Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false)
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008739/0.0008738, allocations: 91.06 kB / 15.06 MB, free: 1.098 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001006/0.001006, allocations: 172.7 kB / 15.95 MB, free: 208 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.275/1.275, allocations: 223.3 MB / 240 MB, free: 5.293 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.1712/0.1712, allocations: 15.27 MB / 306.4 MB, free: 15.73 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0002875/0.0002875, allocations: 8 kB / 371.5 MB, free: 3.949 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.251/0.2513, allocations: 54.62 MB / 426.1 MB, free: 40.01 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65: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 1.4.1-master/package.mo:3019:6-3019:65: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.Examples.ClimateChange.HydrogenotrophicMethanogenesis): time 0.005354/0.2567, allocations: 5.845 MB / 432 MB, free: 39.02 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01253/0.2693, allocations: 15.31 MB / 447.3 MB, free: 27.93 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0008747/0.2702, allocations: 23.94 kB / 447.3 MB, free: 27.92 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007661/0.2709, allocations: 304.7 kB / 447.6 MB, free: 27.76 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00325/0.2742, allocations: 1.325 MB / 448.9 MB, free: 26.97 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.003827/0.2781, allocations: 1.616 MB / 450.5 MB, free: 26.03 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.001396/0.2795, allocations: 1.407 MB / 451.9 MB, free: 25.34 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006449/0.2801, allocations: 0.6555 MB / 452.6 MB, free: 25.09 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0006133/0.2807, allocations: 0.6121 MB / 453.2 MB, free: 24.89 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0007334/0.2815, allocations: 0.7741 MB / 454 MB, free: 24.62 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001282/0.2816, allocations: 70.06 kB / 454.1 MB, free: 24.62 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004208/0.2858, allocations: 1.674 MB / 455.7 MB, free: 24.23 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002522/0.2861, allocations: 256.9 kB / 456 MB, free: 24.11 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002893/0.2864, allocations: 244.9 kB / 456.2 MB, free: 23.97 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.002731/0.2891, allocations: 2.518 MB / 458.7 MB, free: 23.01 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.628e-06/0.2892, allocations: 0 / 458.7 MB, free: 23.01 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.543e-06/0.2892, allocations: 0 / 458.7 MB, free: 23.01 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 2.351e-05/0.2892, allocations: 0 / 458.7 MB, free: 23.01 MB / 350.1 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 0.002424/0.2916, allocations: 1.543 MB / 460.3 MB, free: 22.04 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.447e-05/0.2917, allocations: 9.406 kB / 460.3 MB, free: 22.04 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0009886/0.2927, allocations: 276.5 kB / 460.6 MB, free: 21.95 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006927/0.2934, allocations: 0.6052 MB / 461.2 MB, free: 21.52 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.995e-05/0.2935, allocations: 113.8 kB / 461.3 MB, free: 21.45 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001716/0.2936, allocations: 112.4 kB / 461.4 MB, free: 21.41 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001947/0.2956, allocations: 1.319 MB / 462.7 MB, free: 20.87 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.389e-05/0.2956, allocations: 0 / 462.7 MB, free: 20.87 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001006/0.2957, allocations: 50.2 kB / 462.7 MB, free: 20.83 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.27e-05/0.2958, allocations: 25.41 kB / 462.8 MB, free: 20.83 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00249/0.2983, allocations: 1.688 MB / 464.5 MB, free: 20.34 MB / 350.1 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 0.006281/0.3046, allocations: 4.251 MB / 468.7 MB, free: 17.74 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003149/0.3077, allocations: 2.275 MB / 471 MB, free: 16.73 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008414/0.3086, allocations: 0.5855 MB / 471.6 MB, free: 16.48 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005666/0.3143, allocations: 5.289 MB / 476.9 MB, free: 12.24 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.111e-05/0.3143, allocations: 39.97 kB / 476.9 MB, free: 12.2 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.174e-06/0.3143, allocations: 0 / 476.9 MB, free: 12.2 MB / 350.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01392/0.3282, allocations: 3.596 MB / 480.5 MB, free: 10.68 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.41e-05/0.3283, allocations: 69.81 kB / 480.6 MB, free: 10.61 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006904/0.329, allocations: 0.578 MB / 481.1 MB, free: 10.34 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 5.577e-05/0.3291, allocations: 45.14 kB / 481.2 MB, free: 10.3 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002743/0.3294, allocations: 0.5275 MB / 481.7 MB, free: 9.871 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002279/0.3296, allocations: 335 kB / 482 MB, free: 9.609 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.657e-05/0.3297, allocations: 25.81 kB / 482.1 MB, free: 9.59 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001272/0.3298, allocations: 396.4 kB / 482.5 MB, free: 9.238 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006169/0.3304, allocations: 352.4 kB / 482.8 MB, free: 9.113 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007439/0.3312, allocations: 0.747 MB / 483.5 MB, free: 8.469 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006913/0.3319, allocations: 470.3 kB / 484 MB, free: 8.242 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.973e-06/0.3319, allocations: 3.875 kB / 484 MB, free: 8.242 MB / 350.