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 0.001582/0.001582, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.002215/0.002215, allocations: 173 kB / 23.49 MB, free: 1.059 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 1.056/1.056, allocations: 177.1 MB / 203.8 MB, free: 5.629 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 0.09259/0.09259, allocations: 17.38 MB / 277.7 MB, free: 11.71 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 1.413e-06/1.413e-06, allocations: 0 / 353.4 MB, free: 10.31 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.388e-05/2.529e-05, allocations: 10.25 kB / 353.5 MB, free: 10.3 MB / 282.7 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 0.02847/0.0285, allocations: 29.56 MB / 383 MB, free: 12.88 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01422/0.04271, allocations: 16.77 MB / 399.8 MB, free: 12.05 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000754/0.04347, allocations: 15.88 kB / 399.8 MB, free: 12.03 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0006903/0.04416, allocations: 305.5 kB / 400.1 MB, free: 11.73 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002944/0.0471, allocations: 1.52 MB / 401.6 MB, free: 10.2 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.003987/0.05109, allocations: 2.085 MB / 403.7 MB, free: 8.102 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001584/0.05267, allocations: 1.599 MB / 405.3 MB, free: 6.496 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006835/0.05336, allocations: 0.7194 MB / 406 MB, free: 5.754 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000906/0.05426, allocations: 1.076 MB / 407.1 MB, free: 4.676 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0007883/0.05505, allocations: 0.7133 MB / 407.8 MB, free: 3.961 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002025/0.05525, allocations: 132 kB / 407.9 MB, free: 3.832 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004071/0.05933, allocations: 1.715 MB / 409.7 MB, free: 2.113 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002698/0.0596, allocations: 334.9 kB / 410 MB, free: 1.785 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004454/0.06004, allocations: 0.5067 MB / 410.5 MB, free: 1.277 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.1439/0.2039, allocations: 3.14 MB / 413.6 MB, free: 41.2 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.611e-06/0.2039, allocations: 0 / 413.6 MB, free: 41.2 MB / 330.7 MB
Notification: Performance of FrontEnd: time 9.41e-07/0.2039, allocations: 0 / 413.6 MB, free: 41.2 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 4.979e-05/0.204, allocations: 4.562 kB / 413.6 MB, free: 41.2 MB / 330.7 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 0.003009/0.207, allocations: 1.876 MB / 415.5 MB, free: 40.24 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.885e-05/0.207, allocations: 9.625 kB / 415.5 MB, free: 40.24 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001114/0.2082, allocations: 452.3 kB / 416 MB, free: 40.09 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008743/0.209, allocations: 0.6192 MB / 416.6 MB, free: 39.86 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001049/0.2091, allocations: 142.8 kB / 416.7 MB, free: 39.8 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000148/0.2093, allocations: 116 kB / 416.8 MB, free: 39.79 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0016/0.2109, allocations: 1.067 MB / 417.9 MB, free: 39.64 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.029e-05/0.2109, allocations: 192 / 417.9 MB, free: 39.64 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.327e-05/0.211, allocations: 47.7 kB / 417.9 MB, free: 39.64 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.777e-05/0.211, allocations: 30.22 kB / 418 MB, free: 39.64 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001721/0.2127, allocations: 1.122 MB / 419.1 MB, free: 39.61 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 0.004168/0.2169, allocations: 3.324 MB / 422.4 MB, free: 38.59 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.00218/0.2191, allocations: 2.075 MB / 424.5 MB, free: 38.5 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004328/0.2195, allocations: 369.3 kB / 424.9 MB, free: 38.48 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.003327/0.2228, allocations: 2.755 MB / 427.6 MB, free: 37.98 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.559e-05/0.2229, allocations: 48.98 kB / 427.7 MB, free: 37.93 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.124e-06/0.2229, allocations: 3.531 kB / 427.7 MB, free: 37.93 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.006998/0.2299, allocations: 2.98 MB / 430.6 MB, free: 37.04 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.699e-05/0.2299, allocations: 62.44 kB / 430.7 MB, free: 36.97 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000441/0.2303, allocations: 0.6057 MB / 431.3 MB, free: 36.65 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.423e-05/0.2304, allocations: 41.2 kB / 431.4 MB, free: 36.61 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001901/0.2306, allocations: 0.6112 MB / 432 MB, free: 36.11 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001526/0.2307, allocations: 351.5 kB / 432.3 MB, free: 35.84 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001987/0.2309, allocations: 