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")
[<interactive>:1:1-1:32:writable] Error: Class GC_set_max_heap_size not found in scope <global scope> (looking for a function or record).
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.06384/0.06384, allocations: 15.27 MB / 22.55 MB, free: 1.086 MB / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0009131/0.0009131, allocations: 191.5 kB / 27.31 MB, free: 6.168 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.096/1.096, allocations: 221.4 MB / 253.3 MB, free: 10.54 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008505/0.0008505, allocations: 92.73 kB / 308.4 MB, free: 10.62 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 6.743e-06/6.763e-06, allocations: 8.781 kB / 369 MB, free: 53.95 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.06831/0.06833, allocations: 54.63 MB / 423.7 MB, free: 14.32 MB / 298.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.2291/0.2975, allocations: 99.42 MB / 0.5108 GB, free: 8.266 MB / 362.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0001464/0.2977, allocations: 65.22 kB / 0.5109 GB, free: 8.266 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: time 0.1073/0.405, allocations: 47.74 MB / 0.5575 GB, free: 11.29 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 5.784e-05/0.4051, allocations: 24.31 kB / 0.5575 GB, free: 11.29 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 0.003283/0.4084, allocations: 1.553 MB / 0.559 GB, free: 10.17 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.263e-05/0.4084, allocations: 13.34 kB / 0.5591 GB, free: 10.17 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001352/0.4098, allocations: 354.5 kB / 0.5594 GB, free: 9.973 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001879/0.4117, allocations: 0.9045 MB / 0.5603 GB, free: 9.289 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001031/0.4118, allocations: 73.28 kB / 0.5603 GB, free: 9.254 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001907/0.412, allocations: 63.88 kB / 0.5604 GB, free: 9.254 MB / 378.7 MB
Notification: Performance of preOpt removeEqualFunctionCalls (simulation): time 0.003571/0.4156, allocations: 2.753 MB / 0.5631 GB, free: 7.008 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002053/0.4176, allocations: 1.473 MB / 0.5645 GB, free: 5.492 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.194e-05/0.4177, allocations: 0 / 0.5645 GB, free: 5.492 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.336e-05/0.4177, allocations: 0 / 0.5645 GB, free: 5.492 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.376e-05/0.4178, allocations: 24 kB / 0.5646 GB, free: 5.469 MB / 378.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.008062/0.4258, allocations: 5.662 MB / 0.5701 GB, free: 15.68 MB / 394.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002224/0.4281, allocations: 1.977 MB / 0.572 GB, free: 13.7 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.001044/0.4291, allocations: 0.9505 MB / 0.5729 GB, free: 12.75 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.000432/0.4296, allocations: 326.9 kB / 0.5733 GB, free: 12.44 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.328e-05/0.4296, allocations: 47.86 kB / 0.5733 GB, free: 12.38 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=129): time 2.745e-06/0.4296, allocations: 4 kB / 0.5733 GB, free: 12.38 MB / 394.7 MB
Notification: Performance of matching and sorting (n=175): time 0.02944/0.4591, allocations: 8.7 MB / 0.5818 GB, free: 3.668 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.666e-05/0.4591, allocations: 69.41 kB / 0.5819 GB, free: 3.586 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000733/0.4599, allocations: 0.5974 MB / 0.5825 GB, free: 2.984 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 8.498e-05/0.46, allocations: 29.64 kB / 0.5825 GB, free: 2.949 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002043/0.4602, allocations: 353.2 kB / 0.5828 GB, free: 2.598 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0005509/0.4607, allocations: 0.5541 MB / 0.5834 GB, free: 2.035 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.053e-05/0.4608, allocations: 0 / 0.5834 GB, free: 2.035 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001379/0.461, allocations: 369.8 kB / 0.5837 GB, free: 1.668 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001374/0.4623, allocations: 1.125 MB / 0.5848 GB, free: 0.543 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001474/0.4638, allocations: 1.28 MB / 0.5861 GB, free: 15.23 MB / 410.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003074/0.4669, allocations: 1.511 MB / 0.5875 GB, free: 13.72 MB / 410.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.126e-06/0.4669, allocations: 3.938 kB / 0.5875 GB, free: 13.71 MB / 410.7 MB
