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 1.4.0-master/package.mo", uses=false)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-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 0.000962/0.000962, allocations: 100.1 kB / 15.05 MB, free: 1.105 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0009521/0.0009521, allocations: 177.3 kB / 15.95 MB, free: 216 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.371/1.371, allocations: 223.2 MB / 239.9 MB, free: 5.426 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.2366/0.2366, allocations: 15.25 MB / 306.2 MB, free: 15.73 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.000315/0.000315, allocations: 8 kB / 371.4 MB, free: 3.996 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.4544/0.4547, allocations: 54.62 MB / 426 MB, free: 40.01 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65: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 1.4.0-master/package.mo:3011:6-3011:65: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 0.00551/0.4603, allocations: 5.285 MB / 431.3 MB, free: 39.38 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0163/0.4766, allocations: 14.05 MB / 445.3 MB, free: 29.33 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001924/0.4786, allocations: 24.75 kB / 445.3 MB, free: 29.32 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001167/0.4798, allocations: 313.1 kB / 445.7 MB, free: 29.16 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005234/0.485, allocations: 1.459 MB / 447.1 MB, free: 28.21 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.006158/0.4912, allocations: 1.773 MB / 448.9 MB, free: 27.14 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002231/0.4935, allocations: 1.018 MB / 449.9 MB, free: 26.61 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008659/0.4943, allocations: 0.6565 MB / 450.6 MB, free: 26.36 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000747/0.4951, allocations: 0.5527 MB / 451.1 MB, free: 26.13 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0008359/0.4959, allocations: 0.7394 MB / 451.8 MB, free: 25.87 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001215/0.4961, allocations: 70.19 kB / 451.9 MB, free: 25.87 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007002/0.5031, allocations: 1.96 MB / 453.9 MB, free: 25.52 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002756/0.5034, allocations: 253.5 kB / 454.1 MB, free: 25.39 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004077/0.5038, allocations: 242.6 kB / 454.4 MB, free: 25.26 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.00418/0.508, allocations: 1.958 MB / 456.3 MB, free: 24.63 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.278e-06/0.508, allocations: 3.938 kB / 456.3 MB, free: 24.62 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.806e-06/0.508, allocations: 0 / 456.3 MB, free: 24.62 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.371e-05/0.5081, allocations: 2.781 kB / 456.3 MB, free: 24.62 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 0.00276/0.5108, allocations: 1.513 MB / 457.8 MB, free: 23.67 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.207e-05/0.5109, allocations: 16.88 kB / 457.9 MB, free: 23.66 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001065/0.5119, allocations: 268.7 kB / 458.1 MB, free: 23.58 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008347/0.5128, allocations: 0.5972 MB / 458.7 MB, free: 23.14 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001097/0.5129, allocations: 113.5 kB / 458.8 MB, free: 23.07 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001737/0.5131, allocations: 112.8 kB / 458.9 MB, free: 23.04 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002047/0.5151, allocations: 1.315 MB / 460.3 MB, free: 22.49 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.69e-05/0.5152, allocations: 4.984 kB / 460.3 MB, free: 22.48 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001157/0.5153, allocations: 45.22 kB / 460.3 MB, free: 22.45 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.84e-05/0.5153, allocations: 26.44 kB / 460.3 MB, free: 22.45 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002756/0.5181, allocations: 1.69 MB / 462 MB, free: 21.95 MB / 350.1 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 0.00673/0.5248, allocations: 4.22 MB / 466.2 MB, free: 19.35 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003735/0.5286, allocations: 2.278 MB / 468.5 MB, free: 18.34 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.007029/0.5356, allocations: 5.223 MB / 473.7 MB, free: 14.1 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.546e-05/0.5357, allocations: 43.39 kB / 473.8 MB, free: 14.05 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=78): time 3.136e-06/0.5357, allocations: 0 / 473.8 MB, free: 14.05 MB / 350.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01589/0.5516, allocations: 3.6 MB / 477.4 MB, free: 12.54 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.358e-05/0.5517, allocations: 63.2 kB / 477.4 MB, free: 12.47 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0008281/0.5526, allocations: 0.5863 MB / 478 MB, free: 12.2 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.543e-05/0.5526, allocations: 40.61 kB / 478.1 MB, free: 12.16 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003001/0.5529, allocations: 0.5312 MB / 478.6 MB, free: 11.73 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000253/0.5532, allocations: 335 kB / 478.9 MB, free: 11.46 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.568e-05/0.5533, allocations: 24.03 kB / 479 MB, free: 11.45 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001356/0.5534, allocations: 395.5 kB / 479.3 MB, free: 11.1 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006203/0.554, allocations: 350.1 kB / 479.7 MB, free: 10.97 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000834/0.5549, allocations: 0.7451 MB / 480.4 MB, free: 10.32 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0008038/0.5557, allocations: 466.9 kB / 480.9 MB, free: 10.1 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.743e-06/0.5557, allocations: 3.75 kB / 480.9 MB, free: 10.1 MB / 350.