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 0.1267/0.1267, allocations: 15.25 MB / 27.81 MB, free: 5.406 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001215/0.001215, allocations: 184.4 kB / 32.7 MB, free: 0.5273 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.413/1.413, allocations: 221.4 MB / 258.8 MB, free: 15.99 MB / 218.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008854/0.0008855, allocations: 107.2 kB / 314 MB, free: 15.74 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 3.652e-05/3.656e-05, allocations: 4 kB / 376.5 MB, free: 1.406 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3027/0.3028, allocations: 54.6 MB / 431.1 MB, free: 50.07 MB / 346.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.132/0.4348, allocations: 100.2 MB / 0.5188 GB, free: 15.1 MB / 394.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0002305/0.4351, allocations: 63.97 kB / 0.5189 GB, free: 15.04 MB / 394.7 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 0.1263/0.5614, allocations: 48.41 MB / 0.5661 GB, free: 14.74 MB / 442.7 MB
Notification: Performance of FrontEnd: time 2.024e-06/0.5615, allocations: 0 / 0.5661 GB, free: 14.74 MB / 442.7 MB
Notification: Performance of Transformations before backend: time 6.067e-05/0.5616, allocations: 27.94 kB / 0.5662 GB, free: 14.71 MB / 442.7 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 0.003681/0.5653, allocations: 1.543 MB / 0.5677 GB, free: 13.12 MB / 442.7 MB
Notification: Performance of prepare preOptimizeDAE: time 5.126e-05/0.5653, allocations: 12.03 kB / 0.5677 GB, free: 13.11 MB / 442.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001194/0.5665, allocations: 326.3 kB / 0.568 GB, free: 12.79 MB / 442.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001777/0.5683, allocations: 0.918 MB / 0.5689 GB, free: 11.82 MB / 442.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001192/0.5685, allocations: 111.9 kB / 0.569 GB, free: 11.71 MB / 442.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001904/0.5687, allocations: 111.9 kB / 0.5691 GB, free: 11.6 MB / 442.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002789/0.5715, allocations: 1.938 MB / 0.571 GB, free: 9.613 MB / 442.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.294e-05/0.5715, allocations: 4 kB / 0.571 GB, free: 9.609 MB / 442.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.000112/0.5716, allocations: 44 kB / 0.571 GB, free: 9.566 MB / 442.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.405e-05/0.5716, allocations: 24 kB / 0.5711 GB, free: 9.543 MB / 442.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.003461/0.5751, allocations: 2.796 MB / 0.5738 GB, free: 6.738 MB / 442.7 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 0.008353/0.5835, allocations: 5.75 MB / 0.5794 GB, free: 0.7891 MB / 442.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.2422/0.8257, allocations: 2.769 MB / 0.5821 GB, free: 99.07 MB / 442.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.001422/0.8272, allocations: 0.9861 MB / 0.5831 GB, free: 99.06 MB / 442.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0005652/0.8278, allocations: 333.3 kB / 0.5834 GB, free: 99.06 MB / 442.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.415e-05/0.8278, allocations: 46.95 kB / 0.5834 GB, free: 99.02 MB / 442.7 MB
Notification: Performance of pre-optimization done (n=129): time 3.547e-06/0.8278, allocations: 1 kB / 0.5834 GB, free: 99.02 MB / 442.7 MB
Notification: Performance of matching and sorting (n=180): time 0.02999/0.8578, allocations: 8.655 MB / 0.5919 GB, free: 98.41 MB / 442.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.007434/0.8653, allocations: 2.848 MB / 0.5947 GB, free: 96.93 MB / 442.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001324/0.8667, allocations: 0.6641 MB / 0.5953 GB, free: 96.8 MB / 442.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.000513/0.8672, allocations: 58.27 kB / 0.5954 GB, free: 96.77 MB / 442.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004352/0.8677, allocations: 463.8 kB / 0.5958 GB, free: 96.6 MB / 442.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0009071/0.8686, allocations: 0.6004 MB / 0.5964 GB, free: 96.29 MB / 442.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000147/0.8687, allocations: 32.34 kB / 0.5964 GB, free: 96.29 MB / 442.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001292/0.8689, allocations: 364.5 kB / 0.5968 GB, free: 95.98 MB / 442.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001765/0.8706, allocations: 1.163 MB / 0.5979 GB, free: 95.98 MB / 442.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001821/0.8725, allocations: 1.339 MB / 0.5992 GB, free: 95.86 MB / 442.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00182/0.8743, allocations: 1.27 MB / 0.6005 GB, free: 95.84 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.781e-06/0.8743, allocations: 1.5 kB / 0.6005 GB, free: 95.84 MB / 442.7 MB
