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-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-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(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 0.001124/0.001124, allocations: 108 kB / 15.61 MB, free: 152 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001884/0.001884, allocations: 194.6 kB / 16.53 MB, free: 6.699 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.34/1.34, allocations: 222.9 MB / 240.2 MB, free: 4.406 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1709/0.1709, allocations: 12.27 MB / 302.7 MB, free: 1.254 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001477/0.001477, allocations: 79.86 kB / 365.8 MB, free: 9.793 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1231/0.1246, allocations: 52.08 MB / 417.8 MB, free: 5.625 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.3125/0.4371, allocations: 8.468 MB / 426.3 MB, free: 36.44 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001574/0.4388, allocations: 0.8114 MB / 427.1 MB, free: 36.39 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003083/0.4391, allocations: 40.69 kB / 427.2 MB, free: 36.39 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002755/0.4394, allocations: 141.9 kB / 427.3 MB, free: 36.39 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004291/0.4399, allocations: 210.7 kB / 427.5 MB, free: 36.35 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003414/0.4402, allocations: 190 kB / 427.7 MB, free: 36.35 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005974/0.4408, allocations: 0.8434 MB / 428.5 MB, free: 36.16 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006611/0.4415, allocations: 0.5287 MB / 429.1 MB, free: 36.09 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002541/0.4418, allocations: 366 kB / 429.4 MB, free: 36.02 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003647/0.4421, allocations: 433.8 kB / 429.8 MB, free: 35.91 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001152/0.4423, allocations: 114.8 kB / 430 MB, free: 35.91 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001254/0.4424, allocations: 116.1 kB / 430.1 MB, free: 35.91 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001516/0.4426, allocations: 231.9 kB / 430.3 MB, free: 35.87 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002929/0.4429, allocations: 481.7 kB / 430.8 MB, free: 35.57 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0007471/0.4436, allocations: 1.147 MB / 431.9 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.829e-06/0.4436, allocations: 0 / 431.9 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.074e-06/0.4436, allocations: 0.5625 kB / 431.9 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.151e-05/0.4437, allocations: 0 / 431.9 MB, free: 35.09 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 0.00143/0.4451, allocations: 1.131 MB / 433.1 MB, free: 34.32 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.848e-05/0.4451, allocations: 10.88 kB / 433.1 MB, free: 34.31 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001301/0.4453, allocations: 96.88 kB / 433.2 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002266/0.4455, allocations: 305.1 kB / 433.5 MB, free: 33.98 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.823e-05/0.4456, allocations: 73.31 kB / 433.5 MB, free: 33.95 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001215/0.4457, allocations: 99.97 kB / 433.6 MB, free: 33.91 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001162/0.4469, allocations: 0.8765 MB / 434.5 MB, free: 33.54 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.057e-05/0.4469, allocations: 7.375 kB / 434.5 MB, free: 33.53 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.149e-05/0.447, allocations: 45.88 kB / 434.6 MB, free: 33.5 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.114e-05/0.447, allocations: 22.94 kB / 434.6 MB, free: 33.5 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000946/0.448, allocations: 0.628 MB / 435.2 MB, free: 33.27 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003648/0.4516, allocations: 2.868 MB / 438.1 MB, free: 31.73 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008629/0.4525, allocations: 0.5116 MB / 438.6 MB, free: 31.5 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003695/0.4529, allocations: 322.8 kB / 438.9 MB, free: 31.36 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.911e-05/0.4529, allocations: 3.781 kB / 438.9 MB, free: 31.36 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.674e-05/0.4529, allocations: 38.31 kB / 438.9 MB, free: 31.32 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.833e-06/0.4529, allocations: 0.7812 kB / 438.9 MB, free: 31.32 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004388/0.4573, allocations: 2.179 MB / 441.1 MB, free: 30.31 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.993e-05/0.4574, allocations: 85.42 kB / 441.2 MB, free: 30.21 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002887/0.4577, allocations: 363 kB / 441.6 MB, free: 30.03 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.007e-05/0.4577, allocations: 37.08 kB / 441.6 MB, free: 29.99 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001792/0.4579, allocations: 448.1 kB / 442 MB, free: 29.64 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001386/0.4581, allocations: 222 kB / 442.2 MB, free: 29.46 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001645/0.4582, allocations: 140 kB / 442.4 MB, free: 29.39 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 9.416e-05/0.4583, allocations: 354.2 kB / 442.7 MB, free: 29.05 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003073/0.4586, allocations: 251.5 kB / 443 MB, free: 28.95 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003839/0.459, allocations: 487.9 