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 0.0009105/0.0009105, 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 0.001359/0.001359, allocations: 177.4 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 0.8998/0.8998, allocations: 177.2 MB / 203.8 MB, free: 5.465 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 0.08496/0.08496, allocations: 17.39 MB / 277.6 MB, free: 11.51 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 1.282e-06/1.282e-06, allocations: 0 / 300.7 MB, free: 1.805 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.163e-05/1.291e-05, allocations: 3.406 kB / 300.7 MB, free: 1.801 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 0.02946/0.02948, allocations: 35.04 MB / 335.7 MB, free: 1.492 MB / 298.7 MB
Notification: Performance of NFInst.instExpressions: time 0.00671/0.03619, allocations: 6.297 MB / 342 MB, free: 11.18 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003368/0.03652, allocations: 15.88 kB / 342 MB, free: 11.16 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004129/0.03694, allocations: 190.2 kB / 342.2 MB, free: 10.97 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.001314/0.03825, allocations: 0.8533 MB / 343.1 MB, free: 10.11 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.001358/0.03961, allocations: 0.8633 MB / 343.9 MB, free: 9.246 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001226/0.04083, allocations: 1.595 MB / 345.5 MB, free: 7.645 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005791/0.04141, allocations: 0.7233 MB / 346.3 MB, free: 6.891 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0007082/0.04212, allocations: 1.065 MB / 347.3 MB, free: 5.824 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006435/0.04277, allocations: 0.7016 MB / 348 MB, free: 5.121 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001291/0.04289, allocations: 136 kB / 348.2 MB, free: 4.988 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0007675/0.04366, allocations: 0.6006 MB / 348.8 MB, free: 4.387 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001943/0.04386, allocations: 338.9 kB / 349.1 MB, free: 4.055 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003761/0.04423, allocations: 0.4989 MB / 349.6 MB, free: 3.555 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.001339/0.04557, allocations: 1.72 MB / 351.3 MB, free: 1.828 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.437e-06/0.04558, allocations: 0 / 351.3 MB, free: 1.828 MB / 314.7 MB
Notification: Performance of FrontEnd: time 1.372e-06/0.04558, allocations: 0 / 351.3 MB, free: 1.828 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 1.208e-05/0.04559, allocations: 0 / 351.3 MB, free: 1.828 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 0.001543/0.04713, allocations: 1.512 MB / 352.8 MB, free: 292 kB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.203e-05/0.04716, allocations: 12.02 kB / 352.8 MB, free: 280 kB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0006725/0.04784, allocations: 434.9 kB / 353.3 MB, free: 15.85 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005534/0.04839, allocations: 498.8 kB / 353.7 MB, free: 15.33 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.367e-05/0.04847, allocations: 138.1 kB / 353.9 MB, free: 15.18 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001116/0.04858, allocations: 112.3 kB / 354 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008495/0.04943, allocations: 0.9814 MB / 355 MB, free: 14.04 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.7e-05/0.04945, allocations: 4.188 kB / 355 MB, free: 14.04 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.354e-05/0.04951, allocations: 52.12 kB / 355 MB, free: 13.99 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.502e-05/0.04953, allocations: 24 kB / 355 MB, free: 13.96 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008272/0.05036, allocations: 0.8418 MB / 355.9 MB, free: 13.1 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 0.002924/0.05328, allocations: 2.616 MB / 358.5 MB, free: 10.41 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001822/0.0551, allocations: 1.947 MB / 360.4 MB, free: 8.465 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002544/0.05536, allocations: 274.7 kB / 360.7 MB, free: 8.188 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.002267/0.05763, allocations: 1.967 MB / 362.7 MB, free: 6.203 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.404e-05/0.05765, allocations: 39.22 kB / 362.7 MB, free: 6.156 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 1.633e-06/0.05765, allocations: 0 / 362.7 MB, free: 6.156 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.006411/0.06406, allocations: 2.711 MB / 365.4 MB, free: 3.414 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.909e-05/0.06409, allocations: 60.41 kB / 365.5 MB, free: 3.344 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003252/0.06442, allocations: 0.5347 MB / 366 MB, free: 2.793 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.082e-05/0.06446, allocations: 41.7 kB / 366.1 MB, free: 2.746 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001848/0.06464, allocations: 0.4932 MB / 366.6 MB, free: 2.242 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001621/0.0648, allocations: 349 kB / 366.9 MB, free: 1.898 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002411/0.06504, allocations: 234.7 kB / 367.1 MB, free: 1.664 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001088/0.06515, allocations: 398.6 kB / 367.5 MB, free: 1.266 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001766/0.06533, allocations: 157.4 kB / 367.7 MB, free: 1.109 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003295/0.06566, allocations: 0.5523 MB / 368.2 MB, free: 384 kB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006228/0.06628, allocations: 0.8549 MB / 369.1 MB, free: 15.34 MB / 346.