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 0.001134/0.001133, allocations: 112.6 kB / 16.37 MB, free: 6 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001321/0.001321, allocations: 196 kB / 17.31 MB, free: 5.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.357/1.357, allocations: 222.9 MB / 241 MB, free: 15.18 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08154/0.08154, allocations: 15.3 MB / 306.5 MB, free: 15.45 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001295/0.001295, allocations: 65.39 kB / 371.8 MB, free: 50.86 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1395/0.1408, allocations: 53.62 MB / 425.4 MB, free: 13.35 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 0.03579/0.1766, allocations: 25.19 MB / 450.6 MB, free: 4.277 MB / 318.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02269/0.1993, allocations: 16.67 MB / 467.2 MB, free: 3.539 MB / 334.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001311/0.2007, allocations: 11.94 kB / 467.2 MB, free: 3.527 MB / 334.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001183/0.2019, allocations: 337.5 kB / 467.6 MB, free: 3.195 MB / 334.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005293/0.2072, allocations: 1.47 MB / 469 MB, free: 1.715 MB / 334.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.006795/0.2141, allocations: 1.988 MB / 471 MB, free: 15.71 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002693/0.2168, allocations: 1.545 MB / 472.6 MB, free: 14.16 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001037/0.2178, allocations: 0.859 MB / 473.4 MB, free: 13.29 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009079/0.2187, allocations: 0.7715 MB / 474.2 MB, free: 12.52 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001155/0.2199, allocations: 0.845 MB / 475 MB, free: 11.67 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001977/0.2201, allocations: 136 kB / 475.2 MB, free: 11.54 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007881/0.228, allocations: 1.775 MB / 477 MB, free: 9.762 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.000435/0.2285, allocations: 335 kB / 477.3 MB, free: 9.434 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009271/0.2294, allocations: 0.6806 MB / 478 MB, free: 8.75 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.009435/0.2389, allocations: 3.336 MB / 481.3 MB, free: 5.402 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.623e-06/0.2389, allocations: 3.938 kB / 481.3 MB, free: 5.398 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.863e-06/0.2389, allocations: 4 kB / 481.3 MB, free: 5.395 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 7.983e-05/0.239, allocations: 0 / 481.3 MB, free: 5.395 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 0.00504/0.244, allocations: 1.805 MB / 483.1 MB, free: 3.535 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.942e-05/0.2441, allocations: 8.031 kB / 483.1 MB, free: 3.527 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001521/0.2456, allocations: 267 kB / 483.4 MB, free: 3.266 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001382/0.247, allocations: 0.6726 MB / 484.1 MB, free: 2.551 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001245/0.2472, allocations: 108.4 kB / 484.2 MB, free: 2.438 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002271/0.2474, allocations: 112.3 kB / 484.3 MB, free: 2.328 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002304/0.2497, allocations: 1.341 MB / 485.6 MB, free: 0.9414 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.589e-05/0.2497, allocations: 3.938 kB / 485.6 MB, free: 0.9375 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001068/0.2499, allocations: 47.98 kB / 485.7 MB, free: 0.8906 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.149e-05/0.2499, allocations: 24 kB / 485.7 MB, free: 0.8672 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002585/0.2525, allocations: 1.691 MB / 487.4 MB, free: 15.17 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 0.007611/0.2601, allocations: 4.286 MB / 491.7 MB, free: 10.67 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.00353/0.2636, allocations: 2.279 MB / 493.9 MB, free: 8.305 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008829/0.2645, allocations: 0.5889 MB / 494.5 MB, free: 7.715 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.007261/0.2718, allocations: 5.38 MB / 499.9 MB, free: 1.707 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.414e-05/0.2719, allocations: 43.22 kB / 500 MB, free: 1.656 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 4.559e-06/0.2719, allocations: 0 / 500 MB, free: 1.656 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01556/0.2875, allocations: 3.578 MB / 0.4917 GB, free: 14 MB / 382.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.525e-05/0.2876, allocations: 64.41 kB / 0.4918 GB, free: 13.92 MB / 382.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0008603/0.2884, allocations: 0.5861 MB / 0.4924 GB, free: 13.32 MB / 382.1 MB