Notification: Performance of matching and sorting (n=201) (initialization): time 0.007618/0.4745, allocations: 3.35 MB / 0.5908 GB, free: 10.35 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.317e-05/0.4746, allocations: 4 kB / 0.5908 GB, free: 10.34 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.304e-05/0.4746, allocations: 7.984 kB / 0.5908 GB, free: 10.34 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002659/0.4773, allocations: 402.5 kB / 0.5912 GB, free: 9.934 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001902/0.4792, allocations: 375.4 kB / 0.5916 GB, free: 9.566 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005602/0.4848, allocations: 4.159 MB / 0.5956 GB, free: 5.145 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001628/0.4864, allocations: 103.8 kB / 0.5957 GB, free: 5.043 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001828/0.4866, allocations: 75.92 kB / 0.5958 GB, free: 4.969 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 0.0002965/0.4869, allocations: 141.3 kB / 0.5959 GB, free: 4.828 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002307/0.4872, allocations: 114.5 kB / 0.596 GB, free: 4.715 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01054/0.4977, allocations: 3.816 MB / 0.5998 GB, free: 0.8789 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.009418/0.5071, allocations: 3.459 MB / 0.6031 GB, free: 13.41 MB / 426.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.024e-05/0.5072, allocations: 4 kB / 0.6032 GB, free: 13.4 MB / 426.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.681e-05/0.5072, allocations: 15.88 kB / 0.6032 GB, free: 13.39 MB / 426.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01481/0.522, allocations: 7.581 MB / 0.6106 GB, free: 5.688 MB / 426.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.103e-05/0.522, allocations: 11.94 kB / 0.6106 GB, free: 5.676 MB / 426.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00171/0.5238, allocations: 348.3 kB / 0.6109 GB, free: 5.336 MB / 426.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005627/0.5294, allocations: 0.8958 MB / 0.6118 GB, free: 4.43 MB / 426.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001282/0.5295, allocations: 35.95 kB / 0.6118 GB, free: 4.395 MB / 426.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009979/0.5395, allocations: 6.358 MB / 0.618 GB, free: 13.77 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.005881/0.5454, allocations: 2.308 MB / 0.6203 GB, free: 11.34 MB / 442.7 MB
Notification: Performance of postOpt detectJacobianSparsePattern (simulation): time 0.01134/0.5568, allocations: 5.771 MB / 0.6259 GB, free: 5.262 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003562/0.5571, allocations: 211.6 kB / 0.6261 GB, free: 5.035 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0002222/0.5574, allocations: 15.98 kB / 0.6261 GB, free: 5.02 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001132/0.5585, allocations: 63.83 kB / 0.6262 GB, free: 4.957 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000196/0.5587, allocations: 129.1 kB / 0.6263 GB, free: 4.832 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001268/0.5588, allocations: 71.91 kB / 0.6264 GB, free: 4.762 MB / 442.7 MB
Notification: Performance of sort global known variables: time 0.0005056/0.5594, allocations: 471.1 kB / 0.6268 GB, free: 4.305 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.002486/0.5618, allocations: 0.9759 MB / 0.6278 GB, free: 3.328 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 0.001532/0.5634, allocations: 0.8891 MB / 0.6287 GB, free: 2.473 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.004126/0.5675, allocations: 2.879 MB / 0.6315 GB, free: 15.58 MB / 458.7 MB
Notification: Performance of simCode: created event and clocks part: time 4.378e-06/0.5675, allocations: 4 kB / 0.6315 GB, free: 15.57 MB / 458.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002433/0.57, allocations: 1.743 MB / 0.6332 GB, free: 13.82 MB / 458.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001455/0.5714, allocations: 336.5 kB / 0.6335 GB, free: 13.49 MB / 458.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.007688/0.5791, allocations: 3.234 MB / 0.6367 GB, free: 10.13 MB / 458.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001271/0.5804, allocations: 1.375 MB / 0.638 GB, free: 8.723 MB / 458.7 MB
Notification: Performance of SimCode: time 2.9e-07/0.5804, allocations: 0 / 0.638 GB, free: 8.723 MB / 458.7 MB
Notification: Performance of Templates: time 0.1451/0.7255, allocations: 35.74 MB / 0.6729 GB, free: 167.1 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)