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.978e-06/0.06629, allocations: 4 kB / 369.1 MB, free: 15.34 MB / 346.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.001615/0.0679, allocations: 0.9215 MB / 370 MB, free: 14.4 MB / 346.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.804e-05/0.06792, allocations: 16.25 kB / 370 MB, free: 14.39 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.564e-05/0.06793, allocations: 19.92 kB / 370 MB, free: 14.37 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001305/0.06924, allocations: 325.3 kB / 370.4 MB, free: 14.04 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007384/0.06998, allocations: 363.5 kB / 370.7 MB, free: 13.69 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002441/0.07242, allocations: 3.01 MB / 373.7 MB, free: 10.5 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002917/0.07271, allocations: 43.98 kB / 373.8 MB, free: 10.46 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.665e-05/0.07277, allocations: 55.98 kB / 373.8 MB, free: 10.41 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 0.0001761/0.07294, allocations: 196.2 kB / 374 MB, free: 10.2 MB / 346.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.339e-05/0.07304, allocations: 79.88 kB / 374.1 MB, free: 10.12 MB / 346.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001452/0.07449, allocations: 0.8684 MB / 375 MB, free: 9.246 MB / 346.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.645e-06/0.0745, allocations: 15.98 kB / 375 MB, free: 9.23 MB / 346.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.437e-06/0.0745, allocations: 4 kB / 375 MB, free: 9.227 MB / 346.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.873e-06/0.07451, allocations: 3.984 kB / 375 MB, free: 9.223 MB / 346.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005946/0.0751, allocations: 0.6649 MB / 375.6 MB, free: 8.512 MB / 346.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.888e-06/0.07511, allocations: 0 / 375.6 MB, free: 8.512 MB / 346.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005811/0.07569, allocations: 243.8 kB / 375.9 MB, free: 8.273 MB / 346.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001134/0.07682, allocations: 317.3 kB / 376.2 MB, free: 7.957 MB / 346.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.39e-05/0.07687, allocations: 31.98 kB / 376.2 MB, free: 7.926 MB / 346.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.001972/0.07884, allocations: 2.918 MB / 379.1 MB, free: 4.84 MB / 346.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.733e-06/0.07884, allocations: 3.938 kB / 379.1 MB, free: 4.836 MB / 346.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001451/0.08029, allocations: 1.046 MB / 380.2 MB, free: 3.758 MB / 346.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.892e-05/0.08035, allocations: 67.44 kB / 380.3 MB, free: 3.691 MB / 346.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.242e-05/0.08041, allocations: 23.94 kB / 380.3 MB, free: 3.668 MB / 346.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001983/0.08061, allocations: 24 kB / 380.3 MB, free: 3.645 MB / 346.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001102/0.08072, allocations: 88.78 kB / 380.4 MB, free: 3.555 MB / 346.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.799e-05/0.08076, allocations: 27.98 kB / 380.4 MB, free: 3.527 MB / 346.7 MB
Notification: Performance of sorting global known variables: time 0.0001396/0.0809, allocations: 224.6 kB / 380.6 MB, free: 3.309 MB / 346.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.0809, allocations: 0 / 380.6 MB, free: 3.309 MB / 346.7 MB
Notification: Performance of remove unused functions: time 0.0007146/0.08161, allocations: 407.5 kB / 381 MB, free: 2.91 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 0.000357/0.08197, allocations: 331.7 kB / 381.4 MB, free: 2.574 MB / 346.7 MB
Notification: Performance of simCode: created initialization part: time 0.0007608/0.08273, allocations: 0.8718 MB / 382.2 MB, free: 1.68 MB / 346.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.359e-05/0.08274, allocations: 16.44 kB / 382.2 MB, free: 1.664 MB / 346.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004091/0.08315, allocations: 0.5523 MB / 382.8 MB, free: 1.086 MB / 346.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004808/0.08363, allocations: 235.2 kB / 383 MB, free: 0.8594 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 0.002092/0.08572, allocations: 1.809 MB / 384.8 MB, free: 15 MB / 362.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001167/0.08584, allocations: 197 kB / 385 MB, free: 14.79 MB / 362.7 MB
Notification: Performance of simCode: alias equations: time 0.0004403/0.08628, allocations: 218.5 kB / 385.2 MB, free: 14.57 MB / 362.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004395/0.08672, allocations: 327.1 kB / 385.6 MB, free: 14.25 MB / 362.7 MB
Notification: Performance of SimCode: time 7.52e-07/0.08672, allocations: 0 / 385.6 MB, free: 14.25 MB / 362.7 MB
Notification: Performance of Templates: time 0.01988/0.1066, allocations: 19.3 MB / 404.9 MB, free: 11.13 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: 2.971164369955659]