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 0.1004/0.1004, allocations: 15.26 MB / 30.21 MB, free: 3.297 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001074/0.001074, allocations: 185.1 kB / 35.3 MB, free: 2.375 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.367/1.367, allocations: 223.2 MB / 263.4 MB, free: 6.324 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009656/0.0009656, allocations: 94.44 kB / 318.8 MB, free: 3.254 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003214/0.0003214, allocations: 7.594 kB / 383.9 MB, free: 50.5 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1024/0.1027, allocations: 54.64 MB / 438.6 MB, free: 344 kB / 298.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.3864/0.4892, allocations: 100.2 MB / 0.5262 GB, free: 15.61 MB / 378.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.000291/0.4896, allocations: 71.8 kB / 0.5262 GB, free: 15.61 MB / 378.7 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 0.1113/0.6009, allocations: 48.57 MB / 0.5737 GB, free: 20.25 MB / 394.7 MB
Notification: Performance of FrontEnd: time 2.435e-06/0.601, allocations: 4 kB / 0.5737 GB, free: 20.25 MB / 394.7 MB
Notification: Performance of Transformations before backend: time 0.0001222/0.6011, allocations: 23.38 kB / 0.5737 GB, free: 20.25 MB / 394.7 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 0.004693/0.6058, allocations: 1.66 MB / 0.5753 GB, free: 19.12 MB / 394.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.813e-05/0.6059, allocations: 11.75 kB / 0.5753 GB, free: 19.12 MB / 394.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001513/0.6074, allocations: 328.5 kB / 0.5756 GB, free: 18.99 MB / 394.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.002192/0.6096, allocations: 0.9146 MB / 0.5765 GB, free: 18.46 MB / 394.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001375/0.6097, allocations: 109.9 kB / 0.5766 GB, free: 18.43 MB / 394.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0003881/0.6101, allocations: 116.9 kB / 0.5767 GB, free: 18.42 MB / 394.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.003132/0.6133, allocations: 1.967 MB / 0.5787 GB, free: 17.97 MB / 394.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.846e-05/0.6133, allocations: 4 kB / 0.5787 GB, free: 17.97 MB / 394.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.000134/0.6135, allocations: 45.75 kB / 0.5787 GB, free: 17.97 MB / 394.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.456e-05/0.6135, allocations: 27.19 kB / 0.5787 GB, free: 17.97 MB / 394.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002942/0.6164, allocations: 2.831 MB / 0.5815 GB, free: 17.56 MB / 394.7 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 0.007427/0.6239, allocations: 5.741 MB / 0.5871 GB, free: 15.09 MB / 394.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003055/0.627, allocations: 2.798 MB / 0.5898 GB, free: 13.65 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0005003/0.6275, allocations: 337.2 kB / 0.5902 GB, free: 13.5 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.284e-05/0.6275, allocations: 43.75 kB / 0.5902 GB, free: 13.46 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=129): time 3.026e-06/0.6275, allocations: 0 / 0.5902 GB, free: 13.46 MB / 394.7 MB
Notification: Performance of matching and sorting (n=170): time 0.02554/0.6531, allocations: 8.441 MB / 0.5984 GB, free: 5.816 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.507e-05/0.6532, allocations: 69.41 kB / 0.5985 GB, free: 5.738 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00093/0.6541, allocations: 0.6678 MB / 0.5992 GB, free: 5.066 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.000123/0.6542, allocations: 53.7 kB / 0.5992 GB, free: 5.008 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003139/0.6545, allocations: 469.2 kB / 0.5997 GB, free: 4.543 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0004673/0.655, allocations: 0.5659 MB / 0.6002 GB, free: 3.969 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.849e-05/0.6551, allocations: 32 kB / 0.6002 GB, free: 3.938 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001502/0.6553, allocations: 361.9 kB / 0.6006 GB, free: 3.578 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001278/0.6566, allocations: 0.9839 MB / 0.6015 GB, free: 2.594 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001395/0.658, allocations: 1.162 MB / 0.6027 GB, free: 1.391 MB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001433/0.6594, allocations: 1.084 MB / 0.6037 GB, free: 320 kB / 394.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.136e-06/0.6594, allocations: 0 / 0.6037 GB, free: 320 kB / 394.7 MB
