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 0.005699/0.005699, allocations: 100.7 kB / 15.87 MB, free: 5.867 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001231/0.001231, allocations: 191 kB / 16.79 MB, free: 5.809 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.371/1.371, allocations: 222.9 MB / 240.5 MB, free: 4.574 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2047/0.2047, allocations: 15.31 MB / 305.9 MB, free: 15.33 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001191/0.001191, allocations: 59.91 kB / 370.3 MB, free: 4.422 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09505/0.09626, allocations: 53.6 MB / 423.9 MB, free: 14.77 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 0.3381/0.4344, allocations: 25.79 MB / 449.7 MB, free: 39.45 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.01382/0.4482, allocations: 16.62 MB / 466.3 MB, free: 31.22 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001246/0.4495, allocations: 28.59 kB / 466.4 MB, free: 31.21 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001025/0.4505, allocations: 298.9 kB / 466.7 MB, free: 31.05 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.004343/0.4549, allocations: 1.304 MB / 468 MB, free: 30.37 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.005317/0.4602, allocations: 1.741 MB / 469.7 MB, free: 29.43 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002075/0.4623, allocations: 1.486 MB / 471.2 MB, free: 28.73 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008914/0.4632, allocations: 0.7408 MB / 471.9 MB, free: 28.41 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009947/0.4643, allocations: 0.7541 MB / 472.7 MB, free: 28.18 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001008/0.4653, allocations: 0.8381 MB / 473.5 MB, free: 27.86 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0002091/0.4655, allocations: 88.19 kB / 473.6 MB, free: 27.86 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.005968/0.4715, allocations: 1.748 MB / 475.3 MB, free: 27.43 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0005891/0.4721, allocations: 291.3 kB / 475.6 MB, free: 27.27 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.001081/0.4732, allocations: 0.6412 MB / 476.3 MB, free: 26.92 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.003946/0.4771, allocations: 2.471 MB / 478.7 MB, free: 25.88 MB / 366.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.991e-06/0.4772, allocations: 1.25 kB / 478.7 MB, free: 25.88 MB / 366.1 MB
Notification: Performance of FrontEnd: time 1.733e-06/0.4772, allocations: 0 / 478.7 MB, free: 25.88 MB / 366.1 MB
Notification: Performance of Transformations before backend: time 2.15e-05/0.4772, allocations: 4 kB / 478.7 MB, free: 25.88 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 0.003761/0.481, allocations: 1.802 MB / 480.6 MB, free: 24.77 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.442e-05/0.481, allocations: 9.719 kB / 480.6 MB, free: 24.77 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001467/0.4825, allocations: 270.3 kB / 480.8 MB, free: 24.69 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001125/0.4837, allocations: 0.6498 MB / 481.5 MB, free: 24.25 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001163/0.4838, allocations: 114.1 kB / 481.6 MB, free: 24.18 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002094/0.484, allocations: 108.8 kB / 481.7 MB, free: 24.14 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002264/0.4863, allocations: 1.338 MB / 483 MB, free: 23.59 MB / 366.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.302e-05/0.4863, allocations: 0 / 483 MB, free: 23.59 MB / 366.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001105/0.4864, allocations: 46.25 kB / 483.1 MB, free: 23.55 MB / 366.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.668e-05/0.4865, allocations: 25.66 kB / 483.1 MB, free: 23.55 MB / 366.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.002651/0.4891, allocations: 1.695 MB / 484.8 MB, free: 23.06 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 0.006958/0.4961, allocations: 4.295 MB / 489.1 MB, free: 20.46 MB / 366.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003594/0.4997, allocations: 2.275 MB / 491.4 MB, free: 19.46 MB / 366.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0009132/0.5006, allocations: 0.6025 MB / 492 MB, free: 19.2 MB / 366.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006386/0.507, allocations: 5.405 MB / 497.4 MB, free: 14.94 MB / 366.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.103e-05/0.5071, allocations: 39.78 kB / 497.4 MB, free: 14.9 MB / 366.1 MB
Notification: Performance of pre-optimization done (n=78): time 2.485e-06/0.5071, allocations: 0 / 497.4 MB, free: 14.9 MB / 366.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01549/0.5226, allocations: 3.56 MB / 0.4892 GB, free: 13.39 MB / 366.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.118e-05/0.5227, allocations: 63.72 kB / 0.4893 GB, free: 13.32 MB / 366.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0006088/0.5233, allocations: 0.5875 MB / 0.4899 GB, free: 13.05 MB / 366.1 MB
