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 0.001414/0.001414, allocations: 84.73 kB / 19.44 MB, free: 348 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 0.001617/0.001617, allocations: 161.7 kB / 22.75 MB, free: 1.676 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 1.473/1.473, allocations: 177.1 MB / 203.1 MB, free: 5.617 MB / 186.7 MB
"
[Timeout remaining time 178]
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 0.149/0.149, allocations: 17.45 MB / 277 MB, free: 11.61 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 1.734e-06/1.734e-06, allocations: 0 / 352.8 MB, free: 10.2 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.067e-05/3.24e-05, allocations: 2.312 kB / 352.8 MB, free: 10.2 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 0.04371/0.04374, allocations: 26.67 MB / 379.5 MB, free: 15.67 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.02524/0.06898, allocations: 14.71 MB / 394.2 MB, free: 0.9023 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001346/0.07033, allocations: 15.88 kB / 394.2 MB, free: 0.8867 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001401/0.07173, allocations: 313.4 kB / 394.5 MB, free: 0.5781 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.006143/0.07787, allocations: 1.52 MB / 396 MB, free: 15.05 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.007017/0.08489, allocations: 2.081 MB / 398.1 MB, free: 12.95 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.003199/0.08809, allocations: 1.602 MB / 399.7 MB, free: 11.34 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001492/0.08958, allocations: 0.7193 MB / 400.4 MB, free: 10.6 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.002162/0.09174, allocations: 1.072 MB / 401.5 MB, free: 9.527 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001612/0.09335, allocations: 0.6976 MB / 402.2 MB, free: 8.828 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0004289/0.09378, allocations: 132 kB / 402.3 MB, free: 8.699 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005305/0.09908, allocations: 1.712 MB / 404.1 MB, free: 6.984 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.000473/0.09956, allocations: 334.9 kB / 404.4 MB, free: 6.656 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001096/0.1007, allocations: 0.4989 MB / 404.9 MB, free: 6.156 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.009183/0.1098, allocations: 3.658 MB / 408.5 MB, free: 2.484 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.68e-06/0.1098, allocations: 4 kB / 408.5 MB, free: 2.48 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.502e-06/0.1098, allocations: 0 / 408.5 MB, free: 2.48 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 6.53e-05/0.1099, allocations: 0 / 408.5 MB, free: 2.48 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 0.004747/0.1147, allocations: 1.753 MB / 410.3 MB, free: 0.6875 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.316e-05/0.1147, allocations: 8.031 kB / 410.3 MB, free: 0.6797 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001945/0.1166, allocations: 458.2 kB / 410.8 MB, free: 236 kB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.1455/0.2621, allocations: 0.626 MB / 411.4 MB, free: 62.82 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001879/0.2623, allocations: 136.8 kB / 411.5 MB, free: 62.75 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002536/0.2626, allocations: 111.9 kB / 411.6 MB, free: 62.75 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00235/0.2649, allocations: 1.328 MB / 413 MB, free: 62.27 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.564e-05/0.2649, allocations: 4.125 kB / 413 MB, free: 62.27 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001215/0.2651, allocations: 47.95 kB / 413 MB, free: 62.23 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.71e-05/0.2651, allocations: 27.59 kB / 413 MB, free: 62.23 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002667/0.2678, allocations: 1.672 MB / 414.7 MB, free: 61.74 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 0.006306/0.2741, allocations: 3.407 MB / 418.1 MB, free: 60.03 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003525/0.2776, allocations: 1.879 MB / 420 MB, free: 59.44 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007918/0.2784, allocations: 0.5348 MB / 420.5 MB, free: 59.22 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005774/0.2842, allocations: 2.89 MB / 423.4 MB, free: 58.14 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.439e-05/0.2842, allocations: 42.81 kB / 423.5 MB, free: 58.1 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=78): time 2.284e-06/0.2842, allocations: 0 / 423.5 MB, free: 58.1 MB / 330.7 MB