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004267/0.56, allocations: 1.469 MB / 482.4 MB, free: 9.512 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.631e-05/0.56, allocations: 9.812 kB / 482.4 MB, free: 9.512 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.596e-05/0.5601, allocations: 12.56 kB / 482.4 MB, free: 9.512 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002084/0.5621, allocations: 262.9 kB / 482.6 MB, free: 9.457 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001504/0.5637, allocations: 326.5 kB / 482.9 MB, free: 9.426 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005152/0.5688, allocations: 3.55 MB / 486.5 MB, free: 6.297 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001201/0.5701, allocations: 71.81 kB / 486.6 MB, free: 6.27 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001308/0.5702, allocations: 73.33 kB / 486.6 MB, free: 6.254 MB / 350.1 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 (linear and non-linear blocks): 0
 * Torn equation systems: 2
 * 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: 1 {1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.0005466/0.5708, allocations: 270.3 kB / 486.9 MB, free: 6.039 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000152/0.5709, allocations: 94.78 kB / 487 MB, free: 5.984 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.00438/0.5753, allocations: 1.342 MB / 488.3 MB, free: 5.441 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.25e-05/0.5753, allocations: 13.78 kB / 488.4 MB, free: 5.438 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.899e-06/0.5753, allocations: 1.641 kB / 488.4 MB, free: 5.438 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.193e-05/0.5754, allocations: 5.625 kB / 488.4 MB, free: 5.438 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001701/0.5771, allocations: 1.078 MB / 489.4 MB, free: 4.637 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.171e-06/0.5771, allocations: 4 kB / 489.4 MB, free: 4.633 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001109/0.5782, allocations: 210.6 kB / 489.6 MB, free: 4.457 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001905/0.5801, allocations: 246.1 kB / 489.9 MB, free: 4.281 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.615e-05/0.5802, allocations: 36.22 kB / 489.9 MB, free: 4.25 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004161/0.5844, allocations: 3.451 MB / 493.4 MB, free: 0.707 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.805e-06/0.5844, allocations: 4.031 kB / 493.4 MB, free: 0.7031 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004207/0.5886, allocations: 1.797 MB / 495.2 MB, free: 14.9 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003198/0.589, allocations: 152.1 kB / 495.3 MB, free: 14.73 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001202/0.5891, allocations: 20 kB / 495.3 MB, free: 14.71 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005324/0.5896, allocations: 35.89 kB / 495.4 MB, free: 14.68 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001945/0.5898, allocations: 84.88 kB / 495.5 MB, free: 14.59 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.703e-05/0.5899, allocations: 39.98 kB / 495.5 MB, free: 14.55 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0004871/0.5904, allocations: 383 kB / 495.9 MB, free: 14.18 MB / 366.1 MB
Notification: Performance of sort global known variables: time 2.2e-07/0.5904, allocations: 0 / 495.9 MB, free: 14.18 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.002163/0.5926, allocations: 0.6519 MB / 496.5 MB, free: 13.53 MB / 366.1 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 (linear and non-linear blocks): 0
 * Torn equation systems: 2
 * 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: 1 {1 3}
Notification: Performance of Backend phase and start with SimCode phase: time 0.001303/0.5939, allocations: 0.7789 MB / 497.3 MB, free: 12.75 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.002319/0.5962, allocations: 1.234 MB / 498.5 MB, free: 11.49 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.818e-06/0.5962, allocations: 0 / 498.5 MB, free: 11.49 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001106/0.5974, allocations: 0.75 MB / 499.3 MB, free: 10.71 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0008568/0.5982, allocations: 172.8 kB / 499.5 MB, free: 10.55 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003687/0.6019, allocations: 2.441 MB / 0.4901 GB, free: 8.066 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0006853/0.6026, allocations: 1.063 MB / 0.4912 GB, free: 6.973 MB / 366.1 MB
Notification: Performance of simCode: alias equations: time 0.001/0.6036, allocations: 230.3 kB / 0.4914 GB, free: 6.754 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003181/0.604, allocations: 155.6 kB / 0.4915 GB, free: 6.605 MB / 366.1 MB
Notification: Performance of SimCode: time 5.41e-07/0.604, allocations: 0 / 0.4915 GB, free: 6.605 MB / 366.1 MB
Notification: Performance of Templates: time 0.03629/0.6403, allocations: 21.6 MB / 0.5126 GB, free: 1.125 MB / 382.1 MB
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
Environment - environmentSimulation:
(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)
Environment - environmentSimulation: