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 0.008544/0.008544, allocations: 105.9 kB / 15.73 MB, free: 6.004 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001869/0.001869, allocations: 189 kB / 16.67 MB, free: 5.926 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.366/1.366, allocations: 222.9 MB / 240.4 MB, free: 15.07 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.09786/0.09786, allocations: 15.31 MB / 305.8 MB, free: 15.38 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001236/0.001236, allocations: 71.91 kB / 425.2 MB, free: 11.54 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1216/0.1228, allocations: 53.6 MB / 478.8 MB, free: 5.879 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 0.03603/0.1589, allocations: 25.44 MB / 0.4924 GB, free: 12.53 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2743/0.4332, allocations: 16.65 MB / 0.5087 GB, free: 18.2 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007453/0.434, allocations: 18.61 kB / 0.5087 GB, free: 18.2 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001006/0.435, allocations: 336.7 kB / 0.509 GB, free: 18.2 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004383/0.4394, allocations: 1.495 MB / 0.5105 GB, free: 18.18 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005658/0.4451, allocations: 1.997 MB / 0.5124 GB, free: 17.58 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002349/0.4475, allocations: 1.547 MB / 0.5139 GB, free: 17.28 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001153/0.4486, allocations: 0.8448 MB / 0.5148 GB, free: 17.21 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.001004/0.4496, allocations: 0.7721 MB / 0.5155 GB, free: 17.14 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001212/0.4509, allocations: 0.8471 MB / 0.5163 GB, free: 17.01 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002236/0.4511, allocations: 137.1 kB / 0.5165 GB, free: 17.01 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.00684/0.4579, allocations: 1.78 MB / 0.5182 GB, free: 16.76 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005015/0.4585, allocations: 335.5 kB / 0.5185 GB, free: 16.56 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001083/0.4596, allocations: 0.6824 MB / 0.5192 GB, free: 16.17 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01101/0.4706, allocations: 3.338 MB / 0.5224 GB, free: 14.95 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.596e-06/0.4707, allocations: 4 kB / 0.5225 GB, free: 14.95 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.484e-06/0.4707, allocations: 0 / 0.5225 GB, free: 14.95 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 3.471e-05/0.4707, allocations: 4.094 kB / 0.5225 GB, free: 14.95 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 0.004247/0.475, allocations: 1.8 MB / 0.5242 GB, free: 13.86 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.222e-05/0.475, allocations: 8.781 kB / 0.5242 GB, free: 13.86 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001294/0.4763, allocations: 270.7 kB / 0.5245 GB, free: 13.78 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001043/0.4774, allocations: 0.6791 MB / 0.5251 GB, free: 13.34 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001077/0.4775, allocations: 116.7 kB / 0.5253 GB, free: 13.27 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000189/0.4777, allocations: 108.3 kB / 0.5254 GB, free: 13.23 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002193/0.4799, allocations: 1.335 MB / 0.5267 GB, free: 12.69 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.721e-05/0.4799, allocations: 6.75 kB / 0.5267 GB, free: 12.68 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001114/0.4801, allocations: 43.69 kB / 0.5267 GB, free: 12.65 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.071e-05/0.4801, allocations: 27 kB / 0.5267 GB, free: 12.65 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002517/0.4826, allocations: 1.693 MB / 0.5284 GB, free: 12.16 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 0.005998/0.4886, allocations: 4.291 MB / 0.5326 GB, free: 9.223 MB / 382.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003036/0.4917, allocations: 2.279 MB / 0.5348 GB, free: 8.035 MB / 382.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0007223/0.4924, allocations: 0.5898 MB / 0.5354 GB, free: 7.734 MB / 382.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.005997/0.4984, allocations: 5.384 MB / 0.5406 GB, free: 2.859 MB / 382.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.921e-05/0.4985, allocations: 43.16 kB / 0.5407 GB, free: 2.809 MB / 382.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.244e-06/0.4985, allocations: 0 / 0.5407 GB, free: 2.809 MB / 382.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01428/0.5127, allocations: 3.569 MB / 0.5442 GB, free: 15.21 MB / 398.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.103e-05/0.5128, allocations: 71.05 kB / 0.5442 GB, free: 15.13 MB / 398.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006824/0.5135, allocations: 0.5861 MB / 0.5448 GB, free: 14.54 MB / 398.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.659e-05/0.5136, allocations: 41.7 kB / 0.5448 GB, free: 14.49 MB / 398.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003253/0.5139, allocations: 0.5329 MB / 0.5454 GB, free: 13.95 MB / 398.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002508/0.5142, allocations: 328.5 kB / 0.5457 GB, free: 13.63 MB / 398.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003241/0.5145, allocations: 237.4 kB / 0.5459 GB, free: 13.4 MB / 398.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001694/0.5147, allocations: 392 kB / 0.5463 GB, free: 13.01 MB / 398.