Notification: Performance of matching and sorting (n=191) (initialization): time 0.006651/0.6661, allocations: 2.814 MB / 0.6065 GB, free: 13.48 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.897e-05/0.6661, allocations: 8 kB / 0.6065 GB, free: 13.47 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.8e-05/0.6661, allocations: 7.953 kB / 0.6065 GB, free: 13.46 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003315/0.6695, allocations: 466.3 kB / 0.6069 GB, free: 13 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001844/0.6713, allocations: 351.5 kB / 0.6073 GB, free: 12.66 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.006465/0.6778, allocations: 4.411 MB / 0.6116 GB, free: 7.953 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001341/0.6792, allocations: 67.88 kB / 0.6117 GB, free: 7.887 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001276/0.6793, allocations: 63.97 kB / 0.6117 GB, free: 7.824 MB / 410.7 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 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (177):
 * Single equations (assignments): 174
 * 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 8,1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.0006281/0.6799, allocations: 289.6 kB / 0.612 GB, free: 7.531 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002033/0.6801, allocations: 118.6 kB / 0.6121 GB, free: 7.414 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.006846/0.687, allocations: 2.965 MB / 0.615 GB, free: 4.43 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.496e-05/0.6871, allocations: 19.94 kB / 0.615 GB, free: 4.41 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.174e-06/0.6871, allocations: 4 kB / 0.615 GB, free: 4.406 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.901e-05/0.6871, allocations: 7.969 kB / 0.615 GB, free: 4.398 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01029/0.6974, allocations: 6.016 MB / 0.6209 GB, free: 14.24 MB / 426.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.099e-05/0.6974, allocations: 8 kB / 0.6209 GB, free: 14.23 MB / 426.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001622/0.6991, allocations: 339.5 kB / 0.6212 GB, free: 13.9 MB / 426.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00313/0.7022, allocations: 462.3 kB / 0.6217 GB, free: 13.44 MB / 426.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001223/0.7023, allocations: 47.98 kB / 0.6217 GB, free: 13.39 MB / 426.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.006001/0.7083, allocations: 4.349 MB / 0.626 GB, free: 8.75 MB / 426.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.255e-06/0.7084, allocations: 11.94 kB / 0.626 GB, free: 8.738 MB / 426.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.008772/0.7172, allocations: 4.676 MB / 0.6305 GB, free: 3.824 MB / 426.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0004851/0.7177, allocations: 195.6 kB / 0.6307 GB, free: 3.613 MB / 426.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003145/0.718, allocations: 43.98 kB / 0.6308 GB, free: 3.57 MB / 426.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001116/0.7191, allocations: 59.98 kB / 0.6308 GB, free: 3.512 MB / 426.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002825/0.7194, allocations: 144.9 kB / 0.631 GB, free: 3.371 MB / 426.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001265/0.7196, allocations: 60.11 kB / 0.631 GB, free: 3.312 MB / 426.7 MB
Notification: Performance of sorting global known variables: time 0.0007852/0.7204, allocations: 0.5264 MB / 0.6315 GB, free: 2.781 MB / 426.7 MB
Notification: Performance of sort global known variables: time 1.854e-06/0.7204, allocations: 0 / 0.6315 GB, free: 2.781 MB / 426.7 MB
Notification: Performance of remove unused functions: time 0.00283/0.7232, allocations: 0.8078 MB / 0.6323 GB, free: 1.973 MB / 426.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 25
 * 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 (173):
 * Single equations (assignments): 170
 * 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 3,1 8}
Notification: Performance of Backend phase and start with SimCode phase: time 0.0025/0.7257, allocations: 0.8926 MB / 0.6332 GB, free: 1.066 MB / 426.7 MB
Notification: Performance of simCode: created initialization part: time 0.00411/0.7299, allocations: 2.591 MB / 0.6357 GB, free: 14.45 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.53e-06/0.7299, allocations: 0 / 0.6357 GB, free: 14.45 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002041/0.7319, allocations: 1.482 MB / 0.6372 GB, free: 12.95 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001882/0.7338, allocations: 365.7 kB / 0.6375 GB, free: 12.59 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.005484/0.7393, allocations: 3.574 MB / 0.641 GB, free: 8.918 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0008857/0.7402, allocations: 1.175 MB / 0.6422 GB, free: 7.711 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.001113/0.7413, allocations: 221.8 kB / 0.6424 GB, free: 7.492 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000425/0.7418, allocations: 127.4 kB / 0.6425 GB, free: 7.367 MB / 442.7 MB
Notification: Performance of SimCode: time 1.173e-06/0.7418, allocations: 0 / 0.6425 GB, free: 7.367 MB / 442.7 MB
Notification: Performance of Templates: time 0.04949/0.7913, allocations: 31.63 MB / 0.6734 GB, free: 7.957 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)