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/package.mo", uses=false)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/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 0.001292/0.001292, allocations: 99.75 kB / 15.71 MB, free: 452 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001214/0.001214, allocations: 175 kB / 16.58 MB, free: 6.422 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.572/1.572, allocations: 223.3 MB / 240.6 MB, free: 5.395 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/package.mo): time 0.3352/0.3352, allocations: 15.27 MB / 307 MB, free: 15.73 MB / 254.1 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0004207/0.0004207, allocations: 8 kB / 372.1 MB, free: 3.984 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.4616/0.462, allocations: 54.62 MB / 426.7 MB, free: 39.93 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/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/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 0.008744/0.4708, allocations: 5.834 MB / 432.6 MB, free: 38.89 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02153/0.4924, allocations: 15.19 MB / 447.8 MB, free: 27.88 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.00151/0.4939, allocations: 23.66 kB / 447.8 MB, free: 27.87 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001111/0.4951, allocations: 296.6 kB / 448.1 MB, free: 27.72 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005614/0.5007, allocations: 1.289 MB / 449.4 MB, free: 26.94 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.006916/0.5077, allocations: 1.61 MB / 451 MB, free: 26.01 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.002707/0.5104, allocations: 1.416 MB / 452.4 MB, free: 25.31 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0009869/0.5114, allocations: 0.6525 MB / 453 MB, free: 25.06 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0009222/0.5123, allocations: 0.6165 MB / 453.7 MB, free: 24.86 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.001051/0.5134, allocations: 0.7704 MB / 454.4 MB, free: 24.6 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001625/0.5136, allocations: 71.31 kB / 454.5 MB, free: 24.59 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006481/0.5201, allocations: 1.623 MB / 456.1 MB, free: 24.21 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0002906/0.5204, allocations: 251.9 kB / 456.4 MB, free: 24.09 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003199/0.5207, allocations: 245.6 kB / 456.6 MB, free: 23.95 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.003876/0.5246, allocations: 2.474 MB / 459.1 MB, free: 23.01 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.974e-06/0.5246, allocations: 0 / 459.1 MB, free: 23.01 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.304e-06/0.5246, allocations: 4 kB / 459.1 MB, free: 23 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.313e-05/0.5246, allocations: 3.938 kB / 459.1 MB, free: 23 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 0.003306/0.528, allocations: 1.524 MB / 460.6 MB, free: 22.04 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.42e-05/0.528, allocations: 9.031 kB / 460.6 MB, free: 22.04 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001462/0.5295, allocations: 265.6 kB / 460.9 MB, free: 21.96 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001049/0.5305, allocations: 0.6119 MB / 461.5 MB, free: 21.53 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001314/0.5307, allocations: 114.2 kB / 461.6 MB, free: 21.46 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000249/0.5309, allocations: 112.7 kB / 461.7 MB, free: 21.42 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002854/0.5338, allocations: 1.319 MB / 463 MB, free: 20.88 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.295e-05/0.5339, allocations: 7.891 kB / 463 MB, free: 20.87 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001537/0.534, allocations: 49.86 kB / 463.1 MB, free: 20.83 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.332e-05/0.5341, allocations: 25.91 kB / 463.1 MB, free: 20.83 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.003686/0.5378, allocations: 1.687 MB / 464.8 MB, free: 20.34 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 0.008601/0.5464, allocations: 4.254 MB / 469 MB, free: 17.74 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003377/0.5498, allocations: 2.272 MB / 471.3 MB, free: 16.73 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0009198/0.5507, allocations: 0.5872 MB / 471.9 MB, free: 16.48 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.006224/0.5569, allocations: 5.275 MB / 477.2 MB, free: 12.25 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.504e-05/0.557, allocations: 43.09 kB / 477.2 MB, free: 12.2 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=78): time 1.994e-06/0.557, allocations: 0 / 477.2 MB, free: 12.2 MB / 350.1 MB
Notification: Performance of matching and sorting (n=95): time 0.01393/0.5709, allocations: 3.61 MB / 480.8 MB, free: 10.68 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.978e-05/0.571, allocations: 61.09 kB / 480.9 MB, free: 10.61 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007924/0.5718, allocations: 0.5853 MB / 481.5 MB, free: 10.34 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 6.103e-05/0.5719, allocations: 45.11 kB / 481.5 MB, free: 10.29 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.000314/0.5722, allocations: 0.528 MB / 482.1 MB, free: 9.863 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0002457/0.5725, allocations: 330.2 kB / 482.4 MB, free: 9.605 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.625e-05/0.5725, allocations: 25.47 kB / 482.4 MB, free: 9.586 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001345/0.5727, allocations: 397.1 kB / 482.8 MB, free: 9.234 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006278/0.5733, allocations: 352.2 kB / 483.1 MB, free: 9.109 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008381/0.5741, allocations: 0.7431 MB / 483.9 MB, free: 8.469 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007641/0.5749, allocations: 470.3 kB / 484.3 MB, free: 8.242 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.778e-06/0.5749, allocations: 4.219 kB / 484.3 MB, free: 8.242 MB / 350.1 MB
