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 0.001244/0.001244, 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 0.001642/0.001642, allocations: 169 kB / 23.49 MB, free: 1.062 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 0.9119/0.9119, allocations: 177.1 MB / 203.8 MB, free: 5.652 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 0.1076/0.1076, allocations: 17.46 MB / 277.7 MB, free: 11.64 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 1.763e-06/1.763e-06, allocations: 0 / 353.6 MB, free: 10.18 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.179e-05/2.355e-05, allocations: 2.312 kB / 353.6 MB, free: 10.18 MB / 282.7 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 0.02989/0.02992, allocations: 29.56 MB / 383.1 MB, free: 12.75 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01424/0.04415, allocations: 16.76 MB / 399.9 MB, free: 11.93 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0006721/0.04482, allocations: 15.88 kB / 399.9 MB, free: 11.91 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0006312/0.04545, allocations: 309.5 kB / 400.2 MB, free: 11.61 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002872/0.04833, allocations: 1.528 MB / 401.7 MB, free: 10.07 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004081/0.05241, allocations: 2.077 MB / 403.8 MB, free: 7.98 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.001281/0.05369, allocations: 1.603 MB / 405.4 MB, free: 6.371 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006132/0.0543, allocations: 0.7194 MB / 406.1 MB, free: 5.629 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000741/0.05504, allocations: 1.072 MB / 407.2 MB, free: 4.555 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006744/0.05572, allocations: 0.7172 MB / 407.9 MB, free: 3.836 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001304/0.05585, allocations: 139.9 kB / 408.1 MB, free: 3.699 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.00307/0.05892, allocations: 1.708 MB / 409.8 MB, free: 1.988 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002196/0.05914, allocations: 334.9 kB / 410.1 MB, free: 1.66 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003602/0.0595, allocations: 0.4989 MB / 410.6 MB, free: 1.16 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.146/0.2055, allocations: 3.149 MB / 413.8 MB, free: 40.73 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.737e-06/0.2055, allocations: 4.703 kB / 413.8 MB, free: 40.73 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.333e-06/0.2055, allocations: 1.469 kB / 413.8 MB, free: 40.73 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 4.594e-05/0.2055, allocations: 0 / 413.8 MB, free: 40.73 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 0.002784/0.2083, allocations: 1.878 MB / 415.6 MB, free: 39.78 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.187e-05/0.2084, allocations: 13.19 kB / 415.6 MB, free: 39.78 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0009708/0.2093, allocations: 454.1 kB / 416.1 MB, free: 39.63 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008087/0.2101, allocations: 0.6207 MB / 416.7 MB, free: 39.4 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001073/0.2102, allocations: 138 kB / 416.8 MB, free: 39.33 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001542/0.2104, allocations: 115.5 kB / 417 MB, free: 39.33 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001508/0.2119, allocations: 1.072 MB / 418 MB, free: 39.18 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.102e-05/0.2119, allocations: 4.594 kB / 418 MB, free: 39.18 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.215e-05/0.212, allocations: 43.81 kB / 418.1 MB, free: 39.18 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.506e-05/0.212, allocations: 28.94 kB / 418.1 MB, free: 39.17 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001671/0.2137, allocations: 1.119 MB / 419.2 MB, free: 39.15 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 0.003851/0.2176, allocations: 3.321 MB / 422.5 MB, free: 38.12 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002192/0.2198, allocations: 2.077 MB / 424.6 MB, free: 38.04 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004202/0.2202, allocations: 374.1 kB / 425 MB, free: 38.02 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.003098/0.2233, allocations: 2.75 MB / 427.7 MB, free: 37.44 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.002e-05/0.2233, allocations: 44.03 kB / 427.8 MB, free: 37.39 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.114e-06/0.2233, allocations: 2.75 kB / 427.8 MB, free: 37.39 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.006895/0.2302, allocations: 2.982 MB / 430.8 MB, free: 36.5 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.508e-05/0.2302, allocations: 65.8 kB / 430.8 MB, free: 36.44 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005099/0.2307, allocations: 0.6075 MB / 431.4 MB, free: 36.11 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 4.43e-05/0.2308, allocations: 41.67 kB / 431.5 MB, free: 36.07 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002123/0.231, allocations: 0.6011 MB / 432.1 MB, free: 35.57 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000161/0.2312, allocations: 346.5 kB / 432.4 MB, free: 35.3 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000199/0.2314, allocations: 