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 0.001392/0.001392, allocations: 103.4 kB / 15.33 MB, free: 0.5078 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001703/0.001703, allocations: 193.1 kB / 16.25 MB, free: 6.617 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.368/1.368, allocations: 222.9 MB / 239.9 MB, free: 4.508 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1718/0.1718, allocations: 12.27 MB / 302.3 MB, free: 1.359 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001125/0.001125, allocations: 59.91 kB / 365.3 MB, free: 10.11 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1144/0.1155, allocations: 52.07 MB / 417.3 MB, free: 5.93 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.215/0.3306, allocations: 8.6 MB / 425.9 MB, free: 36.12 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001359/0.332, allocations: 0.8211 MB / 426.8 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003065/0.3324, allocations: 43.72 kB / 426.8 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002733/0.3326, allocations: 103.4 kB / 426.9 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004151/0.3331, allocations: 169.2 kB / 427.1 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003005/0.3334, allocations: 166.2 kB / 427.2 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005974/0.334, allocations: 0.8364 MB / 428.1 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007344/0.3348, allocations: 0.5383 MB / 428.6 MB, free: 35.89 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002903/0.3351, allocations: 368.9 kB / 429 MB, free: 35.82 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003346/0.3354, allocations: 430.2 kB / 429.4 MB, free: 35.71 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.000118/0.3355, allocations: 115.9 kB / 429.5 MB, free: 35.71 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001231/0.3356, allocations: 120 kB / 429.6 MB, free: 35.71 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001429/0.3358, allocations: 223.4 kB / 429.8 MB, free: 35.68 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003169/0.3361, allocations: 483.2 kB / 430.3 MB, free: 35.43 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0008043/0.3369, allocations: 1.146 MB / 431.5 MB, free: 34.96 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.313e-06/0.3369, allocations: 0 / 431.5 MB, free: 34.96 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.264e-06/0.337, allocations: 0.9375 kB / 431.5 MB, free: 34.96 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.486e-05/0.337, allocations: 0.75 kB / 431.5 MB, free: 34.96 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 0.001446/0.3384, allocations: 1.121 MB / 432.6 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.759e-05/0.3385, allocations: 9.469 kB / 432.6 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001227/0.3386, allocations: 94.44 kB / 432.7 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002025/0.3388, allocations: 312.2 kB / 433 MB, free: 33.87 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.138e-05/0.3389, allocations: 77.55 kB / 433.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001001/0.339, allocations: 97.25 kB / 433.2 MB, free: 33.8 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001117/0.3401, allocations: 0.8787 MB / 434 MB, free: 33.42 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.651e-05/0.3401, allocations: 4.094 kB / 434 MB, free: 33.42 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.479e-05/0.3402, allocations: 45.69 kB / 434.1 MB, free: 33.38 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.546e-05/0.3402, allocations: 24.97 kB / 434.1 MB, free: 33.38 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008374/0.3411, allocations: 0.6192 MB / 434.7 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003556/0.3446, allocations: 2.865 MB / 437.6 MB, free: 31.64 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008434/0.3455, allocations: 0.5113 MB / 438.1 MB, free: 31.41 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003389/0.3458, allocations: 319 kB / 438.4 MB, free: 31.27 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.526e-05/0.3459, allocations: 11.06 kB / 438.4 MB, free: 31.27 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.025e-05/0.3459, allocations: 42.78 kB / 438.5 MB, free: 31.22 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.883e-06/0.3459, allocations: 0 / 438.5 MB, free: 31.22 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.00442/0.3504, allocations: 2.171 MB / 440.6 MB, free: 30.21 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.705e-05/0.3504, allocations: 83.89 kB / 440.7 MB, free: 30.12 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002709/0.3507, allocations: 354.7 kB / 441.1 MB, free: 29.94 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.887e-05/0.3507, allocations: 36.7 kB / 441.1 MB, free: 29.9 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001569/0.3509, allocations: 458.3 kB / 441.6 MB, free: 29.54 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001033/0.351, allocations: 218.1 kB / 441.8 MB, free: 29.38 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001568/0.3512, allocations: 