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 0.001296/0.001296, allocations: 105.6 kB / 16.41 MB, free: 6.496 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001051/0.001051, allocations: 189.6 kB / 17.34 MB, free: 5.766 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.318/1.318, allocations: 222.9 MB / 241 MB, free: 15.14 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.07509/0.07509, allocations: 15.31 MB / 306.5 MB, free: 15.41 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001226/0.001226, allocations: 64.27 kB / 425.9 MB, free: 11.46 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09133/0.09257, allocations: 53.62 MB / 479.5 MB, free: 5.789 MB / 350.1 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 0.03511/0.1277, allocations: 25.38 MB / 0.493 GB, free: 12.5 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2179/0.3456, allocations: 16.66 MB / 0.5093 GB, free: 18.19 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0006903/0.3464, allocations: 11.16 kB / 0.5093 GB, free: 18.19 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008586/0.3472, allocations: 338.5 kB / 0.5096 GB, free: 18.19 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.003853/0.3511, allocations: 1.485 MB / 0.5111 GB, free: 18.18 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004998/0.3561, allocations: 1.98 MB / 0.513 GB, free: 17.57 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002034/0.3582, allocations: 1.546 MB / 0.5145 GB, free: 17.27 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.00108/0.3593, allocations: 0.8482 MB / 0.5153 GB, free: 17.21 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009144/0.3602, allocations: 0.7727 MB / 0.5161 GB, free: 17.13 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001151/0.3614, allocations: 0.8442 MB / 0.5169 GB, free: 17 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002646/0.3616, allocations: 137.6 kB / 0.517 GB, free: 17 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006088/0.3677, allocations: 1.789 MB / 0.5188 GB, free: 16.81 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005753/0.3683, allocations: 328.3 kB / 0.5191 GB, free: 16.62 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001135/0.3695, allocations: 0.6821 MB / 0.5198 GB, free: 16.23 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.008075/0.3776, allocations: 3.34 MB / 0.523 GB, free: 15.01 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.422e-06/0.3776, allocations: 3.938 kB / 0.523 GB, free: 15 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.174e-06/0.3776, allocations: 0 / 0.523 GB, free: 15 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 3.653e-05/0.3777, allocations: 0 / 0.523 GB, free: 15 MB / 382.1 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 0.004184/0.3819, allocations: 1.801 MB / 0.5248 GB, free: 13.92 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.745e-05/0.3819, allocations: 9.281 kB / 0.5248 GB, free: 13.92 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001296/0.3832, allocations: 276.8 kB / 0.5251 GB, free: 13.84 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001098/0.3843, allocations: 0.6706 MB / 0.5257 GB, free: 13.4 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.867e-05/0.3844, allocations: 115.1 kB / 0.5258 GB, free: 13.33 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000201/0.3846, allocations: 109.9 kB / 0.5259 GB, free: 13.29 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002214/0.3869, allocations: 1.341 MB / 0.5272 GB, free: 12.75 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.395e-05/0.3869, allocations: 0 / 0.5272 GB, free: 12.75 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001126/0.387, allocations: 45.56 kB / 0.5273 GB, free: 12.71 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.143e-05/0.3871, allocations: 26.75 kB / 0.5273 GB, free: 12.71 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002378/0.3894, allocations: 1.694 MB / 0.529 GB, free: 12.21 MB / 382.1 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 0.006267/0.3957, allocations: 4.293 MB / 0.5332 GB, free: 9.246 MB / 382.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003021/0.3988, allocations: 2.274 MB / 0.5354 GB, free: 8.059 MB / 382.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007352/0.3995, allocations: 0.6005 MB / 0.536 GB, free: 7.754 MB / 382.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006153/0.4057, allocations: 5.377 MB / 0.5412 GB, free: 2.898 MB / 382.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.167e-05/0.4057, allocations: 43.16 kB / 0.5413 GB, free: 2.848 MB / 382.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.675e-06/0.4058, allocations: 3.938 kB / 0.5413 GB, free: 2.844 MB / 382.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01363/0.4194, allocations: 3.573 MB / 0.5448 GB, free: 15.25 MB / 398.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.125e-05/0.4195, allocations: 64.41 kB / 0.5448 GB, free: 15.17 MB / 398.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006801/0.4201, allocations: 0.5925 MB / 0.5454 GB, free: 14.57 MB / 398.1 MB
