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 0.001449/0.001449, allocations: 84.73 kB / 19.44 MB, free: 356 kB / 13.93 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 0.002533/0.002533, allocations: 157.7 kB / 22.75 MB, free: 1.684 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 1.479/1.479, allocations: 177.1 MB / 203.1 MB, free: 5.59 MB / 186.7 MB
"
[Timeout remaining time 178]
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 0.1398/0.1398, allocations: 17.37 MB / 276.9 MB, free: 11.66 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 1.813e-06/1.813e-06, allocations: 0 / 352.7 MB, free: 10.32 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.98e-05/3.161e-05, allocations: 2.312 kB / 352.7 MB, free: 10.31 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 0.04662/0.04665, allocations: 26.68 MB / 379.4 MB, free: 15.77 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.02588/0.07254, allocations: 14.7 MB / 394.1 MB, free: 1.02 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000956/0.07349, allocations: 19.81 kB / 394.1 MB, free: 1 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001249/0.07474, allocations: 309.5 kB / 394.4 MB, free: 0.6953 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.005206/0.07995, allocations: 1.528 MB / 395.9 MB, free: 15.16 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.008226/0.08817, allocations: 2.081 MB / 398 MB, free: 13.06 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.003718/0.09189, allocations: 1.591 MB / 399.6 MB, free: 11.46 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0019/0.09379, allocations: 0.7193 MB / 400.3 MB, free: 10.72 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001912/0.0957, allocations: 1.08 MB / 401.4 MB, free: 9.641 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001208/0.09691, allocations: 0.6899 MB / 402.1 MB, free: 8.949 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002311/0.09714, allocations: 139.9 kB / 402.2 MB, free: 8.812 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005325/0.1025, allocations: 1.708 MB / 403.9 MB, free: 7.102 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004079/0.1029, allocations: 330.9 kB / 404.3 MB, free: 6.777 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0008278/0.1037, allocations: 0.5028 MB / 404.8 MB, free: 6.273 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.008685/0.1124, allocations: 3.658 MB / 408.4 MB, free: 2.602 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.3e-06/0.1124, allocations: 0 / 408.4 MB, free: 2.602 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.833e-06/0.1124, allocations: 0 / 408.4 MB, free: 2.602 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 6.863e-05/0.1125, allocations: 0 / 408.4 MB, free: 2.602 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 0.004688/0.1172, allocations: 1.761 MB / 410.2 MB, free: 0.8008 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.155e-05/0.1172, allocations: 12.03 kB / 410.2 MB, free: 0.7891 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001696/0.1189, allocations: 450.5 kB / 410.6 MB, free: 356 kB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.1354/0.2543, allocations: 0.6239 MB / 411.3 MB, free: 62.83 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001377/0.2544, allocations: 138.5 kB / 411.4 MB, free: 62.76 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002152/0.2547, allocations: 113 kB / 411.5 MB, free: 62.76 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002284/0.2569, allocations: 1.331 MB / 412.8 MB, free: 62.3 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.496e-05/0.257, allocations: 1.094 kB / 412.8 MB, free: 62.3 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001209/0.2571, allocations: 46.66 kB / 412.9 MB, free: 62.27 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.356e-05/0.2571, allocations: 25.97 kB / 412.9 MB, free: 62.27 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002525/0.2596, allocations: 1.673 MB / 414.6 MB, free: 61.78 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 0.005985/0.2656, allocations: 3.411 MB / 418 MB, free: 60.09 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003721/0.2693, allocations: 1.878 MB / 419.9 MB, free: 59.5 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008227/0.2702, allocations: 0.529 MB / 420.4 MB, free: 59.28 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005583/0.2757, allocations: 2.892 MB / 423.3 MB, free: 58.2 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.246e-05/0.2758, allocations: 48.3 kB / 423.3 MB, free: 58.16 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.375e-06/0.2758, allocations: 0 / 423.3 MB, free: 58.16 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.01437/0.2901, allocations: 3.459 MB / 426.8 MB, free: 56.05 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.382e-05/0.2902, allocations: 64.34 kB / 426.9 MB, free: 55.97 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004967/0.2907, allocations: 0.5703 MB / 427.4 MB, free: 55.41 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.633e-05/0.2907, allocations: 41.7 kB / 427.5 MB, free: 55.36 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002126/0.2909, allocations: 0.5516 MB / 428 MB, free: 54.87 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002075/0.2911, allocations: 351.2 kB / 428.4 MB, free: 54.58 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000267/0.2914, allocations: 230.8 kB / 428.6 MB, free: 54.35 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 8.661e-05/0.2915, allocations: 390.6 kB / 429 MB, free: 53.96 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005103/0.292, allocations: 358.5 kB / 429.3 MB, free: 53.61 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000634/0.2926, allocations: 0.7438 MB / 430.1 MB, free: 52.69 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001248/0.2939, allocations: 1.203 MB / 431.3 MB, free: 51.33 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.32e-06/0.2939, allocations: 4 kB / 431.3 MB, free: 51.32 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003746/0.2976, allocations: 1.528 MB / 432.8 MB, free: 49.8 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.951e-05/0.2977, allocations: 8 kB / 432.8 MB, free: 49.79 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.456e-05/0.2977, allocations: 14.72 kB / 432.8 MB, free: 49.78 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003202/0.3009, allocations: 378.6 kB / 433.2 MB, free: 49.41 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00135/0.3022, allocations: 322.2 kB / 433.5 MB, free: 49.1 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004481/0.3067, allocations: 3.597 MB / 437.1 MB, free: 45.32 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008069/0.3075, allocations: 43.98 kB / 437.1 MB, free: 45.27 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.29e-05/0.3076, allocations: 68.86 kB / 437.2 MB, free: 45.21 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 0.0003726/0.308, allocations: 271.1 kB / 437.5 MB, free: 44.94 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001961/0.3082, allocations: 119.4 kB / 437.6 MB, free: 44.82 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003722/0.3119, allocations: 1.334 MB / 438.9 MB, free: 43.52 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.502e-06/0.3119, allocations: 12 kB / 438.9 MB, free: 43.51 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.268e-06/0.3119, allocations: 0 / 438.9 MB, free: 43.51 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.869e-06/0.3119, allocations: 3.984 kB / 438.9 MB, free: 43.5 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001048/0.313, allocations: 0.8029 MB / 439.7 MB, free: 42.68 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.162e-06/0.313, allocations: 7.188 kB / 439.8 MB, free: 42.68 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001132/0.3141, allocations: 214.4 kB / 440 MB, free: 42.47 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.003024/0.3171, allocations: 365.7 kB / 440.3 MB, free: 42.12 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 9.2e-05/0.3172, allocations: 35.92 kB / 440.4 MB, free: 42.09 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004139/0.3214, allocations: 3.486 MB / 443.8 MB, free: 38.41 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.605e-06/0.3214, allocations: 32 / 443.8 MB, free: 38.41 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.003917/0.3253, allocations: 1.768 MB / 445.6 MB, free: 36.62 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001633/0.3254, allocations: 77.81 kB / 445.7 MB, free: 36.55 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001015/0.3255, allocations: 22.69 kB / 445.7 MB, free: 36.53 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005128/0.3261, allocations: 20 kB / 445.7 MB, free: 36.51 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001818/0.3262, allocations: 88.78 kB / 445.8 MB, free: 36.42 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.738e-05/0.3263, allocations: 35.98 kB / 445.9 MB, free: 36.39 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.0003392/0.3266, allocations: 369.8 kB / 446.2 MB, free: 36.03 MB / 330.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.3266, allocations: 0 / 446.2 MB, free: 36.03 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001841/0.3285, allocations: 0.6818 MB / 446.9 MB, free: 35.37 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 0.001196/0.3297, allocations: 0.8484 MB / 447.7 MB, free: 34.66 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001759/0.3314, allocations: 1.196 MB / 448.9 MB, free: 33.45 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.455e-06/0.3314, allocations: 0 / 448.9 MB, free: 33.45 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0008315/0.3323, allocations: 0.7004 MB / 449.6 MB, free: 32.72 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009199/0.3332, allocations: 233.2 kB / 449.9 MB, free: 32.54 MB / 330.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002487/0.3357, allocations: 1.935 MB / 451.8 MB, free: 30.59 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002939/0.336, allocations: 448.8 kB / 452.2 MB, free: 30.14 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0006769/0.3367, allocations: 229.8 kB / 452.5 MB, free: 29.99 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003059/0.337, allocations: 157.6 kB / 452.6 MB, free: 29.84 MB / 330.7 MB
Notification: Performance of SimCode: time 8.41e-07/0.337, allocations: 0 / 452.6 MB, free: 29.84 MB / 330.7 MB
Notification: Performance of Templates: time 0.02853/0.3655, allocations: 24.08 MB / 476.7 MB, free: 6.875 MB / 330.7 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=480 -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.811911066994071]