Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.CircadianOscillator.Container.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/BioChem 1.1.2/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/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(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008682/0.000868, allocations: 103 kB / 15.71 MB, free: 460 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001174/0.001174, allocations: 177.3 kB / 16.58 MB, free: 6.402 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.52/1.52, allocations: 223.2 MB / 240.6 MB, free: 5.434 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.2729/0.2729, allocations: 12.21 MB / 303.9 MB, free: 1.871 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.000327/0.0003271, allocations: 11.98 kB / 367.5 MB, free: 9.645 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1325/0.1328, allocations: 53.08 MB / 420.6 MB, free: 4.473 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.2849/0.4178, allocations: 7.667 MB / 428.3 MB, free: 34.93 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.002246/0.4201, allocations: 0.8182 MB / 429.1 MB, free: 34.75 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0004033/0.4205, allocations: 43.53 kB / 429.1 MB, free: 34.75 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002403/0.4207, allocations: 111 kB / 429.2 MB, free: 34.71 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004451/0.4212, allocations: 165.9 kB / 429.4 MB, free: 34.64 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003488/0.4215, allocations: 114.3 kB / 429.5 MB, free: 34.64 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0007226/0.4223, allocations: 0.7645 MB / 430.3 MB, free: 34.45 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007017/0.423, allocations: 408.3 kB / 430.7 MB, free: 34.42 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002228/0.4232, allocations: 256.7 kB / 430.9 MB, free: 34.35 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002937/0.4235, allocations: 313 kB / 431.2 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 6.735e-05/0.4236, allocations: 40.56 kB / 431.3 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 8.014e-05/0.4237, allocations: 41.72 kB / 431.3 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 8.76e-05/0.4238, allocations: 129.6 kB / 431.4 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000132/0.4239, allocations: 178.1 kB / 431.6 MB, free: 34.17 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006802/0.4246, allocations: 0.8754 MB / 432.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.63e-06/0.4246, allocations: 0 / 432.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of FrontEnd: time 3.267e-06/0.4246, allocations: 0.5938 kB / 432.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.247e-05/0.4246, allocations: 5.469 kB / 432.5 MB, free: 34.12 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: 252
 * Number of variables: 252
Notification: Performance of Generate backend data structure: time 0.001306/0.426, allocations: 0.9573 MB / 433.4 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.962e-05/0.426, allocations: 8.125 kB / 433.4 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001295/0.4261, allocations: 95.22 kB / 433.5 MB, free: 33.47 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002568/0.4264, allocations: 298.4 kB / 433.8 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.969e-05/0.4265, allocations: 73.69 kB / 433.9 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001144/0.4266, allocations: 103.1 kB / 434 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001321/0.4279, allocations: 0.8689 MB / 434.9 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.83e-05/0.428, allocations: 3.938 kB / 434.9 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.31e-05/0.428, allocations: 38.23 kB / 434.9 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.085e-05/0.4281, allocations: 29.2 kB / 434.9 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009917/0.4291, allocations: 0.6167 MB / 435.6 MB, free: 33.11 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003887/0.433, allocations: 2.841 MB / 438.4 MB, free: 32.1 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008338/0.4338, allocations: 0.5126 MB / 438.9 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000381/0.4342, allocations: 322.6 kB / 439.2 MB, free: 31.73 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.352e-05/0.4343, allocations: 7.812 kB / 439.2 MB, free: 31.72 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.279e-05/0.4343, allocations: 38.41 kB / 439.3 MB, free: 31.68 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 3.587e-06/0.4343, allocations: 1.078 kB / 439.3 MB, free: 31.68 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004352/0.4386, allocations: 2.168 MB / 441.4 MB, free: 30.69 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.944e-05/0.4387, allocations: 90.05 kB / 441.5 MB, free: 30.59 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003334/0.439, allocations: 367.1 kB / 441.9 MB, free: 30.39 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.792e-05/0.4391, allocations: 37.98 kB / 441.9 MB, free: 30.36 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002272/0.4393, allocations: 443.5 kB / 442.4 MB, free: 30.01 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001211/0.4395, allocations: 217 kB / 442.6 MB, free: 29.84 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 2.665e-05/0.4395, allocations: 15.34 kB / 442.6 MB, free: 29.83 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 9.413e-05/0.4396, allocations: 366.6 kB / 442.9 MB, free: 29.5 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003038/0.4399, allocations: 242.4 kB / 443.2 MB, free: 29.39 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003898/0.4403, allocations: 482.5 kB / 443.6 MB, free: 28.97 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003855/0.4407, allocations: 308.4 kB / 444 MB, free: 28.81 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.208e-06/0.4407, allocations: 4.938 kB / 444 MB, free: 28.81 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009771/0.4417, allocations: 0.7974 MB / 444.8 MB, free: 28.44 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.37e-05/0.4417, allocations: 8.781 kB / 444.8 MB, free: 28.44 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.309e-05/0.4417, allocations: 9.094 kB / 444.8 MB, free: 28.44 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.691e-05/0.4418, allocations: 16 kB / 444.8 MB, free: 28.44 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006168/0.4424, allocations: 181.6 kB / 445 MB, free: 28.42 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.022e-05/0.4424, allocations: 19.66 kB / 445 MB, free: 28.42 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003219/0.4427, allocations: 48.78 kB / 445 MB, free: 28.39 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.617e-05/0.4428, allocations: 41.28 kB / 445.1 MB, free: 28.38 MB / 350.1 MB
Warning: Assuming fixed start value for the following 12 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         cytoplasm.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.y5.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.y4.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.y6.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         nucleus.y3.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.y7.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         cytoplasm.y1.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.y2.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 39
 * 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 (107):
 * Single equations (assignments): 107
 * 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: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.000465/0.4433, allocations: 282.5 kB / 445.3 MB, free: 28.17 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.606e-05/0.4434, allocations: 51.91 kB / 445.4 MB, free: 28.14 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001532/0.4435, allocations: 65.88 kB / 445.5 MB, free: 28.09 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.244e-06/0.4435, allocations: 6.188 kB / 445.5 MB, free: 28.09 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.411e-05/0.4436, allocations: 0 / 445.5 MB, free: 28.09 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.804e-06/0.4436, allocations: 3.469 kB / 445.5 MB, free: 28.09 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009694/0.4445, allocations: 0.7655 MB / 446.2 MB, free: 27.68 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.325e-06/0.4446, allocations: 0 / 446.2 MB, free: 27.68 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004894/0.445, allocations: 106.8 kB / 446.3 MB, free: 27.67 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 7.083e-06/0.4451, allocations: 9.031 kB / 446.3 MB, free: 27.67 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.77e-05/0.4451, allocations: 17.55 kB / 446.4 MB, free: 27.66 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.086e-06/0.4451, allocations: 4 kB / 446.4 MB, free: 27.66 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.385e-06/0.4451, allocations: 2.875 kB / 446.4 MB, free: 27.66 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009911/0.4461, allocations: 0.9313 MB / 447.3 MB, free: 27.12 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.963e-05/0.4462, allocations: 116.7 kB / 447.4 MB, free: 27 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.644e-05/0.4463, allocations: 11.19 kB / 447.4 MB, free: 27 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002845/0.4466, allocations: 36.03 kB / 447.5 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.82e-05/0.4466, allocations: 33.94 kB / 447.5 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.62e-05/0.4467, allocations: 14.38 kB / 447.5 MB, free: 26.97 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001932/0.4469, allocations: 244.9 kB / 447.8 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.4469, allocations: 0 / 447.8 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005909/0.4475, allocations: 154.9 kB / 447.9 MB, free: 26.82 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 2
 * Number of states: 12 (nucleus.V,nucleus.y3.n,nucleus.y6.n,nucleus.y7.n,nucleus.ambientSubstance.n,cytoplasm.V,cytoplasm.y1.n,cytoplasm.y2.n,cytoplasm.y4.n,cytoplasm.y5.n,cytoplasm.ambientSubstance.n,V)
 * 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 (59):
 * Single equations (assignments): 59
 * 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: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001114/0.4476, allocations: 115.3 kB / 448 MB, free: 26.71 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0007678/0.4483, allocations: 0.5925 MB / 448.6 MB, free: 26.5 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.415e-06/0.4484, allocations: 4.125 kB / 448.6 MB, free: 26.49 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002846/0.4487, allocations: 258.4 kB / 448.9 MB, free: 26.4 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004754/0.4491, allocations: 61.69 kB / 448.9 MB, free: 26.37 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002792/0.4519, allocations: 2.279 MB / 451.2 MB, free: 24.86 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003422/0.4523, allocations: 0.9427 MB / 452.1 MB, free: 24.14 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001629/0.4525, allocations: 50.2 kB / 452.2 MB, free: 24.14 MB / 350.1 MB
Notification: Performance of SimCode: time 6.51e-07/0.4525, allocations: 0 / 452.2 MB, free: 24.14 MB / 350.1 MB
Notification: Performance of Templates: time 0.008862/0.4613, allocations: 7.335 MB / 459.5 MB, free: 23.38 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.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 OMCppBioChem_BioChem.Examples.CircadianOscillator.ContainerCalcHelperMain.o OMCppBioChem_BioChem.Examples.CircadianOscillator.ContainerCalcHelperMain.cpp
clang: error: no such file or directory: 'NOTFOUND'
make: *** [<builtin>: OMCppBioChem_BioChem.Examples.CircadianOscillator.ContainerCalcHelperMain.o] Error 1