Notification: Performance of collectPreVariables (initialization): time 8.73e-05/0.2885, allocations: 41.7 kB / 0.4924 GB, free: 13.28 MB / 382.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004436/0.289, allocations: 0.5294 MB / 0.4929 GB, free: 12.74 MB / 382.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003024/0.2893, allocations: 335.2 kB / 0.4932 GB, free: 12.41 MB / 382.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003322/0.2896, allocations: 226.8 kB / 0.4935 GB, free: 12.18 MB / 382.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001956/0.2898, allocations: 390.7 kB / 0.4938 GB, free: 11.79 MB / 382.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006314/0.2905, allocations: 362.5 kB / 0.4942 GB, free: 11.43 MB / 382.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0009315/0.2914, allocations: 0.744 MB / 0.4949 GB, free: 10.51 MB / 382.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001614/0.2931, allocations: 1.212 MB / 0.4961 GB, free: 9.125 MB / 382.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.123e-06/0.2931, allocations: 4 kB / 0.4961 GB, free: 9.121 MB / 382.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004099/0.2972, allocations: 1.467 MB / 0.4975 GB, free: 7.641 MB / 382.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.491e-05/0.2972, allocations: 11.28 kB / 0.4975 GB, free: 7.633 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.219e-05/0.2973, allocations: 16 kB / 0.4975 GB, free: 7.617 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001966/0.2992, allocations: 249.4 kB / 0.4978 GB, free: 7.367 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001433/0.3007, allocations: 327.5 kB / 0.4981 GB, free: 7.047 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005854/0.3065, allocations: 3.869 MB / 0.5019 GB, free: 2.902 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001023/0.3076, allocations: 40 kB / 0.5019 GB, free: 2.863 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.000142/0.3077, allocations: 67.98 kB / 0.502 GB, free: 2.797 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 0.000554/0.3083, allocations: 285.4 kB / 0.5022 GB, free: 2.508 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001795/0.3085, allocations: 82.97 kB / 0.5023 GB, free: 2.426 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004048/0.3125, allocations: 1.336 MB / 0.5036 GB, free: 1.074 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.026e-05/0.3126, allocations: 11.94 kB / 0.5036 GB, free: 1.062 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.817e-06/0.3126, allocations: 0 / 0.5036 GB, free: 1.062 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.055e-05/0.3126, allocations: 3.984 kB / 0.5036 GB, free: 1.059 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.2918/0.6044, allocations: 1.065 MB / 0.5047 GB, free: 77.84 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.09e-05/0.6044, allocations: 0 / 0.5047 GB, free: 77.84 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001357/0.6058, allocations: 218.8 kB / 0.5049 GB, free: 77.84 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.0017/0.6075, allocations: 234.1 kB / 0.5051 GB, free: 77.83 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001102/0.6076, allocations: 29.14 kB / 0.5051 GB, free: 77.83 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004263/0.6119, allocations: 3.768 MB / 0.5088 GB, free: 74.89 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.087e-06/0.6119, allocations: 1.375 kB / 0.5088 GB, free: 74.89 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004523/0.6165, allocations: 1.736 MB / 0.5105 GB, free: 74.7 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002565/0.6167, allocations: 153.9 kB / 0.5107 GB, free: 74.6 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001179/0.6169, allocations: 23.03 kB / 0.5107 GB, free: 74.6 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0004719/0.6173, allocations: 24.16 kB / 0.5107 GB, free: 74.6 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002177/0.6176, allocations: 82.41 kB / 0.5108 GB, free: 74.6 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.012e-05/0.6177, allocations: 39.61 kB / 0.5108 GB, free: 74.6 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0004383/0.6181, allocations: 391 kB / 0.5112 GB, free: 74.51 MB / 382.1 MB
Notification: Performance of sort global known variables: time 2.5e-07/0.6181, allocations: 2.688 kB / 0.5112 GB, free: 74.51 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.001971/0.6201, allocations: 0.6687 MB / 0.5119 GB, free: 74.51 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 0.001731/0.6218, allocations: 0.8066 MB / 0.5126 GB, free: 74.39 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002569/0.6244, allocations: 1.255 MB / 0.5139 GB, free: 73.81 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.689e-06/0.6244, allocations: 0 / 0.5139 GB, free: 73.81 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001152/0.6256, allocations: 0.7425 MB / 0.5146 GB, free: 73.41 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001102/0.6267, allocations: 206.4 kB / 0.5148 GB, free: 73.34 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003431/0.6301, allocations: 1.969 MB / 0.5167 GB, free: 72.37 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009429/0.6311, allocations: 1.04 MB / 0.5177 GB, free: 71.66 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.001/0.6321, allocations: 231.1 kB / 0.518 GB, free: 71.65 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003752/0.6325, allocations: 165.5 kB / 0.5181 GB, free: 71.63 MB / 382.1 MB
Notification: Performance of SimCode: time 1.603e-06/0.6325, allocations: 0 / 0.5181 GB, free: 71.63 MB / 382.1 MB
Notification: Performance of Templates: time 0.035/0.6675, allocations: 23.44 MB / 0.541 GB, free: 55.79 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 cvode -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)