Notification: Performance of matching and sorting (n=95): time 0.01438/0.2986, allocations: 3.455 MB / 426.9 MB, free: 55.88 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.189e-05/0.2986, allocations: 64.34 kB / 427 MB, free: 55.8 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005284/0.2991, allocations: 0.5714 MB / 427.5 MB, free: 55.24 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 5.95e-05/0.2992, allocations: 45.64 kB / 427.6 MB, free: 55.19 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002279/0.2994, allocations: 0.5559 MB / 428.1 MB, free: 54.69 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002013/0.2996, allocations: 351.3 kB / 428.5 MB, free: 54.4 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002674/0.2999, allocations: 226.8 kB / 428.7 MB, free: 54.17 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 9.037e-05/0.3, allocations: 386.8 kB / 429.1 MB, free: 53.79 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005409/0.3005, allocations: 358.5 kB / 429.4 MB, free: 53.43 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007241/0.3012, allocations: 0.7477 MB / 430.2 MB, free: 52.51 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001339/0.3026, allocations: 1.206 MB / 431.4 MB, free: 51.14 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.486e-06/0.3026, allocations: 4 kB / 431.4 MB, free: 51.14 MB / 330.7 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003843/0.3064, allocations: 1.528 MB / 432.9 MB, free: 49.61 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.523e-05/0.3064, allocations: 10.19 kB / 432.9 MB, free: 49.61 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.77e-05/0.3065, allocations: 14.69 kB / 432.9 MB, free: 49.59 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003253/0.3097, allocations: 374.6 kB / 433.3 MB, free: 49.23 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001407/0.3111, allocations: 326.2 kB / 433.6 MB, free: 48.92 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004831/0.316, allocations: 3.594 MB / 437.2 MB, free: 45.14 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0009251/0.3169, allocations: 44.86 kB / 437.3 MB, free: 45.09 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001393/0.317, allocations: 67.98 kB / 437.3 MB, free: 45.03 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 0.0004882/0.3175, allocations: 273.4 kB / 437.6 MB, free: 44.75 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002753/0.3178, allocations: 122 kB / 437.7 MB, free: 44.63 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003938/0.3217, allocations: 1.328 MB / 439 MB, free: 43.33 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.604e-06/0.3217, allocations: 12 kB / 439.1 MB, free: 43.32 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.56e-06/0.3217, allocations: 0 / 439.1 MB, free: 43.32 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.728e-06/0.3217, allocations: 3.984 kB / 439.1 MB, free: 43.32 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00115/0.3229, allocations: 0.8091 MB / 439.9 MB, free: 42.49 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.584e-06/0.3229, allocations: 3.188 kB / 439.9 MB, free: 42.49 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001156/0.3241, allocations: 214.5 kB / 440.1 MB, free: 42.28 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.003139/0.3272, allocations: 366.5 kB / 440.4 MB, free: 41.93 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.646e-05/0.3273, allocations: 35.92 kB / 440.5 MB, free: 41.89 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004132/0.3314, allocations: 3.493 MB / 444 MB, free: 38.21 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.155e-06/0.3314, allocations: 0 / 444 MB, free: 38.21 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004058/0.3355, allocations: 1.767 MB / 445.7 MB, free: 36.43 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001801/0.3357, allocations: 82.11 kB / 445.8 MB, free: 36.35 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001306/0.3358, allocations: 19.83 kB / 445.8 MB, free: 36.33 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005614/0.3364, allocations: 20 kB / 445.9 MB, free: 36.31 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001843/0.3365, allocations: 84.84 kB / 445.9 MB, free: 36.23 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.244e-05/0.3366, allocations: 39.98 kB / 446 MB, free: 36.19 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 0.000332/0.3369, allocations: 365.7 kB / 446.3 MB, free: 35.84 MB / 330.7 MB
Notification: Performance of sort global known variables: time 7e-08/0.3369, allocations: 0 / 446.3 MB, free: 35.84 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.001803/0.3387, allocations: 0.6856 MB / 447 MB, free: 35.15 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 0.001511/0.3403, allocations: 0.8465 MB / 447.9 MB, free: 34.45 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.001867/0.3421, allocations: 1.196 MB / 449.1 MB, free: 33.23 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 2.886e-06/0.3421, allocations: 0 / 449.1 MB, free: 33.23 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.000896/0.343, allocations: 0.6927 MB / 449.8 MB, free: 32.51 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001005/0.344, allocations: 228.4 kB / 450 MB, free: 32.32 MB / 330.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002868/0.3469, allocations: 1.939 MB / 451.9 MB, free: 30.38 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003468/0.3472, allocations: 452.5 kB / 452.4 MB, free: 29.92 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 0.0007628/0.348, allocations: 229.3 kB / 452.6 MB, free: 29.77 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003199/0.3483, allocations: 161.5 kB / 452.7 MB, free: 29.62 MB / 330.7 MB
Notification: Performance of SimCode: time 1.082e-06/0.3483, allocations: 0 / 452.7 MB, free: 29.62 MB / 330.7 MB
Notification: Performance of Templates: time 0.02988/0.3782, allocations: 24.07 MB / 476.8 MB, free: 6.66 MB / 330.7 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=480 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.787086162948981]