234.8 kB / 432.5 MB, free: 35.72 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001021/0.231, allocations: 0.5588 MB / 433.1 MB, free: 35.2 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003244/0.2313, allocations: 230.8 kB / 433.3 MB, free: 35.16 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004376/0.2318, allocations: 0.7894 MB / 434.1 MB, free: 34.41 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0008758/0.2327, allocations: 1.104 MB / 435.2 MB, free: 33.55 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.54e-06/0.2327, allocations: 6.594 kB / 435.2 MB, free: 33.55 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.002043/0.2347, allocations: 1.264 MB / 436.5 MB, free: 33.24 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.634e-05/0.2347, allocations: 11.97 kB / 436.5 MB, free: 33.24 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.874e-05/0.2348, allocations: 16.47 kB / 436.5 MB, free: 33.23 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001428/0.2362, allocations: 344.6 kB / 436.8 MB, free: 33.2 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007715/0.237, allocations: 327 kB / 437.2 MB, free: 33.18 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.003075/0.24, allocations: 4.374 MB / 441.5 MB, free: 28.87 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0007512/0.2408, allocations: 42.66 kB / 441.6 MB, free: 28.83 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 8.487e-05/0.2409, allocations: 66.61 kB / 441.6 MB, free: 28.77 MB / 330.7 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 0.0003856/0.2412, allocations: 241.6 kB / 441.9 MB, free: 28.55 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001608/0.2414, allocations: 115.4 kB / 442 MB, free: 28.43 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001924/0.2433, allocations: 1.112 MB / 443.1 MB, free: 27.43 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.853e-06/0.2433, allocations: 12 kB / 443.1 MB, free: 27.41 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.068e-06/0.2433, allocations: 0 / 443.1 MB, free: 27.41 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.758e-06/0.2434, allocations: 3.984 kB / 443.1 MB, free: 27.41 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008616/0.2442, allocations: 0.7564 MB / 443.9 MB, free: 26.63 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.035e-06/0.2442, allocations: 4 kB / 443.9 MB, free: 26.62 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005593/0.2448, allocations: 214.8 kB / 444.1 MB, free: 26.43 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00128/0.2461, allocations: 333.4 kB / 444.4 MB, free: 26.11 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.886e-05/0.2461, allocations: 31.98 kB / 444.5 MB, free: 26.08 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002232/0.2484, allocations: 4.272 MB / 448.7 MB, free: 21.6 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.733e-06/0.2484, allocations: 0 / 448.7 MB, free: 21.6 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001977/0.2503, allocations: 1.389 MB / 450.1 MB, free: 20.18 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001409/0.2505, allocations: 70.91 kB / 450.2 MB, free: 20.11 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.137e-05/0.2506, allocations: 24 kB / 450.2 MB, free: 20.09 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002336/0.2508, allocations: 20 kB / 450.2 MB, free: 20.07 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001456/0.2509, allocations: 88.78 kB / 450.3 MB, free: 19.98 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.608e-05/0.251, allocations: 39.98 kB / 450.4 MB, free: 19.94 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0002384/0.2512, allocations: 365.6 kB / 450.7 MB, free: 19.59 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.2512, allocations: 0 / 450.7 MB, free: 19.59 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001754/0.253, allocations: 0.6851 MB / 451.4 MB, free: 18.91 MB / 330.7 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 0.001273/0.2542, allocations: 0.8487 MB / 452.2 MB, free: 18.21 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001282/0.2555, allocations: 1.122 MB / 453.4 MB, free: 17.11 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.615e-06/0.2555, allocations: 0 / 453.4 MB, free: 17.11 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0005332/0.2561, allocations: 0.7375 MB / 454.1 MB, free: 16.36 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006307/0.2567, allocations: 228.5 kB / 454.3 MB, free: 16.16 MB / 330.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0027/0.2594, allocations: 1.837 MB / 456.2 MB, free: 14.32 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000112/0.2595, allocations: 193 kB / 456.4 MB, free: 14.12 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0005203/0.26, allocations: 220.3 kB / 456.6 MB, free: 13.97 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002114/0.2602, allocations: 163.3 kB / 456.7 MB, free: 13.82 MB / 330.7 MB
Notification: Performance of SimCode: time 1.202e-06/0.2602, allocations: 0 / 456.7 MB, free: 13.82 MB / 330.7 MB
Notification: Performance of Templates: time 0.02406/0.2843, allocations: 24.31 MB / 481 MB, free: 6.703 MB / 346.7 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: 3.827289290027693]