235.1 kB / 432.7 MB, free: 35.19 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001322/0.2315, allocations: 0.5715 MB / 433.2 MB, free: 34.66 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003129/0.2318, allocations: 226.5 kB / 433.4 MB, free: 34.62 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004628/0.2323, allocations: 0.785 MB / 434.2 MB, free: 33.87 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009442/0.2332, allocations: 1.118 MB / 435.3 MB, free: 33.01 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.901e-06/0.2332, allocations: 4.562 kB / 435.4 MB, free: 33.01 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.002104/0.2353, allocations: 1.254 MB / 436.6 MB, free: 32.7 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.228e-05/0.2353, allocations: 14.61 kB / 436.6 MB, free: 32.7 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.135e-05/0.2354, allocations: 21.12 kB / 436.6 MB, free: 32.7 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001387/0.2367, allocations: 347.1 kB / 437 MB, free: 32.66 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007696/0.2375, allocations: 329.3 kB / 437.3 MB, free: 32.64 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00294/0.2405, allocations: 4.366 MB / 441.7 MB, free: 28.34 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003817/0.2408, allocations: 40 kB / 441.7 MB, free: 28.3 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.03e-05/0.2409, allocations: 67.47 kB / 441.8 MB, free: 28.24 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 0.0002375/0.2411, allocations: 236.8 kB / 442 MB, free: 28.02 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001256/0.2413, allocations: 119.4 kB / 442.1 MB, free: 27.9 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.00193/0.2432, allocations: 1.108 MB / 443.2 MB, free: 26.9 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.461e-06/0.2432, allocations: 8 kB / 443.2 MB, free: 26.89 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.138e-06/0.2432, allocations: 6.656 kB / 443.2 MB, free: 26.89 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.746e-06/0.2432, allocations: 3.984 kB / 443.2 MB, free: 26.88 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007543/0.244, allocations: 0.7554 MB / 444 MB, free: 26.11 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.911e-06/0.244, allocations: 3.891 kB / 444 MB, free: 26.11 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005688/0.2446, allocations: 221 kB / 444.2 MB, free: 25.91 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001284/0.2458, allocations: 330.9 kB / 444.5 MB, free: 25.59 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 5.017e-05/0.2459, allocations: 31.98 kB / 444.6 MB, free: 25.56 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002271/0.2482, allocations: 4.267 MB / 448.8 MB, free: 21.08 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.304e-06/0.2482, allocations: 4 kB / 448.8 MB, free: 21.08 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00191/0.2501, allocations: 1.379 MB / 450.2 MB, free: 19.67 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.158e-05/0.2501, allocations: 82.11 kB / 450.3 MB, free: 19.59 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.89e-05/0.2502, allocations: 16 kB / 450.3 MB, free: 19.57 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000233/0.2504, allocations: 24 kB / 450.3 MB, free: 19.55 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001289/0.2506, allocations: 94.92 kB / 450.4 MB, free: 19.46 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.101e-05/0.2506, allocations: 35.98 kB / 450.5 MB, free: 19.43 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0001937/0.2508, allocations: 367 kB / 450.8 MB, free: 19.07 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.2508, allocations: 0 / 450.8 MB, free: 19.07 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001586/0.2524, allocations: 0.6805 MB / 451.5 MB, free: 18.39 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 0.00101/0.2534, allocations: 0.849 MB / 452.4 MB, free: 17.7 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.00103/0.2544, allocations: 1.129 MB / 453.5 MB, free: 16.59 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.054e-06/0.2544, allocations: 0 / 453.5 MB, free: 16.59 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0004767/0.2549, allocations: 0.7293 MB / 454.2 MB, free: 15.84 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006211/0.2555, allocations: 235.3 kB / 454.4 MB, free: 15.64 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 0.002515/0.258, allocations: 1.833 MB / 456.3 MB, free: 13.8 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001026/0.2581, allocations: 199.8 kB / 456.5 MB, free: 13.59 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0004742/0.2586, allocations: 220.9 kB / 456.7 MB, free: 13.45 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002134/0.2588, allocations: 170.2 kB / 456.9 MB, free: 13.29 MB / 330.7 MB
Notification: Performance of SimCode: time 1.333e-06/0.2588, allocations: 0 / 456.9 MB, free: 13.29 MB / 330.7 MB
Notification: Performance of Templates: time 0.0233/0.2821, allocations: 24.3 MB / 481.2 MB, free: 6.188 MB / 346.7 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  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.7507090168073773]