, free: 7.438 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.00055/0.03832, allocations: 0.7233 MB / 346.4 MB, free: 6.684 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009472/0.03927, allocations: 1.072 MB / 347.4 MB, free: 5.609 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006364/0.03991, allocations: 0.7094 MB / 348.1 MB, free: 4.898 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001279/0.04003, allocations: 132 kB / 348.3 MB, free: 4.77 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0007231/0.04076, allocations: 0.5968 MB / 348.9 MB, free: 4.172 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001925/0.04095, allocations: 342.9 kB / 349.2 MB, free: 3.836 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003212/0.04127, allocations: 0.4989 MB / 349.7 MB, free: 3.336 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001265/0.04254, allocations: 1.716 MB / 351.4 MB, free: 1.613 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.775e-06/0.04254, allocations: 0 / 351.4 MB, free: 1.613 MB / 314.7 MB
Notification: Performance of FrontEnd: time 9.92e-07/0.04254, allocations: 4 kB / 351.4 MB, free: 1.609 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 8.716e-06/0.04255, allocations: 4 kB / 351.4 MB, free: 1.605 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 0.001481/0.04403, allocations: 1.504 MB / 352.9 MB, free: 72 kB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 2.939e-05/0.04406, allocations: 8.031 kB / 352.9 MB, free: 64 kB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0007512/0.04481, allocations: 430.9 kB / 353.4 MB, free: 15.64 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005583/0.04537, allocations: 498.8 kB / 353.8 MB, free: 15.12 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.241e-05/0.04546, allocations: 138.1 kB / 354 MB, free: 14.98 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001254/0.04559, allocations: 116.3 kB / 354.1 MB, free: 14.86 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001242/0.04683, allocations: 0.9814 MB / 355.1 MB, free: 13.83 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.859e-05/0.04685, allocations: 192 / 355.1 MB, free: 13.83 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.515e-05/0.04691, allocations: 52.12 kB / 355.1 MB, free: 13.78 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.521e-05/0.04693, allocations: 28 kB / 355.2 MB, free: 13.75 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008616/0.04779, allocations: 0.8496 MB / 356 MB, free: 12.88 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 0.002936/0.05073, allocations: 2.62 MB / 358.6 MB, free: 10.19 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.00209/0.05281, allocations: 1.951 MB / 360.6 MB, free: 8.238 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002719/0.05309, allocations: 270.8 kB / 360.8 MB, free: 7.965 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002522/0.05561, allocations: 1.955 MB / 362.8 MB, free: 5.992 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.241e-05/0.05563, allocations: 39.22 kB / 362.8 MB, free: 5.945 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 1.794e-06/0.05563, allocations: 0 / 362.8 MB, free: 5.945 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.006527/0.06216, allocations: 2.712 MB / 365.5 MB, free: 3.199 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.209e-05/0.06219, allocations: 64.41 kB / 365.6 MB, free: 3.125 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003115/0.0625, allocations: 0.5269 MB / 366.1 MB, free: 2.582 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.34e-05/0.06255, allocations: 41.7 kB / 366.2 MB, free: 2.535 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001958/0.06274, allocations: 0.501 MB / 366.7 MB, free: 2.023 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001839/0.06293, allocations: 353 kB / 367 MB, free: 1.676 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001979/0.06312, allocations: 230.8 kB / 367.2 MB, free: 1.445 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001119/0.06324, allocations: 394.6 kB / 367.6 MB, free: 1.051 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001804/0.06342, allocations: 157.4 kB / 367.8 MB, free: 0.8945 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003374/0.06375, allocations: 0.5485 MB / 368.3 MB, free: 168 kB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0008811/0.06464, allocations: 0.8587 MB / 369.2 MB, free: 15.13 MB / 346.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.04e-06/0.06464, allocations: 7.938 kB / 369.2 MB, free: 15.12 MB / 346.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001455/0.06609, allocations: 0.917 MB / 370.1 MB, free: 14.19 MB / 346.