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 0.001162/0.001162, allocations: 111.3 kB / 15.23 MB, free: 0.6406 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001706/0.001706, allocations: 196.7 kB / 16.14 MB, free: 6.703 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 / 239.8 MB, free: 4.609 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2365/0.2365, allocations: 15.32 MB / 305.3 MB, free: 15.3 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001357/0.001357, allocations: 63.89 kB / 369.7 MB, free: 4.426 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1204/0.1218, allocations: 53.61 MB / 423.3 MB, free: 14.76 MB / 366.1 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 0.3992/0.521, allocations: 25.14 MB / 448.4 MB, free: 39.55 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01396/0.535, allocations: 16.62 MB / 465 MB, free: 31.31 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001232/0.5363, allocations: 27 kB / 465.1 MB, free: 31.3 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009372/0.5372, allocations: 302.7 kB / 465.3 MB, free: 31.15 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.003748/0.541, allocations: 1.303 MB / 466.7 MB, free: 30.46 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005657/0.5466, allocations: 1.746 MB / 468.4 MB, free: 29.51 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.001944/0.5486, allocations: 1.486 MB / 469.9 MB, free: 28.81 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008413/0.5495, allocations: 0.7334 MB / 470.6 MB, free: 28.49 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001001/0.5505, allocations: 0.7605 MB / 471.4 MB, free: 28.25 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001055/0.5515, allocations: 0.8356 MB / 472.2 MB, free: 27.94 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002023/0.5517, allocations: 87.19 kB / 472.3 MB, free: 27.94 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005886/0.5576, allocations: 1.748 MB / 474 MB, free: 27.51 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0003384/0.558, allocations: 289.7 kB / 474.3 MB, free: 27.35 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0007879/0.5588, allocations: 0.6498 MB / 475 MB, free: 27 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.006409/0.5652, allocations: 3.143 MB / 478.1 MB, free: 25.68 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.38e-06/0.5652, allocations: 0 / 478.1 MB, free: 25.68 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.202e-06/0.5653, allocations: 0 / 478.1 MB, free: 25.68 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 1.882e-05/0.5653, allocations: 0 / 478.1 MB, free: 25.68 MB / 366.1 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 0.003286/0.5686, allocations: 1.802 MB / 479.9 MB, free: 24.57 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.035e-05/0.5686, allocations: 9.656 kB / 479.9 MB, free: 24.57 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001165/0.5698, allocations: 274.8 kB / 480.2 MB, free: 24.49 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0008378/0.5706, allocations: 0.6517 MB / 480.9 MB, free: 24.04 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.386e-05/0.5707, allocations: 114.7 kB / 481 MB, free: 23.97 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001774/0.5709, allocations: 109.3 kB / 481.1 MB, free: 23.93 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002004/0.5729, allocations: 1.338 MB / 482.4 MB, free: 23.38 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.139e-05/0.573, allocations: 0 / 482.4 MB, free: 23.38 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001067/0.5731, allocations: 41.12 kB / 482.4 MB, free: 23.35 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.309e-05/0.5731, allocations: 26.34 kB / 482.5 MB, free: 23.35 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002656/0.5758, allocations: 1.699 MB / 484.2 MB, free: 22.85 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 0.006477/0.5823, allocations: 4.296 MB / 488.5 MB, free: 20.25 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003395/0.5857, allocations: 2.274 MB / 490.7 MB, free: 19.25 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0008108/0.5865, allocations: 0.595 MB / 491.3 MB, free: 19 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00633/0.5928, allocations: 5.409 MB / 496.7 MB, free: 14.74 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.986e-05/0.5929, allocations: 43.59 kB / 496.8 MB, free: 14.69 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.094e-06/0.5929, allocations: 3.938 kB / 496.8 MB, free: 14.69 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01511/0.608, allocations: 3.556 MB / 0.4886 GB, free: 13.18 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.904e-05/0.6081, allocations: 63.28 kB / 0.4887 GB, free: 13.11 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006541/0.6087, allocations: 0.5877 MB / 0.4893 GB, free: 12.84 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.205e-05/0.6088, allocations: 41.3 kB / 0.4893 GB, free: 12.8 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002483/0.6091, allocations: 0.5269 MB / 0.4898 GB, free: 12.38 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002017/0.6093, allocations: 333.9 kB / 0.4901 GB, free: 12.11 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002791/0.6095, allocations: 234.7 kB / 0.4904 GB, free: 12 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001162/0.6097, allocations: 395.6 kB / 0.4907 GB, free: 11.65 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005628/0.6102, allocations: 359.7 kB / 0.4911 GB, free: 11.52 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007189/0.611, allocations: 0.753 MB / 0.4918 GB, free: 10.87 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00129/0.6123, allocations: 1.205 MB / 0.493 GB, free: 9.957 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.06e-06/0.6123, allocations: 7.406 kB / 0.493 GB, free: 9.953 MB / 366.