140.5 kB / 441.9 MB, free: 29.3 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 7.422e-05/0.3512, allocations: 361.8 kB / 442.3 MB, free: 28.96 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002896/0.3515, allocations: 251.5 kB / 442.5 MB, free: 28.85 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003653/0.3519, allocations: 480.4 kB / 443 MB, free: 28.43 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005226/0.3571, allocations: 1.711 MB / 444.7 MB, free: 27.62 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.989e-06/0.3572, allocations: 3.094 kB / 444.7 MB, free: 27.62 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001009/0.3582, allocations: 0.802 MB / 445.5 MB, free: 27.26 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.474e-05/0.3582, allocations: 14.19 kB / 445.5 MB, free: 27.26 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.237e-05/0.3582, allocations: 9.062 kB / 445.5 MB, free: 27.26 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 4.221e-05/0.3583, allocations: 13.12 kB / 445.5 MB, free: 27.26 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006008/0.3589, allocations: 185 kB / 445.7 MB, free: 27.23 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.709e-05/0.3589, allocations: 19.44 kB / 445.7 MB, free: 27.23 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003746/0.3593, allocations: 48.75 kB / 445.8 MB, free: 27.21 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.904e-05/0.3593, allocations: 33.22 kB / 445.8 MB, free: 27.2 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 0.0004341/0.3598, allocations: 287.3 kB / 446.1 MB, free: 26.99 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.528e-05/0.3599, allocations: 46.5 kB / 446.1 MB, free: 26.96 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001194/0.36, allocations: 73.03 kB / 446.2 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.561e-06/0.36, allocations: 7.531 kB / 446.2 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.287e-05/0.36, allocations: 0 / 446.2 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.502e-06/0.36, allocations: 3.422 kB / 446.2 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008908/0.3609, allocations: 0.764 MB / 447 MB, free: 26.48 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.876e-06/0.361, allocations: 0 / 447 MB, free: 26.48 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005157/0.3615, allocations: 112.2 kB / 447.1 MB, free: 26.47 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.95e-06/0.3615, allocations: 3.125 kB / 447.1 MB, free: 26.47 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.685e-05/0.3615, allocations: 21.67 kB / 447.1 MB, free: 26.46 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.406e-06/0.3615, allocations: 0 / 447.1 MB, free: 26.46 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.816e-06/0.3616, allocations: 5.25 kB / 447.1 MB, free: 26.46 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009865/0.3625, allocations: 0.9315 MB / 448 MB, free: 25.92 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 8.633e-05/0.3626, allocations: 113.3 kB / 448.2 MB, free: 25.8 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.01e-05/0.3627, allocations: 19.16 kB / 448.2 MB, free: 25.79 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003121/0.363, allocations: 31.3 kB / 448.2 MB, free: 25.78 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.794e-05/0.3631, allocations: 35.92 kB / 448.2 MB, free: 25.77 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.823e-05/0.3631, allocations: 19.91 kB / 448.3 MB, free: 25.77 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.000184/0.3633, allocations: 240.2 kB / 448.5 MB, free: 25.64 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.3633, allocations: 4 kB / 448.5 MB, free: 25.64 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005935/0.3639, allocations: 156 kB / 448.7 MB, free: 25.62 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 0.0001116/0.364, allocations: 111.5 kB / 448.8 MB, free: 25.52 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0009746/0.365, allocations: 0.6235 MB / 449.4 MB, free: 25.27 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.394e-06/0.365, allocations: 0 / 449.4 MB, free: 25.27 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002723/0.3653, allocations: 261.1 kB / 449.6 MB, free: 25.18 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005178/0.3658, allocations: 79.42 kB / 449.7 MB, free: 25.13 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002695/0.3685, allocations: 2.173 MB / 451.9 MB, free: 23.64 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003047/0.3689, allocations: 0.9427 MB / 452.8 MB, free: 22.93 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002944/0.3692, allocations: 61.42 kB / 452.9 MB, free: 22.91 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000129/0.3693, allocations: 46.78 kB / 452.9 MB, free: 22.9 MB / 350.1 MB
Notification: Performance of SimCode: time 7.41e-07/0.3693, allocations: 0 / 452.9 MB, free: 22.9 MB / 350.1 MB
Notification: Performance of Templates: time 0.008631/0.378, allocations: 5.35 MB / 458.3 MB, free: 22.55 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)