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 0.001526/0.001526, allocations: 107.7 kB / 15.99 MB, free: 6.355 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001502/0.001502, allocations: 190.4 kB / 16.91 MB, free: 6.195 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.68/1.68, allocations: 222.9 MB / 240.6 MB, free: 15.44 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06278/0.06278, allocations: 12.28 MB / 303 MB, free: 3.488 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001303/0.001303, allocations: 63.91 kB / 365.9 MB, free: 4.496 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3143/0.3156, allocations: 52.08 MB / 418 MB, free: 22.04 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.009579/0.3253, allocations: 8.613 MB / 426.6 MB, free: 13.4 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001433/0.3268, allocations: 0.8167 MB / 427.4 MB, free: 12.59 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003167/0.3271, allocations: 40 kB / 427.5 MB, free: 12.55 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002764/0.3274, allocations: 109.2 kB / 427.6 MB, free: 12.45 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.000414/0.3278, allocations: 165.1 kB / 427.7 MB, free: 12.29 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003733/0.3282, allocations: 176.5 kB / 427.9 MB, free: 12.12 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.000592/0.3288, allocations: 0.8307 MB / 428.7 MB, free: 11.29 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006542/0.3295, allocations: 0.5332 MB / 429.3 MB, free: 10.73 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000253/0.3297, allocations: 370.7 kB / 429.6 MB, free: 10.37 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003328/0.3301, allocations: 438 kB / 430.1 MB, free: 9.941 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001077/0.3302, allocations: 117.3 kB / 430.2 MB, free: 9.828 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.000108/0.3303, allocations: 116 kB / 430.3 MB, free: 9.715 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.000133/0.3304, allocations: 219.3 kB / 430.5 MB, free: 9.5 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002864/0.3307, allocations: 486.6 kB / 431 MB, free: 9.023 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005826/0.3313, allocations: 0.9139 MB / 431.9 MB, free: 8.109 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.342e-06/0.3313, allocations: 0 / 431.9 MB, free: 8.109 MB / 302.1 MB
Notification: Performance of FrontEnd: time 2.244e-06/0.3314, allocations: 0.8438 kB / 431.9 MB, free: 8.109 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.316e-05/0.3314, allocations: 3.938 kB / 431.9 MB, free: 8.105 MB / 302.1 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 0.001436/0.3328, allocations: 1.122 MB / 433 MB, free: 6.938 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.723e-05/0.3329, allocations: 12.03 kB / 433 MB, free: 6.926 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001312/0.333, allocations: 99.72 kB / 433.1 MB, free: 6.828 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002371/0.3333, allocations: 302.8 kB / 433.4 MB, free: 6.496 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.226e-05/0.3333, allocations: 74.38 kB / 433.5 MB, free: 6.426 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001185/0.3334, allocations: 104.3 kB / 433.6 MB, free: 6.324 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001175/0.3346, allocations: 0.8797 MB / 434.5 MB, free: 5.434 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.086e-05/0.3347, allocations: 192 / 434.5 MB, free: 5.434 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.746e-05/0.3347, allocations: 43.94 kB / 434.5 MB, free: 5.391 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.672e-05/0.3348, allocations: 24 kB / 434.5 MB, free: 5.367 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008427/0.3356, allocations: 0.6208 MB / 435.2 MB, free: 4.746 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00355/0.3392, allocations: 2.87 MB / 438 MB, free: 1.805 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008455/0.34, allocations: 0.5299 MB / 438.6 MB, free: 1.258 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003472/0.3404, allocations: 319.5 kB / 438.9 MB, free: 0.9414 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.074e-05/0.3404, allocations: 4.438 kB / 438.9 MB, free: 0.9375 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.064e-05/0.3404, allocations: 46.92 kB / 438.9 MB, free: 0.8828 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.974e-06/0.3405, allocations: 0 / 438.9 MB, free: 0.8828 MB / 302.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004815/0.3453, allocations: 2.159 MB / 441.1 MB, free: 14.68 MB / 318.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.199e-05/0.3453, allocations: 81.67 kB / 441.2 MB, free: 14.58 MB / 318.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003937/0.3457, allocations: 361.5 kB / 441.5 MB, free: 14.22 MB / 318.1 MB
Notification: Performance of collectPreVariables (initialization): time 4.113e-05/0.3458, allocations: 33.7 kB / 441.6 MB, free: 14.18 MB / 318.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003344/0.3461, allocations: 454.1 kB / 442 MB, free: 13.73 MB / 318.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001823/0.3463, allocations: 216.8 kB / 442.2 MB, free: 13.51 MB / 318.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000189/0.3465, allocations: 142.6 kB / 442.3 MB, free: 13.37 MB / 318.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001905/0.3467, allocations: 358.8 kB / 442.7 MB, free: 13.01 MB / 318.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00037/0.3471, allocations: 247.7 kB / 442.9 MB, free: 12.76 MB / 318.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005562/0.3477, allocations: 484.9 kB / 443.4 MB, free: 12.17 MB / 318.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005815/0.3535, allocations: 1.716 MB / 445.1 MB, free: 10.33 MB / 318.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.226e-06/0.3535, allocations: 4 kB / 445.1 MB, free: 10.33 MB / 318.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001193/0.3547, allocations: 0.8031 MB / 445.9 MB, free: 9.52 MB / 318.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.579e-05/0.3547, allocations: 8 kB / 445.9 MB, free: 9.512 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.441e-05/0.3548, allocations: 8 kB / 446 MB, free: 9.504 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.26e-05/0.3548, allocations: 12 kB / 446 MB, free: 9.492 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006729/0.3555, allocations: 187.7 kB / 446.1 MB, free: 9.309 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.067e-05/0.3555, allocations: 19.94 kB / 446.2 MB, free: 9.289 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003694/0.3559, allocations: 52.31 kB / 446.2 MB, free: 9.238 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.103e-05/0.356, allocations: 39.94 kB / 446.3 MB, free: 9.199 MB / 318.1 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 0.0005745/0.3565, allocations: 279.3 kB / 446.5 MB, free: 8.922 MB / 318.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000103/0.3566, allocations: 43.44 kB / 446.6 MB, free: 8.879 MB / 318.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001537/0.3568, allocations: 72.89 kB / 446.6 MB, free: 8.809 MB / 318.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.963e-06/0.3568, allocations: 4 kB / 446.6 MB, free: 8.805 MB / 318.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.668e-06/0.3568, allocations: 4 kB / 446.7 MB, free: 8.801 MB / 318.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.993e-06/0.3568, allocations: 0 / 446.7 MB, free: 8.801 MB / 318.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001148/0.358, allocations: 0.7554 MB / 447.4 MB, free: 7.996 MB / 318.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.515e-06/0.358, allocations: 4 kB / 447.4 MB, free: 7.992 MB / 318.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005545/0.3586, allocations: 111.8 kB / 447.5 MB, free: 7.883 MB / 318.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.888e-06/0.3586, allocations: 4 kB / 447.5 MB, free: 7.879 MB / 318.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.132e-05/0.3586, allocations: 16 kB / 447.5 MB, free: 7.863 MB / 318.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.725e-06/0.3586, allocations: 0 / 447.5 MB, free: 7.863 MB / 318.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.436e-06/0.3587, allocations: 4 kB / 447.5 MB, free: 7.859 MB / 318.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001281/0.3599, allocations: 0.936 MB / 448.5 MB, free: 6.902 MB / 318.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001008/0.36, allocations: 120.5 kB / 448.6 MB, free: 6.766 MB / 318.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.676e-05/0.3601, allocations: 16 kB / 448.6 MB, free: 6.75 MB / 318.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003129/0.3604, allocations: 35.83 kB / 448.6 MB, free: 6.715 MB / 318.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.298e-05/0.3605, allocations: 36.45 kB / 448.7 MB, free: 6.68 MB / 318.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.3e-05/0.3606, allocations: 19.98 kB / 448.7 MB, free: 6.66 MB / 318.1 MB
Notification: Performance of sorting global known variables: time 0.0002473/0.3608, allocations: 239.2 kB / 448.9 MB, free: 6.43 MB / 318.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.3608, allocations: 0 / 448.9 MB, free: 6.43 MB / 318.1 MB
Notification: Performance of remove unused functions: time 0.0005794/0.3614, allocations: 160 kB / 449.1 MB, free: 6.273 MB / 318.1 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 0.00017/0.3616, allocations: 118.2 kB / 449.2 MB, free: 6.152 MB / 318.1 MB
Notification: Performance of simCode: created initialization part: time 0.001157/0.3628, allocations: 0.6219 MB / 449.8 MB, free: 5.531 MB / 318.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.206e-06/0.3628, allocations: 0 / 449.8 MB, free: 5.531 MB / 318.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003537/0.3631, allocations: 259.1 kB / 450.1 MB, free: 5.281 MB / 318.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005161/0.3637, allocations: 66.03 kB / 450.1 MB, free: 5.215 MB / 318.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003449/0.3671, allocations: 2.21 MB / 452.4 MB, free: 2.961 MB / 318.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005967/0.3677, allocations: 0.9503 MB / 453.3 MB, free: 1.984 MB / 318.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001771/0.3679, allocations: 51.42 kB / 453.4 MB, free: 1.934 MB / 318.1 MB
Notification: Performance of SimCode: time 5.11e-07/0.3679, allocations: 0 / 453.4 MB, free: 1.934 MB / 318.1 MB
Notification: Performance of Templates: time 0.0114/0.3793, allocations: 7.417 MB / 460.8 MB, free: 10.53 MB / 334.1 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)