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 0.00836/0.008359, allocations: 96.72 kB / 15.73 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 0.002077/0.002077, allocations: 185.4 kB / 16.67 MB, free: 5.93 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.438/1.438, allocations: 222.9 MB / 240.4 MB, free: 4.316 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.282/0.282, allocations: 15.32 MB / 305.9 MB, free: 15.26 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001587/0.001587, allocations: 67.91 kB / 425.2 MB, free: 13.11 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3816/0.3832, allocations: 53.61 MB / 478.8 MB, free: 25.84 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 0.0462/0.4295, allocations: 25.5 MB / 0.4925 GB, free: 9.176 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01957/0.4491, allocations: 16.67 MB / 0.5088 GB, free: 8.445 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002222/0.4514, allocations: 11.94 kB / 0.5088 GB, free: 8.434 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001333/0.4527, allocations: 337.5 kB / 0.5091 GB, free: 8.102 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.006275/0.459, allocations: 1.482 MB / 0.5105 GB, free: 6.609 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.007757/0.4668, allocations: 1.977 MB / 0.5125 GB, free: 4.617 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.003407/0.4702, allocations: 1.541 MB / 0.514 GB, free: 3.07 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001165/0.4714, allocations: 0.8629 MB / 0.5148 GB, free: 2.184 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009641/0.4724, allocations: 0.7637 MB / 0.5156 GB, free: 1.418 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001168/0.4735, allocations: 0.8488 MB / 0.5164 GB, free: 0.5664 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002149/0.4738, allocations: 136 kB / 0.5165 GB, free: 444 kB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007906/0.4817, allocations: 1.783 MB / 0.5183 GB, free: 14.65 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0004117/0.4821, allocations: 339 kB / 0.5186 GB, free: 14.32 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0009184/0.4831, allocations: 0.6845 MB / 0.5193 GB, free: 13.63 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01266/0.4957, allocations: 3.346 MB / 0.5225 GB, free: 10.27 MB / 398.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.09e-05/0.4958, allocations: 0 / 0.5225 GB, free: 10.27 MB / 398.1 MB
Notification: Performance of FrontEnd: time 7.223e-06/0.4959, allocations: 4 kB / 0.5225 GB, free: 10.27 MB / 398.1 MB
Notification: Performance of Transformations before backend: time 0.0001204/0.496, allocations: 0 / 0.5225 GB, free: 10.27 MB / 398.1 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 0.007104/0.5031, allocations: 1.848 MB / 0.5243 GB, free: 8.359 MB / 398.1 MB
Notification: Performance of prepare preOptimizeDAE: time 6.686e-05/0.5032, allocations: 12.02 kB / 0.5244 GB, free: 8.348 MB / 398.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001849/0.505, allocations: 279.4 kB / 0.5246 GB, free: 8.074 MB / 398.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001773/0.5068, allocations: 0.6691 MB / 0.5253 GB, free: 7.363 MB / 398.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002007/0.5071, allocations: 116.4 kB / 0.5254 GB, free: 7.242 MB / 398.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000443/0.5075, allocations: 116.3 kB / 0.5255 GB, free: 7.129 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00298/0.5105, allocations: 1.337 MB / 0.5268 GB, free: 5.746 MB / 398.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.578e-05/0.5106, allocations: 0 / 0.5268 GB, free: 5.746 MB / 398.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001099/0.5107, allocations: 40 kB / 0.5268 GB, free: 5.707 MB / 398.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.703e-05/0.5107, allocations: 28 kB / 0.5269 GB, free: 5.68 MB / 398.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002682/0.5134, allocations: 1.695 MB / 0.5285 GB, free: 3.977 MB / 398.1 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 0.007219/0.5206, allocations: 4.303 MB / 0.5327 GB, free: 15.46 MB / 414.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003715/0.5244, allocations: 2.274 MB / 0.5349 GB, free: 13.11 MB / 414.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.00104/0.5254, allocations: 0.5928 MB / 0.5355 GB, free: 12.52 MB / 414.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.00867/0.5341, allocations: 5.381 MB / 0.5408 GB, free: 6.508 MB / 414.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.387e-05/0.5342, allocations: 43.22 kB / 0.5408 GB, free: 6.457 MB / 414.1 MB
Notification: Performance of pre-optimization done (n=78): time 3.937e-06/0.5342, allocations: 0 / 0.5408 GB, free: 6.457 MB / 414.1 MB
Notification: Performance of matching and sorting (n=95): time 0.0153/0.5495, allocations: 3.587 MB / 0.5443 GB, free: 2.801 MB / 414.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.117e-05/0.5497, allocations: 64.41 kB / 0.5444 GB, free: 2.723 MB / 414.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001113/0.5508, allocations: 0.5862 MB / 0.545 GB, free: 2.125 MB / 414.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.366e-05/0.5509, allocations: 41.7 kB / 0.545 GB, free: 2.078 MB / 414.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004544/0.5513, allocations: 0.5429 MB / 0.5455 GB, free: 1.527 MB / 414.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003853/0.5517, allocations: 357 kB / 0.5459 GB, free: 1.176 MB / 414.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0004246/0.5522, allocations: 234.8 kB / 0.5461 GB, free: 0.9414 MB / 414.