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 0.001064/0.001064, allocations: 115 kB / 16.37 MB, free: 6.016 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001014/0.001014, allocations: 193.2 kB / 17.31 MB, free: 5.609 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.309/1.309, allocations: 222.9 MB / 241 MB, free: 15 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08332/0.08332, allocations: 15.31 MB / 306.5 MB, free: 15.41 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001252/0.001252, allocations: 65.78 kB / 371.8 MB, free: 50.71 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09199/0.09326, allocations: 53.61 MB / 425.4 MB, free: 13.29 MB / 302.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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:4740:7-4740:66: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 0.03128/0.1246, allocations: 25.19 MB / 450.6 MB, free: 4.207 MB / 318.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01845/0.143, allocations: 16.67 MB / 467.2 MB, free: 3.473 MB / 334.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001038/0.1441, allocations: 15.94 kB / 467.2 MB, free: 3.457 MB / 334.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009909/0.1451, allocations: 325.5 kB / 467.6 MB, free: 3.137 MB / 334.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.003713/0.1489, allocations: 1.482 MB / 469 MB, free: 1.645 MB / 334.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005038/0.1539, allocations: 1.984 MB / 471 MB, free: 15.65 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0019/0.1558, allocations: 1.545 MB / 472.6 MB, free: 14.1 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0009476/0.1568, allocations: 0.8552 MB / 473.4 MB, free: 13.23 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009731/0.1578, allocations: 0.7715 MB / 474.2 MB, free: 12.46 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001015/0.1588, allocations: 0.845 MB / 475 MB, free: 11.61 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001677/0.159, allocations: 136 kB / 475.2 MB, free: 11.48 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004953/0.1639, allocations: 1.786 MB / 477 MB, free: 9.688 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0003018/0.1643, allocations: 323 kB / 477.3 MB, free: 9.371 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0007163/0.165, allocations: 0.6884 MB / 478 MB, free: 8.68 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.00546/0.1704, allocations: 3.328 MB / 481.3 MB, free: 5.34 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.399e-06/0.1705, allocations: 0 / 481.3 MB, free: 5.34 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.976e-06/0.1705, allocations: 3.984 kB / 481.3 MB, free: 5.336 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.826e-05/0.1705, allocations: 0 / 481.3 MB, free: 5.336 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 0.002952/0.1735, allocations: 1.805 MB / 483.1 MB, free: 3.477 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.82e-05/0.1735, allocations: 12.03 kB / 483.1 MB, free: 3.465 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001121/0.1746, allocations: 267 kB / 483.4 MB, free: 3.203 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001081/0.1757, allocations: 0.6648 MB / 484 MB, free: 2.496 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001043/0.1758, allocations: 112.4 kB / 484.2 MB, free: 2.379 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002027/0.1761, allocations: 116.3 kB / 484.3 MB, free: 2.266 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002062/0.1781, allocations: 1.341 MB / 485.6 MB, free: 0.8789 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.334e-05/0.1782, allocations: 0 / 485.6 MB, free: 0.8789 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001067/0.1783, allocations: 44 kB / 485.6 MB, free: 0.8359 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.393e-05/0.1783, allocations: 28 kB / 485.7 MB, free: 0.8086 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002624/0.1809, allocations: 1.687 MB / 487.4 MB, free: 15.11 MB / 366.1 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 0.006605/0.1875, allocations: 4.286 MB / 491.7 MB, free: 10.61 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003515/0.1911, allocations: 2.279 MB / 493.9 MB, free: 8.25 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008905/0.192, allocations: 0.5967 MB / 494.5 MB, free: 7.652 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.007433/0.1994, allocations: 5.381 MB / 499.9 MB, free: 1.645 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.32e-05/0.1995, allocations: 43.16 kB / 499.9 MB, free: 1.594 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.595e-06/0.1995, allocations: 7.875 kB / 500 MB, free: 1.586 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01498/0.2145, allocations: 3.575 MB / 0.4917 GB, free: 13.93 MB / 382.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.545e-05/0.2146, allocations: 60.41 kB / 0.4918 GB, free: 13.86 MB / 382.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006852/0.2153, allocations: 0.59 MB / 0.4924 GB, free: 13.26 MB / 382.1 MB