Notification: Performance of matching and sorting (n=158) (initialization): time 0.004069/0.579, allocations: 1.474 MB / 485.8 MB, free: 7.645 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.773e-05/0.5791, allocations: 11.56 kB / 485.8 MB, free: 7.645 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.13e-05/0.5791, allocations: 12.38 kB / 485.8 MB, free: 7.645 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.001963/0.581, allocations: 262.8 kB / 486.1 MB, free: 7.59 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001346/0.5824, allocations: 326.1 kB / 486.4 MB, free: 7.559 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004796/0.5872, allocations: 3.521 MB / 489.9 MB, free: 4.441 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.001033/0.5883, allocations: 76.92 kB / 490 MB, free: 4.41 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001272/0.5884, allocations: 65.05 kB / 490.1 MB, free: 4.402 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 0.0004773/0.5889, allocations: 274.3 kB / 490.3 MB, free: 4.184 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001458/0.589, allocations: 87.47 kB / 490.4 MB, free: 4.137 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.004011/0.5931, allocations: 1.35 MB / 491.8 MB, free: 3.148 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.135e-06/0.5931, allocations: 8 kB / 491.8 MB, free: 3.141 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.838e-06/0.5931, allocations: 0 / 491.8 MB, free: 3.141 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.7e-05/0.5931, allocations: 5.297 kB / 491.8 MB, free: 3.141 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001541/0.5947, allocations: 1.069 MB / 492.9 MB, free: 2.211 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.472e-06/0.5947, allocations: 8.125 kB / 492.9 MB, free: 2.203 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001055/0.5957, allocations: 219.2 kB / 493.1 MB, free: 2.02 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.001847/0.5976, allocations: 241.4 kB / 493.3 MB, free: 1.797 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.79e-05/0.5977, allocations: 39.97 kB / 493.4 MB, free: 1.758 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.004384/0.6021, allocations: 3.41 MB / 496.8 MB, free: 14.08 MB / 366.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.264e-06/0.6021, allocations: 0 / 496.8 MB, free: 14.08 MB / 366.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.004407/0.6065, allocations: 1.74 MB / 498.5 MB, free: 12.31 MB / 366.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0003651/0.6069, allocations: 152 kB / 498.6 MB, free: 12.14 MB / 366.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000124/0.607, allocations: 31.94 kB / 498.7 MB, free: 12.11 MB / 366.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005009/0.6075, allocations: 31.92 kB / 498.7 MB, free: 12.08 MB / 366.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002047/0.6078, allocations: 84.83 kB / 498.8 MB, free: 11.99 MB / 366.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.379e-05/0.6078, allocations: 39.98 kB / 498.8 MB, free: 11.95 MB / 366.1 MB
Notification: Performance of sorting global known variables: time 0.0005384/0.6084, allocations: 387.1 kB / 499.2 MB, free: 11.58 MB / 366.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.6084, allocations: 0 / 499.2 MB, free: 11.58 MB / 366.1 MB
Notification: Performance of remove unused functions: time 0.00256/0.611, allocations: 0.6519 MB / 499.9 MB, free: 10.93 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 0.001479/0.6125, allocations: 0.7831 MB / 0.4889 GB, free: 10.14 MB / 366.1 MB
Notification: Performance of simCode: created initialization part: time 0.0024/0.6149, allocations: 1.243 MB / 0.4901 GB, free: 8.871 MB / 366.1 MB
Notification: Performance of simCode: created event and clocks part: time 6.342e-06/0.6149, allocations: 4.188 kB / 0.4901 GB, free: 8.867 MB / 366.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.001104/0.616, allocations: 0.7333 MB / 0.4908 GB, free: 8.109 MB / 366.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001076/0.6171, allocations: 195.5 kB / 0.491 GB, free: 7.922 MB / 366.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003793/0.6209, allocations: 2.478 MB / 0.4935 GB, free: 5.395 MB / 366.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0008082/0.6217, allocations: 1.038 MB / 0.4945 GB, free: 4.328 MB / 366.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0005608/0.6223, allocations: 204.1 kB / 0.4947 GB, free: 4.133 MB / 366.1 MB
Notification: Performance of SimCode: time 1.874e-06/0.6223, allocations: 4 kB / 0.4947 GB, free: 4.129 MB / 366.1 MB
Notification: Performance of Templates: time 0.03522/0.6575, allocations: 25.95 MB / 0.52 GB, free: 10.25 MB / 398.1 MB
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile clang++  NOTFOUND  -Winvalid-pch -O0 -g -DNDEBUG -fPIC   -std=c++11 -DBOOST_ALL_DYN_LINK   -DUSE_DGESV -DUSE_LOGGER -DOMC_BUILD -DUSE_THREAD -DSUNDIALS_MAJOR_VERSION=5 -DSUNDIALS_MINOR_VERSION=4 -DPMC_USE_SUNDIALS -I"." -I"/var/lib/jenkins1/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/bin/../include/omc/cpp/" -I.  -I"." -I"." -I"/var/lib/jenkins1/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/include/omc/c/sundials"     -DMEASURETIME_PROFILEBLOCKS -DUSE_LOGGER  -c -o OMCppChemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesisCalcHelperMain.o OMCppChemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesisCalcHelperMain.cpp
clang: error: no such file or directory: 'NOTFOUND'
make: *** [<builtin>: OMCppChemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesisCalcHelperMain.o] Error 1