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/Chemical 1.4.0-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/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/Chemical 1.4.0-master/package.mo): time 0.101/0.101, allocations: 15.26 MB / 22.73 MB, free: 0.9727 MB / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001211/0.001211, allocations: 185 kB / 27.52 MB, free: 6.117 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.466/1.466, allocations: 221.5 MB / 253.7 MB, free: 10.97 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008497/0.0008497, allocations: 97.55 kB / 308.8 MB, free: 10.94 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 1.514e-05/1.509e-05, allocations: 2.781 kB / 369.6 MB, free: 53.88 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1013/0.1013, allocations: 54.64 MB / 424.2 MB, free: 14.28 MB / 298.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.3915/0.4929, allocations: 99.49 MB / 0.5114 GB, free: 12.47 MB / 362.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0002001/0.4932, allocations: 69.34 kB / 0.5115 GB, free: 12.47 MB / 362.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System solution.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Solution.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System CH4.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$CH4.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System CO2.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$CO2.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2O.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2O.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
Notification: Performance of FrontEnd - DAE generated: time 0.1103/0.6035, allocations: 47.72 MB / 0.5581 GB, free: 16.16 MB / 378.7 MB
Notification: Performance of FrontEnd: time 1.272e-06/0.6036, allocations: 4 kB / 0.5581 GB, free: 16.16 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 6.627e-05/0.6036, allocations: 27.28 kB / 0.5581 GB, free: 16.16 MB / 378.7 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 0.003395/0.607, allocations: 1.542 MB / 0.5596 GB, free: 15.12 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.781e-05/0.6071, allocations: 7.75 kB / 0.5596 GB, free: 15.12 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001285/0.6084, allocations: 332.3 kB / 0.56 GB, free: 14.99 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001842/0.6102, allocations: 0.9024 MB / 0.5608 GB, free: 14.34 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.735e-05/0.6103, allocations: 77.44 kB / 0.5609 GB, free: 14.3 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002127/0.6106, allocations: 79.86 kB / 0.561 GB, free: 14.28 MB / 378.7 MB
Notification: Performance of preOpt removeEqualFunctionCalls (simulation): time 0.003336/0.6139, allocations: 2.729 MB / 0.5637 GB, free: 12.57 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002231/0.6161, allocations: 1.458 MB / 0.5651 GB, free: 11.07 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.562e-05/0.6162, allocations: 11.98 kB / 0.5651 GB, free: 11.05 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.703e-05/0.6163, allocations: 0 / 0.5651 GB, free: 11.05 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.166e-05/0.6163, allocations: 28 kB / 0.5651 GB, free: 11.03 MB / 378.7 MB
Warning: The model contains alias variables with conflicting start and/or 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 0.008386/0.6247, allocations: 5.546 MB / 0.5705 GB, free: 5.348 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003471/0.6282, allocations: 2.736 MB / 0.5732 GB, free: 2.535 MB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.001124/0.6293, allocations: 0.9489 MB / 0.5741 GB, free: 1.582 MB / 378.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0005113/0.6299, allocations: 328.1 kB / 0.5744 GB, free: 1.27 MB / 378.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.351e-05/0.6299, allocations: 43.88 kB / 0.5745 GB, free: 1.219 MB / 378.7 MB
Notification: Performance of pre-optimization done (n=129): time 3.807e-06/0.6299, allocations: 0 / 0.5745 GB, free: 1.219 MB / 378.7 MB
Notification: Performance of matching and sorting (n=175): time 0.029/0.6589, allocations: 8.614 MB / 0.5829 GB, free: 8.59 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.456e-05/0.659, allocations: 69.41 kB / 0.583 GB, free: 8.508 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001014/0.66, allocations: 0.5936 MB / 0.5835 GB, free: 7.91 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.000196/0.6603, allocations: 25.7 kB / 0.5836 GB, free: 7.879 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003474/0.6606, allocations: 473.2 kB / 0.584 GB, free: 7.41 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000622/0.6613, allocations: 0.5579 MB / 0.5846 GB, free: 6.844 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001038/0.6614, allocations: 3.938 kB / 0.5846 GB, free: 6.84 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001711/0.6616, allocations: 369.9 kB / 0.5849 GB, free: 6.473 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001564/0.6631, allocations: 1.109 MB / 0.586 GB, free: 5.363 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001617/0.6648, allocations: 1.267 MB / 0.5872 GB, free: 4.059 MB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003295/0.6681, allocations: 1.48 MB / 0.5887 GB, free: 2.582 MB / 394.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.131e-06/0.6681, allocations: 4 kB / 0.5887 GB, free: 2.578 MB / 394.7 MB