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006091/0.5153, allocations: 358.5 kB / 0.5466 GB, free: 12.66 MB / 398.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008597/0.5162, allocations: 0.7466 MB / 0.5474 GB, free: 11.75 MB / 398.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001618/0.5178, allocations: 1.206 MB / 0.5485 GB, free: 10.4 MB / 398.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.367e-06/0.5178, allocations: 7.938 kB / 0.5485 GB, free: 10.39 MB / 398.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004051/0.5219, allocations: 1.472 MB / 0.55 GB, free: 8.922 MB / 398.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.482e-05/0.5219, allocations: 8 kB / 0.55 GB, free: 8.914 MB / 398.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.702e-05/0.5219, allocations: 16 kB / 0.55 GB, free: 8.898 MB / 398.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002055/0.524, allocations: 249.4 kB / 0.5502 GB, free: 8.656 MB / 398.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001492/0.5255, allocations: 327.5 kB / 0.5505 GB, free: 8.336 MB / 398.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.005313/0.5308, allocations: 3.846 MB / 0.5543 GB, free: 4.238 MB / 398.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001019/0.5319, allocations: 48.39 kB / 0.5543 GB, free: 4.195 MB / 398.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001259/0.532, allocations: 76.05 kB / 0.5544 GB, free: 4.125 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 0.0005229/0.5325, allocations: 273.4 kB / 0.5547 GB, free: 3.848 MB / 398.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000193/0.5327, allocations: 90.88 kB / 0.5548 GB, free: 3.758 MB / 398.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004016/0.5368, allocations: 1.34 MB / 0.5561 GB, free: 2.441 MB / 398.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.556e-05/0.5368, allocations: 11.94 kB / 0.5561 GB, free: 2.43 MB / 398.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.616e-06/0.5368, allocations: 0 / 0.5561 GB, free: 2.43 MB / 398.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.736e-06/0.5368, allocations: 3.984 kB / 0.5561 GB, free: 2.426 MB / 398.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001501/0.5383, allocations: 1.066 MB / 0.5571 GB, free: 1.324 MB / 398.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.759e-06/0.5383, allocations: 0 / 0.5571 GB, free: 1.324 MB / 398.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001168/0.5395, allocations: 225.1 kB / 0.5573 GB, free: 1.109 MB / 398.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001894/0.5414, allocations: 230.3 kB / 0.5576 GB, free: 0.8867 MB / 398.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.36e-05/0.5415, allocations: 30.67 kB / 0.5576 GB, free: 0.8594 MB / 398.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004999/0.5465, allocations: 3.77 MB / 0.5613 GB, free: 12.83 MB / 414.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.126e-06/0.5465, allocations: 2.625 kB / 0.5613 GB, free: 12.83 MB / 414.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004175/0.5507, allocations: 1.736 MB / 0.563 GB, free: 11.06 MB / 414.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0002627/0.551, allocations: 156 kB / 0.5631 GB, free: 10.89 MB / 414.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001032/0.5511, allocations: 16 kB / 0.5631 GB, free: 10.88 MB / 414.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0004897/0.5516, allocations: 27.98 kB / 0.5632 GB, free: 10.85 MB / 414.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001688/0.5518, allocations: 79.55 kB / 0.5632 GB, free: 10.77 MB / 414.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.457e-05/0.5518, allocations: 39.98 kB / 0.5633 GB, free: 10.73 MB / 414.1 MB
Notification: Performance of sorting global known variables: time 0.0004409/0.5523, allocations: 391 kB / 0.5637 GB, free: 10.36 MB / 414.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.5523, allocations: 0 / 0.5637 GB, free: 10.36 MB / 414.1 MB
Notification: Performance of remove unused functions: time 0.002505/0.5548, allocations: 0.6714 MB / 0.5643 GB, free: 9.688 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 0.001476/0.5563, allocations: 0.8118 MB / 0.5651 GB, free: 9.008 MB / 414.1 MB
Notification: Performance of simCode: created initialization part: time 0.002066/0.5584, allocations: 1.255 MB / 0.5663 GB, free: 7.734 MB / 414.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.536e-06/0.5584, allocations: 2.688 kB / 0.5663 GB, free: 7.734 MB / 414.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001019/0.5594, allocations: 0.7479 MB / 0.5671 GB, free: 6.969 MB / 414.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0008915/0.5603, allocations: 205.8 kB / 0.5673 GB, free: 6.793 MB / 414.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003059/0.5634, allocations: 1.959 MB / 0.5692 GB, free: 4.836 MB / 414.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005446/0.5639, allocations: 1.041 MB / 0.5702 GB, free: 3.785 MB / 414.1 MB
Notification: Performance of simCode: alias equations: time 0.0006876/0.5646, allocations: 227.5 kB / 0.5704 GB, free: 3.637 MB / 414.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003252/0.565, allocations: 162.3 kB / 0.5706 GB, free: 3.484 MB / 414.1 MB
Notification: Performance of SimCode: time 2.4e-07/0.565, allocations: 0 / 0.5706 GB, free: 3.484 MB / 414.1 MB
Notification: Performance of Templates: time 0.03566/0.6007, allocations: 23.66 MB / 0.5937 GB, free: 12.41 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)