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002287/0.5524, allocations: 394.7 kB / 0.5465 GB, free: 0.5469 MB / 414.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0007079/0.5531, allocations: 358.5 kB / 0.5468 GB, free: 200 kB / 414.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001096/0.5542, allocations: 0.748 MB / 0.5475 GB, free: 15.27 MB / 430.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001881/0.5561, allocations: 1.204 MB / 0.5487 GB, free: 13.89 MB / 430.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.119e-05/0.5562, allocations: 4 kB / 0.5487 GB, free: 13.88 MB / 430.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004237/0.5604, allocations: 1.479 MB / 0.5502 GB, free: 12.39 MB / 430.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.587e-05/0.5605, allocations: 12 kB / 0.5502 GB, free: 12.38 MB / 430.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.564e-05/0.5605, allocations: 12 kB / 0.5502 GB, free: 12.37 MB / 430.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001897/0.5624, allocations: 245.8 kB / 0.5504 GB, free: 12.12 MB / 430.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001436/0.5638, allocations: 331.5 kB / 0.5507 GB, free: 11.8 MB / 430.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00591/0.5698, allocations: 3.861 MB / 0.5545 GB, free: 7.668 MB / 430.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001107/0.5709, allocations: 43.98 kB / 0.5545 GB, free: 7.625 MB / 430.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002073/0.5711, allocations: 71.92 kB / 0.5546 GB, free: 7.555 MB / 430.1 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 0.0006972/0.5718, allocations: 277.5 kB / 0.5549 GB, free: 7.273 MB / 430.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0003351/0.5722, allocations: 87.44 kB / 0.555 GB, free: 7.188 MB / 430.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004315/0.5765, allocations: 1.34 MB / 0.5563 GB, free: 5.828 MB / 430.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.379e-05/0.5765, allocations: 11.94 kB / 0.5563 GB, free: 5.816 MB / 430.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.155e-06/0.5766, allocations: 3.938 kB / 0.5563 GB, free: 5.812 MB / 430.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.495e-05/0.5766, allocations: 15.97 kB / 0.5563 GB, free: 5.797 MB / 430.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001845/0.5784, allocations: 1.069 MB / 0.5573 GB, free: 4.66 MB / 430.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.512e-05/0.5785, allocations: 0 / 0.5573 GB, free: 4.66 MB / 430.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001215/0.5797, allocations: 215.7 kB / 0.5576 GB, free: 4.449 MB / 430.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001806/0.5815, allocations: 233.6 kB / 0.5578 GB, free: 4.215 MB / 430.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001211/0.5816, allocations: 35.98 kB / 0.5578 GB, free: 4.18 MB / 430.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.005267/0.5869, allocations: 3.776 MB / 0.5615 GB, free: 128 kB / 430.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.447e-06/0.5869, allocations: 0 / 0.5615 GB, free: 128 kB / 430.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004357/0.5913, allocations: 1.74 MB / 0.5632 GB, free: 14.35 MB / 446.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003833/0.5917, allocations: 156.6 kB / 0.5633 GB, free: 14.18 MB / 446.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0002068/0.5919, allocations: 20 kB / 0.5634 GB, free: 14.16 MB / 446.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0006108/0.5925, allocations: 20 kB / 0.5634 GB, free: 14.14 MB / 446.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000218/0.5928, allocations: 84.89 kB / 0.5635 GB, free: 14.05 MB / 446.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.331e-05/0.5929, allocations: 39.92 kB / 0.5635 GB, free: 14.02 MB / 446.1 MB
Notification: Performance of sorting global known variables: time 0.0005897/0.5935, allocations: 391.1 kB / 0.5639 GB, free: 13.64 MB / 446.1 MB
Notification: Performance of sort global known variables: time 1.41e-07/0.5935, allocations: 0 / 0.5639 GB, free: 13.64 MB / 446.1 MB
Notification: Performance of remove unused functions: time 0.002635/0.5961, allocations: 0.6818 MB / 0.5645 GB, free: 12.96 MB / 446.1 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 0.002714/0.5988, allocations: 0.813 MB / 0.5653 GB, free: 12.13 MB / 446.1 MB
Notification: Performance of simCode: created initialization part: time 0.002816/0.6017, allocations: 1.259 MB / 0.5666 GB, free: 10.85 MB / 446.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.849e-06/0.6017, allocations: 0 / 0.5666 GB, free: 10.85 MB / 446.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001271/0.603, allocations: 0.7449 MB / 0.5673 GB, free: 10.08 MB / 446.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001279/0.6043, allocations: 207.6 kB / 0.5675 GB, free: 9.875 MB / 446.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00406/0.6083, allocations: 2.005 MB / 0.5694 GB, free: 7.824 MB / 446.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0008016/0.6092, allocations: 1.038 MB / 0.5705 GB, free: 6.762 MB / 446.1 MB
Notification: Performance of simCode: alias equations: time 0.0009182/0.6101, allocations: 223.2 kB / 0.5707 GB, free: 6.539 MB / 446.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003912/0.6105, allocations: 159.9 kB / 0.5708 GB, free: 6.387 MB / 446.1 MB
Notification: Performance of SimCode: time 1.242e-06/0.6105, allocations: 0 / 0.5708 GB, free: 6.387 MB / 446.1 MB
Notification: Performance of Templates: time 0.04179/0.6523, allocations: 23.67 MB / 0.5939 GB, free: 14.8 MB / 478.1 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)