Notification: Performance of collectPreVariables (initialization): time 5.961e-05/0.2153, allocations: 37.7 kB / 0.4924 GB, free: 13.21 MB / 382.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003398/0.2157, allocations: 0.5333 MB / 0.4929 GB, free: 12.67 MB / 382.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002561/0.2159, allocations: 335.2 kB / 0.4932 GB, free: 12.34 MB / 382.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003112/0.2162, allocations: 234.8 kB / 0.4935 GB, free: 12.11 MB / 382.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001641/0.2164, allocations: 394.7 kB / 0.4938 GB, free: 11.71 MB / 382.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00061/0.217, allocations: 358.5 kB / 0.4942 GB, free: 11.36 MB / 382.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008627/0.2179, allocations: 0.7479 MB / 0.4949 GB, free: 10.43 MB / 382.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001548/0.2195, allocations: 1.2 MB / 0.4961 GB, free: 9.059 MB / 382.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.779e-06/0.2195, allocations: 0 / 0.4961 GB, free: 9.059 MB / 382.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004026/0.2235, allocations: 1.474 MB / 0.4975 GB, free: 7.57 MB / 382.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.589e-05/0.2235, allocations: 18.48 kB / 0.4975 GB, free: 7.555 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.587e-05/0.2236, allocations: 12 kB / 0.4976 GB, free: 7.543 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002015/0.2256, allocations: 241.8 kB / 0.4978 GB, free: 7.301 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001433/0.227, allocations: 327.5 kB / 0.4981 GB, free: 6.98 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005405/0.2324, allocations: 3.861 MB / 0.5019 GB, free: 2.844 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008672/0.2333, allocations: 40 kB / 0.5019 GB, free: 2.805 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001099/0.2335, allocations: 63.98 kB / 0.502 GB, free: 2.742 MB / 382.1 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 (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.000446/0.2339, allocations: 285.4 kB / 0.5022 GB, free: 2.453 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001707/0.2341, allocations: 86.91 kB / 0.5023 GB, free: 2.367 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004011/0.2381, allocations: 1.34 MB / 0.5036 GB, free: 1.012 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.182e-05/0.2381, allocations: 15.94 kB / 0.5036 GB, free: 0.9961 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.587e-06/0.2381, allocations: 0 / 0.5036 GB, free: 0.9961 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.897e-06/0.2382, allocations: 3.984 kB / 0.5036 GB, free: 0.9922 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.192/0.4302, allocations: 1.069 MB / 0.5047 GB, free: 77.91 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.953e-05/0.4303, allocations: 2.844 kB / 0.5047 GB, free: 77.91 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001322/0.4316, allocations: 216.4 kB / 0.5049 GB, free: 77.91 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001906/0.4335, allocations: 229.8 kB / 0.5051 GB, free: 77.9 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000122/0.4336, allocations: 34.8 kB / 0.5052 GB, free: 77.9 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004291/0.4379, allocations: 3.763 MB / 0.5088 GB, free: 74.96 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.264e-06/0.438, allocations: 3.188 kB / 0.5088 GB, free: 74.96 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004434/0.4424, allocations: 1.742 MB / 0.5105 GB, free: 74.77 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002032/0.4426, allocations: 154.2 kB / 0.5107 GB, free: 74.67 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001149/0.4427, allocations: 20.3 kB / 0.5107 GB, free: 74.67 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005073/0.4433, allocations: 22.23 kB / 0.5107 GB, free: 74.67 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001924/0.4435, allocations: 78.61 kB / 0.5108 GB, free: 74.67 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.511e-05/0.4435, allocations: 41.83 kB / 0.5108 GB, free: 74.67 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0003857/0.4439, allocations: 393.4 kB / 0.5112 GB, free: 74.58 MB / 382.1 MB
Notification: Performance of sort global known variables: time 5.11e-07/0.4439, allocations: 0 / 0.5112 GB, free: 74.58 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.00162/0.4456, allocations: 0.6685 MB / 0.5119 GB, free: 74.58 MB / 382.1 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 (not torn): 0
 * Torn equation systems: 2
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 1 system
   {(1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 1 system
   {(1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001256/0.4468, allocations: 0.8053 MB / 0.5126 GB, free: 74.46 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.001902/0.4487, allocations: 1.256 MB / 0.5139 GB, free: 73.96 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.765e-06/0.4488, allocations: 1.25 kB / 0.5139 GB, free: 73.96 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0009899/0.4498, allocations: 0.7469 MB / 0.5146 GB, free: 73.55 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009177/0.4507, allocations: 200 kB / 0.5148 GB, free: 73.5 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003021/0.4537, allocations: 1.976 MB / 0.5167 GB, free: 72.52 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006159/0.4543, allocations: 1.036 MB / 0.5177 GB, free: 71.81 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0008399/0.4552, allocations: 225.5 kB / 0.518 GB, free: 71.8 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003499/0.4555, allocations: 165.4 kB / 0.5181 GB, free: 71.78 MB / 382.1 MB
Notification: Performance of SimCode: time 9.22e-07/0.4556, allocations: 0 / 0.5181 GB, free: 71.78 MB / 382.1 MB
Notification: Performance of Templates: time 0.02815/0.4837, allocations: 23.44 MB / 0.541 GB, free: 55.86 MB / 382.1 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 -s gbode -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)