Notification: Performance of matching and sorting (n=201) (initialization): time 0.007852/0.676, allocations: 3.27 MB / 0.5919 GB, free: 15.29 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.721e-05/0.676, allocations: 8 kB / 0.5919 GB, free: 15.29 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.798e-05/0.676, allocations: 4 kB / 0.5919 GB, free: 15.28 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002506/0.6785, allocations: 398.4 kB / 0.5923 GB, free: 14.88 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001892/0.6805, allocations: 367.5 kB / 0.5926 GB, free: 14.52 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.0058/0.6863, allocations: 4.211 MB / 0.5967 GB, free: 10.05 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002037/0.6884, allocations: 155.7 kB / 0.5969 GB, free: 9.902 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0003569/0.6887, allocations: 75.92 kB / 0.597 GB, free: 9.828 MB / 410.7 MB
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         CH4.solution.n:DUMMY_STATE(flow=false min = 0.0 max = 0.0 unit = "mol" )  "Amount of the solution" type: Real
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         CH4.solution.I:VARIABLE(flow=false min = 0.0 max = 0.0 unit = "1" )  "Mole fraction based ionic strength of the solution" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 14
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (179):
 * Single equations (assignments): 174
 * Array equations: 2
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * 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: 2 {1 8,1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.0004765/0.6892, allocations: 143.7 kB / 0.5971 GB, free: 9.684 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0003586/0.6896, allocations: 110.6 kB / 0.5972 GB, free: 9.574 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01081/0.7004, allocations: 3.754 MB / 0.6009 GB, free: 5.789 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.009766/0.7102, allocations: 3.435 MB / 0.6042 GB, free: 2.34 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.389e-05/0.7103, allocations: 0 / 0.6042 GB, free: 2.34 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.95e-05/0.7103, allocations: 7.969 kB / 0.6042 GB, free: 2.332 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0161/0.7264, allocations: 7.609 MB / 0.6117 GB, free: 10.61 MB / 426.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.867e-05/0.7265, allocations: 8 kB / 0.6117 GB, free: 10.6 MB / 426.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001641/0.7281, allocations: 335.5 kB / 0.612 GB, free: 10.27 MB / 426.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005388/0.7335, allocations: 0.9092 MB / 0.6129 GB, free: 9.355 MB / 426.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001838/0.7338, allocations: 35.95 kB / 0.6129 GB, free: 9.32 MB / 426.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01024/0.744, allocations: 6.459 MB / 0.6192 GB, free: 2.598 MB / 426.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.005795/0.7498, allocations: 2.367 MB / 0.6215 GB, free: 108 kB / 426.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01267/0.7626, allocations: 5.694 MB / 0.6271 GB, free: 10.1 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0005695/0.7632, allocations: 215.6 kB / 0.6273 GB, free: 9.867 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003799/0.7636, allocations: 12 kB / 0.6273 GB, free: 9.855 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001508/0.7651, allocations: 83.86 kB / 0.6274 GB, free: 9.773 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0004341/0.7656, allocations: 156.9 kB / 0.6275 GB, free: 9.621 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001888/0.7658, allocations: 71.95 kB / 0.6276 GB, free: 9.551 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.0008276/0.7666, allocations: 475.1 kB / 0.6281 GB, free: 9.082 MB / 442.7 MB
Notification: Performance of sort global known variables: time 3.6e-07/0.7666, allocations: 4 kB / 0.6281 GB, free: 9.078 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.003961/0.7706, allocations: 0.9876 MB / 0.629 GB, free: 8.09 MB / 442.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 32
 * Number of states: 5 ($STATESET1.x[5],$STATESET1.x[4],$STATESET1.x[3],$STATESET1.x[2],$STATESET1.x[1])
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (167):
 * Single equations (assignments): 164
 * 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: 3
 * 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: 2 {1 8,6 9}
Notification: Performance of Backend phase and start with SimCode phase: time 0.002549/0.7731, allocations: 0.8736 MB / 0.6299 GB, free: 7.25 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.00449/0.7776, allocations: 2.801 MB / 0.6326 GB, free: 4.438 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.016e-05/0.7777, allocations: 4 kB / 0.6326 GB, free: 4.434 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.00315/0.7808, allocations: 1.791 MB / 0.6344 GB, free: 2.625 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002402/0.7833, allocations: 349.4 kB / 0.6347 GB, free: 2.285 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.008418/0.7917, allocations: 3.314 MB / 0.6379 GB, free: 14.84 MB / 458.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001028/0.7928, allocations: 1.224 MB / 0.6391 GB, free: 13.58 MB / 458.7 MB
Notification: Performance of simCode: alias equations: time 0.001418/0.7942, allocations: 249.5 kB / 0.6394 GB, free: 13.33 MB / 458.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0006134/0.7948, allocations: 147.3 kB / 0.6395 GB, free: 13.18 MB / 458.7 MB
Notification: Performance of SimCode: time 7.51e-07/0.7948, allocations: 0 / 0.6395 GB, free: 13.18 MB / 458.7 MB
Notification: Performance of Templates: time 0.3185/1.113, allocations: 33.06 MB / 0.6718 GB, free: 132 MB / 474.7 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)