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003842/0.3357, allocations: 1.467 MB / 485.5 MB, free: 7.652 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.404e-05/0.3358, allocations: 10.06 kB / 485.5 MB, free: 7.652 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.719e-05/0.3358, allocations: 14.28 kB / 485.5 MB, free: 7.652 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001917/0.3377, allocations: 265.9 kB / 485.8 MB, free: 7.594 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00129/0.339, allocations: 330.2 kB / 486.1 MB, free: 7.559 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00454/0.3436, allocations: 3.514 MB / 489.6 MB, free: 4.441 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008715/0.3445, allocations: 72.61 kB / 489.7 MB, free: 4.414 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001059/0.3446, allocations: 64.95 kB / 489.7 MB, free: 4.406 MB / 350.1 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 (linear and non-linear blocks): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 1 {(1,100.0%) 3}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.0003945/0.345, allocations: 278.4 kB / 490 MB, free: 4.184 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001365/0.3451, allocations: 86.8 kB / 490.1 MB, free: 4.137 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003758/0.3489, allocations: 1.342 MB / 491.4 MB, free: 3.133 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.905e-06/0.3489, allocations: 16.14 kB / 491.4 MB, free: 3.117 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.418e-06/0.3489, allocations: 0 / 491.4 MB, free: 3.117 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.102e-05/0.3489, allocations: 7.969 kB / 491.5 MB, free: 3.109 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001115/0.3501, allocations: 1.077 MB / 492.5 MB, free: 1.961 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.819e-06/0.3501, allocations: 3.953 kB / 492.5 MB, free: 1.957 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001024/0.3511, allocations: 223.8 kB / 492.8 MB, free: 1.738 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001775/0.3529, allocations: 237.4 kB / 493 MB, free: 1.5 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.003e-05/0.353, allocations: 35.98 kB / 493 MB, free: 1.465 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004135/0.3571, allocations: 3.421 MB / 496.4 MB, free: 13.78 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.144e-06/0.3571, allocations: 0 / 496.4 MB, free: 13.78 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004005/0.3611, allocations: 1.744 MB / 498.2 MB, free: 12 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002022/0.3614, allocations: 152 kB / 498.3 MB, free: 11.83 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001155/0.3615, allocations: 24 kB / 498.4 MB, free: 11.81 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0004798/0.362, allocations: 31.98 kB / 498.4 MB, free: 11.78 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001529/0.3621, allocations: 80.84 kB / 498.5 MB, free: 11.7 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.021e-05/0.3622, allocations: 39.98 kB / 498.5 MB, free: 11.66 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0004127/0.3626, allocations: 387.1 kB / 498.9 MB, free: 11.28 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.3626, allocations: 0 / 498.9 MB, free: 11.28 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.001899/0.3645, allocations: 0.6675 MB / 499.6 MB, free: 10.61 MB / 366.1 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 (linear and non-linear blocks): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 1 {(1,100.0%) 3}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001245/0.3658, allocations: 0.8001 MB / 0.4886 GB, free: 9.809 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.001933/0.3677, allocations: 1.242 MB / 0.4898 GB, free: 8.543 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.435e-06/0.3678, allocations: 1.188 kB / 0.4898 GB, free: 8.543 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0009823/0.3687, allocations: 0.7413 MB / 0.4906 GB, free: 7.777 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0008871/0.3696, allocations: 187.3 kB / 0.4907 GB, free: 7.598 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003109/0.3728, allocations: 2.446 MB / 0.4931 GB, free: 5.109 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005453/0.3733, allocations: 1.041 MB / 0.4941 GB, free: 4.039 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 0.0009154/0.3742, allocations: 221.8 kB / 0.4944 GB, free: 3.828 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000315/0.3746, allocations: 162.1 kB / 0.4945 GB, free: 3.676 MB / 366.1 MB
Notification: Performance of SimCode: time 3.51e-07/0.3746, allocations: 0 / 0.4945 GB, free: 3.676 MB / 366.1 MB
Notification: Performance of Templates: time 0.03038/0.405, allocations: 21.96 MB / 0.516 GB, free: 13.84 MB / 398.1 MB
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
(rm -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)