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003917/0.6162, allocations: 1.468 MB / 0.4944 GB, free: 9.359 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.136e-05/0.6162, allocations: 11.56 kB / 0.4944 GB, free: 9.359 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.318e-05/0.6163, allocations: 14.66 kB / 0.4945 GB, free: 9.359 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002136/0.6184, allocations: 242.9 kB / 0.4947 GB, free: 9.305 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001359/0.6198, allocations: 333.5 kB / 0.495 GB, free: 9.27 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004648/0.6244, allocations: 3.487 MB / 0.4984 GB, free: 6.164 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0009731/0.6254, allocations: 73.92 kB / 0.4985 GB, free: 6.137 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001007/0.6255, allocations: 65.86 kB / 0.4985 GB, free: 6.125 MB / 366.1 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 0.0004096/0.6259, allocations: 280 kB / 0.4988 GB, free: 5.902 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001654/0.6261, allocations: 85.72 kB / 0.4989 GB, free: 5.855 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004086/0.6302, allocations: 1.335 MB / 0.5002 GB, free: 5.301 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.008e-05/0.6302, allocations: 10.97 kB / 0.5002 GB, free: 5.301 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.362e-06/0.6302, allocations: 0 / 0.5002 GB, free: 5.301 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.326e-05/0.6303, allocations: 5.203 kB / 0.5002 GB, free: 5.301 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001415/0.6317, allocations: 1.081 MB / 0.5013 GB, free: 4.41 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.773e-06/0.6317, allocations: 0.7031 kB / 0.5013 GB, free: 4.41 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001195/0.6329, allocations: 222.6 kB / 0.5015 GB, free: 4.223 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002035/0.6349, allocations: 225.7 kB / 0.5017 GB, free: 4.062 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.161e-05/0.635, allocations: 38.94 kB / 0.5017 GB, free: 4.027 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004036/0.6391, allocations: 3.397 MB / 0.505 GB, free: 0.5273 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.595e-06/0.6391, allocations: 3.938 kB / 0.505 GB, free: 0.5234 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004331/0.6434, allocations: 1.736 MB / 0.5067 GB, free: 14.9 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002513/0.6437, allocations: 156 kB / 0.5069 GB, free: 14.73 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001232/0.6438, allocations: 20 kB / 0.5069 GB, free: 14.71 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000589/0.6444, allocations: 31.98 kB / 0.5069 GB, free: 14.68 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002133/0.6446, allocations: 88.77 kB / 0.507 GB, free: 14.59 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.08e-05/0.6447, allocations: 39.98 kB / 0.5071 GB, free: 14.55 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0004714/0.6452, allocations: 387.1 kB / 0.5074 GB, free: 14.18 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.51e-07/0.6452, allocations: 0 / 0.5074 GB, free: 14.18 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.00228/0.6475, allocations: 0.6675 MB / 0.5081 GB, free: 13.51 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 0.001467/0.649, allocations: 0.7963 MB / 0.5089 GB, free: 12.7 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002108/0.6511, allocations: 1.25 MB / 0.5101 GB, free: 11.43 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.645e-06/0.6511, allocations: 4 kB / 0.5101 GB, free: 11.43 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001099/0.6522, allocations: 0.7495 MB / 0.5108 GB, free: 10.65 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009659/0.6532, allocations: 184.4 kB / 0.511 GB, free: 10.47 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003392/0.6566, allocations: 2.448 MB / 0.5134 GB, free: 7.988 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005704/0.6572, allocations: 1.045 MB / 0.5144 GB, free: 6.918 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0009653/0.6582, allocations: 231.3 kB / 0.5146 GB, free: 6.688 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003297/0.6585, allocations: 156.2 kB / 0.5148 GB, free: 6.539 MB / 382.1 MB
Notification: Performance of SimCode: time 4.71e-07/0.6585, allocations: 0 / 0.5148 GB, free: 6.539 MB / 382.1 MB
Notification: Performance of Templates: time 0.03148/0.69, allocations: 22.63 MB / 0.5369 GB, free: 0 / 398.1 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)