Notification: Performance of collectPreVariables (initialization): time 8.437e-05/0.4202, allocations: 41.7 kB / 0.5454 GB, free: 14.52 MB / 398.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003158/0.4206, allocations: 0.5248 MB / 0.5459 GB, free: 13.99 MB / 398.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000264/0.4208, allocations: 332.8 kB / 0.5463 GB, free: 13.67 MB / 398.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003089/0.4212, allocations: 234.8 kB / 0.5465 GB, free: 13.43 MB / 398.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001663/0.4213, allocations: 393.4 kB / 0.5469 GB, free: 13.04 MB / 398.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005939/0.4219, allocations: 358.5 kB / 0.5472 GB, free: 12.69 MB / 398.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008511/0.4228, allocations: 0.7517 MB / 0.5479 GB, free: 11.78 MB / 398.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001566/0.4244, allocations: 1.202 MB / 0.5491 GB, free: 10.43 MB / 398.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.086e-06/0.4244, allocations: 7.938 kB / 0.5491 GB, free: 10.43 MB / 398.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003847/0.4282, allocations: 1.469 MB / 0.5506 GB, free: 8.957 MB / 398.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.47e-05/0.4283, allocations: 11.94 kB / 0.5506 GB, free: 8.945 MB / 398.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.845e-05/0.4283, allocations: 18.66 kB / 0.5506 GB, free: 8.93 MB / 398.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001869/0.4302, allocations: 248.6 kB / 0.5508 GB, free: 8.691 MB / 398.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001493/0.4317, allocations: 330.2 kB / 0.5511 GB, free: 8.371 MB / 398.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005254/0.4369, allocations: 3.85 MB / 0.5549 GB, free: 4.27 MB / 398.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001003/0.438, allocations: 40 kB / 0.5549 GB, free: 4.23 MB / 398.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001439/0.4381, allocations: 71.98 kB / 0.555 GB, free: 4.16 MB / 398.1 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 0.0004998/0.4387, allocations: 280.1 kB / 0.5553 GB, free: 3.879 MB / 398.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002156/0.4389, allocations: 86.88 kB / 0.5553 GB, free: 3.793 MB / 398.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.003872/0.4428, allocations: 1.336 MB / 0.5567 GB, free: 2.477 MB / 398.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.105e-05/0.4428, allocations: 14.59 kB / 0.5567 GB, free: 2.465 MB / 398.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.609e-06/0.4428, allocations: 0 / 0.5567 GB, free: 2.465 MB / 398.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.089e-05/0.4428, allocations: 3.984 kB / 0.5567 GB, free: 2.461 MB / 398.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001519/0.4443, allocations: 1.067 MB / 0.5577 GB, free: 1.359 MB / 398.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.25e-06/0.4444, allocations: 0 / 0.5577 GB, free: 1.359 MB / 398.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001194/0.4456, allocations: 219.7 kB / 0.5579 GB, free: 1.145 MB / 398.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001809/0.4474, allocations: 232.5 kB / 0.5581 GB, free: 0.9219 MB / 398.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.664e-05/0.4475, allocations: 27.98 kB / 0.5582 GB, free: 0.8945 MB / 398.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00478/0.4523, allocations: 3.774 MB / 0.5619 GB, free: 12.86 MB / 414.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.655e-06/0.4523, allocations: 0 / 0.5619 GB, free: 12.86 MB / 414.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004231/0.4565, allocations: 1.746 MB / 0.5636 GB, free: 11.09 MB / 414.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003019/0.4569, allocations: 152 kB / 0.5637 GB, free: 10.93 MB / 414.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000125/0.457, allocations: 16 kB / 0.5637 GB, free: 10.91 MB / 414.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005148/0.4575, allocations: 27.98 kB / 0.5637 GB, free: 10.88 MB / 414.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001853/0.4577, allocations: 79.55 kB / 0.5638 GB, free: 10.81 MB / 414.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.963e-05/0.4578, allocations: 39.98 kB / 0.5639 GB, free: 10.77 MB / 414.1 MB
Notification: Performance of sorting global known variables: time 0.0004777/0.4583, allocations: 395 kB / 0.5642 GB, free: 10.39 MB / 414.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.4583, allocations: 0 / 0.5642 GB, free: 10.39 MB / 414.1 MB
Notification: Performance of remove unused functions: time 0.00219/0.4605, allocations: 0.6675 MB / 0.5649 GB, free: 9.723 MB / 414.1 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 0.00153/0.462, allocations: 0.8063 MB / 0.5657 GB, free: 9.043 MB / 414.1 MB
Notification: Performance of simCode: created initialization part: time 0.002127/0.4642, allocations: 1.259 MB / 0.5669 GB, free: 7.766 MB / 414.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.316e-06/0.4642, allocations: 0 / 0.5669 GB, free: 7.766 MB / 414.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001059/0.4652, allocations: 0.7436 MB / 0.5676 GB, free: 7.004 MB / 414.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001119/0.4664, allocations: 200.3 kB / 0.5678 GB, free: 6.828 MB / 414.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003272/0.4697, allocations: 2.008 MB / 0.5698 GB, free: 4.824 MB / 414.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005668/0.4703, allocations: 1.035 MB / 0.5708 GB, free: 3.777 MB / 414.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005179/0.4708, allocations: 209.2 kB / 0.571 GB, free: 3.586 MB / 414.1 MB
Notification: Performance of SimCode: time 9.82e-07/0.4708, allocations: 0 / 0.571 GB, free: 3.586 MB / 414.1 MB
Notification: Performance of Templates: time 0.03239/0.5032, allocations: 26.42 MB / 0.5968 GB, free: 9.781 MB / 446.1 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 -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)