Notification: Performance of collectPreVariables (initialization): time 7.729e-05/0.5234, allocations: 41.23 kB / 0.4899 GB, free: 13.01 MB / 366.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002481/0.5236, allocations: 0.5275 MB / 0.4904 GB, free: 12.58 MB / 366.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002118/0.5239, allocations: 340.9 kB / 0.4907 GB, free: 12.32 MB / 366.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002963/0.5242, allocations: 230.7 kB / 0.491 GB, free: 12.21 MB / 366.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001111/0.5243, allocations: 392.4 kB / 0.4913 GB, free: 11.86 MB / 366.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005746/0.5249, allocations: 357.2 kB / 0.4917 GB, free: 11.73 MB / 366.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007326/0.5256, allocations: 0.7523 MB / 0.4924 GB, free: 11.08 MB / 366.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001286/0.5269, allocations: 1.209 MB / 0.4936 GB, free: 10.16 MB / 366.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.971e-06/0.5269, allocations: 3.656 kB / 0.4936 GB, free: 10.16 MB / 366.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.003942/0.5309, allocations: 1.477 MB / 0.495 GB, free: 9.562 MB / 366.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.493e-05/0.5309, allocations: 11.52 kB / 0.4951 GB, free: 9.562 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.633e-05/0.5309, allocations: 14.91 kB / 0.4951 GB, free: 9.559 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.002051/0.533, allocations: 247.6 kB / 0.4953 GB, free: 9.504 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001375/0.5344, allocations: 329.4 kB / 0.4956 GB, free: 9.469 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.00477/0.5391, allocations: 3.485 MB / 0.499 GB, free: 6.367 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001199/0.5404, allocations: 77.2 kB / 0.4991 GB, free: 6.336 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001502/0.5405, allocations: 64.3 kB / 0.4992 GB, free: 6.328 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 0.0005222/0.5411, allocations: 282.8 kB / 0.4994 GB, free: 6.102 MB / 366.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001887/0.5413, allocations: 82.3 kB / 0.4995 GB, free: 6.059 MB / 366.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004204/0.5455, allocations: 1.327 MB / 0.5008 GB, free: 5.289 MB / 366.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.348e-06/0.5455, allocations: 12.66 kB / 0.5008 GB, free: 5.277 MB / 366.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.433e-06/0.5455, allocations: 0 / 0.5008 GB, free: 5.277 MB / 366.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.565e-05/0.5455, allocations: 8.547 kB / 0.5008 GB, free: 5.273 MB / 366.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001634/0.5472, allocations: 1.081 MB / 0.5019 GB, free: 4.332 MB / 366.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.47e-06/0.5472, allocations: 4 kB / 0.5019 GB, free: 4.328 MB / 366.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001155/0.5483, allocations: 211.2 kB / 0.5021 GB, free: 4.152 MB / 366.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.00202/0.5504, allocations: 232 kB / 0.5023 GB, free: 3.984 MB / 366.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 8.709e-05/0.5505, allocations: 35.89 kB / 0.5023 GB, free: 3.953 MB / 366.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004236/0.5547, allocations: 3.392 MB / 0.5056 GB, free: 468 kB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.32e-06/0.5548, allocations: 10.08 kB / 0.5057 GB, free: 460 kB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004943/0.5597, allocations: 1.738 MB / 0.5074 GB, free: 14.86 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003708/0.5601, allocations: 154.7 kB / 0.5075 GB, free: 14.7 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001998/0.5603, allocations: 20.19 kB / 0.5075 GB, free: 14.68 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0007143/0.5611, allocations: 29.95 kB / 0.5075 GB, free: 14.65 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002546/0.5613, allocations: 94.92 kB / 0.5076 GB, free: 14.58 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.96e-05/0.5614, allocations: 40.17 kB / 0.5077 GB, free: 14.55 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0006104/0.5621, allocations: 387.1 kB / 0.508 GB, free: 14.18 MB / 382.1 MB
Notification: Performance of sort global known variables: time 1.3e-07/0.5621, allocations: 0 / 0.508 GB, free: 14.18 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.00269/0.5648, allocations: 0.6675 MB / 0.5087 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 0.002215/0.567, allocations: 0.8001 MB / 0.5095 GB, free: 12.7 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.002739/0.5697, allocations: 1.259 MB / 0.5107 GB, free: 11.42 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 4.709e-06/0.5698, allocations: 0 / 0.5107 GB, free: 11.42 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001368/0.5711, allocations: 0.741 MB / 0.5114 GB, free: 10.65 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001595/0.5728, allocations: 191.7 kB / 0.5116 GB, free: 10.46 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004775/0.5776, allocations: 2.477 MB / 0.514 GB, free: 7.945 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007648/0.5784, allocations: 1.038 MB / 0.515 GB, free: 6.883 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0006311/0.579, allocations: 204.3 kB / 0.5152 GB, free: 6.688 MB / 382.1 MB
Notification: Performance of SimCode: time 9.61e-07/0.579, allocations: 0 / 0.5152 GB, free: 6.688 MB / 382.1 MB
Notification: Performance of Templates: time 0.03936/0.6184, allocations: 26.22 MB / 0.5408 GB, free: 12.5 MB / 414.1 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)