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.796e-05/0.06611, allocations: 16.88 kB / 370.1 MB, free: 14.17 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.148e-05/0.06612, allocations: 12 kB / 370.1 MB, free: 14.16 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001204/0.06733, allocations: 337.3 kB / 370.5 MB, free: 13.82 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007684/0.0681, allocations: 359.5 kB / 370.8 MB, free: 13.47 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002361/0.07046, allocations: 3.014 MB / 373.8 MB, free: 10.29 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003042/0.07076, allocations: 44.03 kB / 373.9 MB, free: 10.24 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.402e-05/0.07083, allocations: 55.98 kB / 373.9 MB, free: 10.19 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 0.0001823/0.07101, allocations: 192.2 kB / 374.1 MB, free: 9.988 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000106/0.07111, allocations: 83.86 kB / 374.2 MB, free: 9.906 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001492/0.07261, allocations: 0.8646 MB / 375.1 MB, free: 9.031 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.22e-06/0.07261, allocations: 8 kB / 375.1 MB, free: 9.023 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.218e-06/0.07262, allocations: 4 kB / 375.1 MB, free: 9.02 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.514e-06/0.07262, allocations: 7.984 kB / 375.1 MB, free: 9.012 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008416/0.07346, allocations: 0.6687 MB / 375.8 MB, free: 8.297 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.539e-06/0.07347, allocations: 4 kB / 375.8 MB, free: 8.293 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006066/0.07408, allocations: 239.7 kB / 376 MB, free: 8.059 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001165/0.07524, allocations: 317.4 kB / 376.3 MB, free: 7.742 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.423e-05/0.07528, allocations: 31.98 kB / 376.3 MB, free: 7.711 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002008/0.07729, allocations: 2.922 MB / 379.3 MB, free: 4.621 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.833e-06/0.07729, allocations: 4 kB / 379.3 MB, free: 4.617 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00149/0.07878, allocations: 1.046 MB / 380.3 MB, free: 3.539 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.719e-05/0.07884, allocations: 67.44 kB / 380.4 MB, free: 3.473 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.718e-05/0.07891, allocations: 27.94 kB / 380.4 MB, free: 3.445 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002108/0.07912, allocations: 20 kB / 380.4 MB, free: 3.426 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000113/0.07923, allocations: 80.84 kB / 380.5 MB, free: 3.344 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.31e-05/0.07928, allocations: 35.98 kB / 380.5 MB, free: 3.309 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001431/0.07942, allocations: 220.6 kB / 380.8 MB, free: 3.094 MB / 346.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.07942, allocations: 0 / 380.8 MB, free: 3.094 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.000777/0.0802, allocations: 411.5 kB / 381.2 MB, free: 2.691 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 0.0003836/0.08058, allocations: 331.5 kB / 381.5 MB, free: 2.355 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.0008147/0.08139, allocations: 0.8746 MB / 382.4 MB, free: 1.457 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.274e-05/0.08141, allocations: 8.5 kB / 382.4 MB, free: 1.449 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0006636/0.08207, allocations: 0.5575 MB / 382.9 MB, free: 0.8672 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005011/0.08257, allocations: 230.5 kB / 383.1 MB, free: 0.6445 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 0.002363/0.08493, allocations: 1.817 MB / 385 MB, free: 14.77 MB / 362.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001159/0.08505, allocations: 197 kB / 385.2 MB, free: 14.56 MB / 362.7 MB
Notification: Performance of simCode: alias equations: time 0.0004827/0.08553, allocations: 214.8 kB / 385.4 MB, free: 14.35 MB / 362.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0008868/0.08642, allocations: 329.5 kB / 385.7 MB, free: 14.04 MB / 362.7 MB
Notification: Performance of SimCode: time 1.563e-06/0.08642, allocations: 0 / 385.7 MB, free: 14.04 MB / 362.7 MB
Notification: Performance of Templates: time 0.02072/0.1071, allocations: 19.29 MB / 405 MB, free: 10.92 MB / 378.7 MB
"
[Timeout remaining time 660]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.199091229122132]