kB / 443.5 MB, free: 28.52 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005005/0.464, allocations: 1.718 MB / 445.2 MB, free: 27.7 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.528e-06/0.4641, allocations: 3.156 kB / 445.2 MB, free: 27.7 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001016/0.4651, allocations: 0.7973 MB / 446 MB, free: 27.34 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.037e-05/0.4651, allocations: 9.188 kB / 446 MB, free: 27.34 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.373e-05/0.4651, allocations: 10.62 kB / 446 MB, free: 27.34 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.86e-05/0.4652, allocations: 16.41 kB / 446 MB, free: 27.34 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005858/0.4658, allocations: 191.2 kB / 446.2 MB, free: 27.32 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.788e-05/0.4658, allocations: 16.78 kB / 446.2 MB, free: 27.31 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002917/0.4661, allocations: 21.5 kB / 446.2 MB, free: 27.3 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.12e-05/0.4661, allocations: 42.39 kB / 446.3 MB, free: 27.29 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
         nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         cytoplasm.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
         cytoplasm.y2.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" 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
         nucleus.ambientSubstance.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.y6.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" 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
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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0004856/0.4666, allocations: 286.7 kB / 446.5 MB, free: 27.07 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.037e-05/0.4667, allocations: 47.91 kB / 446.6 MB, free: 27.05 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001257/0.4669, allocations: 73.39 kB / 446.7 MB, free: 27 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.673e-06/0.4669, allocations: 6.156 kB / 446.7 MB, free: 27 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.185e-05/0.4669, allocations: 0 / 446.7 MB, free: 27 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.923e-06/0.4669, allocations: 3.281 kB / 446.7 MB, free: 27 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009077/0.4678, allocations: 0.7604 MB / 447.4 MB, free: 26.57 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.434e-06/0.4678, allocations: 3.938 kB / 447.4 MB, free: 26.57 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004915/0.4683, allocations: 110.5 kB / 447.5 MB, free: 26.56 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.549e-06/0.4683, allocations: 3 kB / 447.6 MB, free: 26.56 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.563e-05/0.4684, allocations: 17.66 kB / 447.6 MB, free: 26.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.006e-06/0.4684, allocations: 3.188 kB / 447.6 MB, free: 26.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.124e-06/0.4684, allocations: 0.8594 kB / 447.6 MB, free: 26.55 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009595/0.4694, allocations: 0.9323 MB / 448.5 MB, free: 26.02 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.969e-05/0.4694, allocations: 120.3 kB / 448.6 MB, free: 25.9 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.046e-05/0.4695, allocations: 18.09 kB / 448.6 MB, free: 25.89 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002511/0.4697, allocations: 8 kB / 448.6 MB, free: 25.88 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.325e-05/0.4698, allocations: 38.05 kB / 448.7 MB, free: 25.88 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.417e-05/0.4698, allocations: 17.25 kB / 448.7 MB, free: 25.87 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001665/0.47, allocations: 243.3 kB / 448.9 MB, free: 25.74 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.47, allocations: 0 / 448.9 MB, free: 25.74 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005539/0.4706, allocations: 155.6 kB / 449.1 MB, free: 25.72 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001072/0.4707, allocations: 115.5 kB / 449.2 MB, free: 25.61 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.001005/0.4717, allocations: 0.6118 MB / 449.8 MB, free: 25.38 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.625e-06/0.4717, allocations: 0.75 kB / 449.8 MB, free: 25.38 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002874/0.472, allocations: 272.1 kB / 450.1 MB, free: 25.28 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005001/0.4725, allocations: 65.73 kB / 450.1 MB, free: 25.25 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002806/0.4753, allocations: 1.796 MB / 451.9 MB, free: 24.13 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003871/0.4757, allocations: 0.9375 MB / 452.9 MB, free: 23.42 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002875/0.476, allocations: 69.84 kB / 452.9 MB, free: 23.4 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001309/0.4762, allocations: 42.62 kB / 453 MB, free: 23.39 MB / 350.1 MB
Notification: Performance of SimCode: time 2e-07/0.4762, allocations: 0 / 453 MB, free: 23.39 MB / 350.1 MB
Notification: Performance of Templates: time 0.009821/0.486, allocations: 5.361 MB / 458.4 MB, free: 23.05 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile
(rm -f BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; mkfifo BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CircadianOscillator.Container.pipe >> ../files/BioChem_BioChem.Examples.CircadianOscillator.Container.sim & ./BioChem_BioChem.Examples.CircadianOscillator.Container  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)