Notification: Performance of matching and sorting (n=206) (initialization): time 0.007008/0.8813, allocations: 3.18 MB / 0.6036 GB, free: 95.67 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.987e-05/0.8814, allocations: 11.69 kB / 0.6036 GB, free: 95.67 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.933e-05/0.8814, allocations: 4.797 kB / 0.6036 GB, free: 95.67 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002901/0.8843, allocations: 438.4 kB / 0.604 GB, free: 95.64 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00221/0.8866, allocations: 385.4 kB / 0.6044 GB, free: 95.64 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005857/0.8924, allocations: 4.325 MB / 0.6086 GB, free: 92.39 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00235/0.8948, allocations: 178.3 kB / 0.6088 GB, free: 92.36 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002696/0.8951, allocations: 80.52 kB / 0.6089 GB, free: 92.35 MB / 442.7 MB
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 (184):
 * Single equations (assignments): 179
 * 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 0.0003628/0.8955, allocations: 190.3 kB / 0.609 GB, free: 92.2 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0004391/0.8959, allocations: 120.5 kB / 0.6091 GB, free: 92.13 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.008993/0.9049, allocations: 3.706 MB / 0.6128 GB, free: 90.88 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.007755/0.9127, allocations: 3.323 MB / 0.616 GB, free: 89.78 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.013e-05/0.9128, allocations: 3.469 kB / 0.616 GB, free: 89.78 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.1e-05/0.9128, allocations: 14.98 kB / 0.616 GB, free: 89.78 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01324/0.9261, allocations: 7.69 MB / 0.6235 GB, free: 86.71 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.303e-05/0.9261, allocations: 7.875 kB / 0.6235 GB, free: 86.71 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001626/0.9278, allocations: 345.2 kB / 0.6239 GB, free: 86.7 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005298/0.9331, allocations: 0.9515 MB / 0.6248 GB, free: 86.56 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000209/0.9333, allocations: 63.89 kB / 0.6249 GB, free: 86.53 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.008802/0.9421, allocations: 6.441 MB / 0.6312 GB, free: 82.32 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.005513/0.9477, allocations: 2.465 MB / 0.6336 GB, free: 80.54 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01009/0.9578, allocations: 5.636 MB / 0.6391 GB, free: 77.71 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0006149/0.9584, allocations: 219.7 kB / 0.6393 GB, free: 77.54 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003871/0.9588, allocations: 42.28 kB / 0.6393 GB, free: 77.52 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001589/0.9604, allocations: 120.4 kB / 0.6394 GB, free: 77.49 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0003665/0.9608, allocations: 164.7 kB / 0.6396 GB, free: 77.46 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001579/0.961, allocations: 71.2 kB / 0.6397 GB, free: 77.45 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.000684/0.9617, allocations: 0.5235 MB / 0.6402 GB, free: 77.2 MB / 442.7 MB
Notification: Performance of sort global known variables: time 2.41e-07/0.9617, allocations: 0 / 0.6402 GB, free: 77.2 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.003251/0.965, allocations: 1.009 MB / 0.6412 GB, free: 77.07 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 (172):
 * Single equations (assignments): 169
 * 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 0.001622/0.9666, allocations: 0.9029 MB / 0.642 GB, free: 76.81 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.003691/0.9703, allocations: 2.955 MB / 0.6449 GB, free: 75.56 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 6.001e-06/0.9703, allocations: 0 / 0.6449 GB, free: 75.56 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002477/0.9728, allocations: 1.871 MB / 0.6467 GB, free: 74.75 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001869/0.9747, allocations: 378.9 kB / 0.6471 GB, free: 74.66 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00724/0.982, allocations: 3.482 MB / 0.6505 GB, free: 71.87 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005682/0.9826, allocations: 1.226 MB / 0.6517 GB, free: 70.81 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.001281/0.9839, allocations: 251.3 kB / 0.6519 GB, free: 70.62 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0004646/0.9843, allocations: 151.7 kB / 0.6521 GB, free: 70.5 MB / 442.7 MB
Notification: Performance of SimCode: time 1.011e-06/0.9843, allocations: 0 / 0.6521 GB, free: 70.5 MB / 442.7 MB
Notification: Performance of Templates: time 0.04939/1.034, allocations: 36.52 MB / 0.6878 GB, free: 39.98 MB / 442.7 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)