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 0.0008663/0.0008659, allocations: 91.77 kB / 15.36 MB, free: 0.7383 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.007707/0.007707, allocations: 172.4 kB / 16.26 MB, free: 6.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.37/1.37, allocations: 223.3 MB / 240.3 MB, free: 5.352 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1913/0.1913, allocations: 12.25 MB / 303.7 MB, free: 2.004 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003502/0.0003502, allocations: 8 kB / 367.5 MB, free: 9.457 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1218/0.1222, allocations: 53.08 MB / 420.6 MB, free: 4.27 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.264/0.3863, allocations: 8.029 MB / 428.6 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.002108/0.3884, allocations: 0.819 MB / 429.5 MB, free: 34.81 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003534/0.3888, allocations: 40.16 kB / 429.5 MB, free: 34.81 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002392/0.389, allocations: 108.7 kB / 429.6 MB, free: 34.77 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004702/0.3895, allocations: 166.9 kB / 429.8 MB, free: 34.7 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003802/0.3899, allocations: 165.3 kB / 429.9 MB, free: 34.7 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0006595/0.3906, allocations: 0.7864 MB / 430.7 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006609/0.3912, allocations: 474.7 kB / 431.2 MB, free: 34.45 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002394/0.3915, allocations: 256.1 kB / 431.4 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003225/0.3918, allocations: 332.3 kB / 431.8 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 7.001e-05/0.3919, allocations: 43.88 kB / 431.8 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.72e-05/0.392, allocations: 41.06 kB / 431.8 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 9.169e-05/0.3921, allocations: 134.7 kB / 432 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000299/0.3924, allocations: 414.8 kB / 432.4 MB, free: 34.06 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0009735/0.3934, allocations: 1.057 MB / 433.4 MB, free: 33.91 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.42e-06/0.3934, allocations: 2.938 kB / 433.4 MB, free: 33.91 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.104e-06/0.3934, allocations: 3.75 kB / 433.4 MB, free: 33.91 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.948e-05/0.3934, allocations: 0 / 433.4 MB, free: 33.91 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 0.001423/0.3949, allocations: 0.9352 MB / 434.4 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.117e-05/0.3949, allocations: 10 kB / 434.4 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001562/0.3951, allocations: 96.56 kB / 434.5 MB, free: 33.27 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002709/0.3954, allocations: 310.3 kB / 434.8 MB, free: 32.99 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.513e-05/0.3954, allocations: 74.84 kB / 434.9 MB, free: 32.98 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000148/0.3956, allocations: 101.7 kB / 435 MB, free: 32.98 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001462/0.397, allocations: 0.8804 MB / 435.8 MB, free: 32.9 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.917e-05/0.3971, allocations: 5.375 kB / 435.8 MB, free: 32.9 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.335e-05/0.3972, allocations: 41.81 kB / 435.9 MB, free: 32.9 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.183e-05/0.3972, allocations: 23.25 kB / 435.9 MB, free: 32.9 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009911/0.3982, allocations: 0.6162 MB / 436.5 MB, free: 32.89 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004012/0.4022, allocations: 2.843 MB / 439.4 MB, free: 31.94 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009042/0.4031, allocations: 0.5219 MB / 439.9 MB, free: 31.7 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003886/0.4035, allocations: 319.3 kB / 440.2 MB, free: 31.55 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.037e-05/0.4036, allocations: 6.969 kB / 440.2 MB, free: 31.55 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.676e-05/0.4036, allocations: 48.12 kB / 440.3 MB, free: 31.51 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 3.566e-06/0.4036, allocations: 0 / 440.3 MB, free: 31.51 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004771/0.4084, allocations: 2.166 MB / 442.4 MB, free: 30.52 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.655e-05/0.4085, allocations: 89.05 kB / 442.5 MB, free: 30.42 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003339/0.4088, allocations: 362.9 kB / 442.9 MB, free: 30.23 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.125e-05/0.4088, allocations: 38.14 kB / 442.9 MB, free: 30.19 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002089/0.409, allocations: 447.4 kB / 443.3 MB, free: 29.84 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001182/0.4092, allocations: 216.6 kB / 443.5 MB, free: 29.68 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.928e-05/0.4093, allocations: 74.75 kB / 443.6 MB, free: 29.64 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 9.988e-05/0.4094, allocations: 358.1 kB / 444 MB, free: 29.3 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003147/0.4097, allocations: 252.5 kB / 444.2 MB, free: 29.2 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003974/0.4101, allocations: 489.5 kB / 444.7 MB, free: 28.77 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005746/0.4158, allocations: 1.755 MB / 446.4 MB, free: 27.96 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.42e-06/0.4159, allocations: 3.219 kB / 446.5 MB, free: 27.96 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001104/0.417, allocations: 0.8004 MB / 447.3 MB, free: 27.6 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.721e-05/0.417, allocations: 9.094 kB / 447.3 MB, free: 27.6 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.506e-05/0.417, allocations: 9.812 kB / 447.3 MB, free: 27.6 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.749e-05/0.4171, allocations: 12.44 kB / 447.3 MB, free: 27.6 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006134/0.4177, allocations: 185.7 kB / 447.5 MB, free: 27.58 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.928e-05/0.4177, allocations: 23.31 kB / 447.5 MB, free: 27.57 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003973/0.4181, allocations: 43.23 kB / 447.5 MB, free: 27.55 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.044e-05/0.4182, allocations: 41.47 kB / 447.6 MB, free: 27.54 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 0.0005297/0.4187, allocations: 282.5 kB / 447.8 MB, free: 27.33 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.939e-05/0.4188, allocations: 45.41 kB / 447.9 MB, free: 27.3 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001586/0.419, allocations: 69.11 kB / 448 MB, free: 27.25 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.204e-06/0.419, allocations: 6.562 kB / 448 MB, free: 27.25 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.233e-05/0.419, allocations: 0 / 448 MB, free: 27.25 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.994e-06/0.419, allocations: 3.938 kB / 448 MB, free: 27.25 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009844/0.42, allocations: 0.7693 MB / 448.7 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.987e-06/0.42, allocations: 3.984 kB / 448.7 MB, free: 26.83 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005046/0.4205, allocations: 114.8 kB / 448.9 MB, free: 26.82 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.278e-06/0.4205, allocations: 3.25 kB / 448.9 MB, free: 26.82 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.606e-05/0.4206, allocations: 18.19 kB / 448.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.42e-06/0.4206, allocations: 3.094 kB / 448.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.954e-06/0.4206, allocations: 0 / 448.9 MB, free: 26.81 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001016/0.4216, allocations: 0.9299 MB / 449.8 MB, free: 26.28 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 9.455e-05/0.4217, allocations: 117.5 kB / 449.9 MB, free: 26.16 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.946e-05/0.4218, allocations: 18.39 kB / 449.9 MB, free: 26.14 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003016/0.4221, allocations: 24.02 kB / 450 MB, free: 26.14 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.812e-05/0.4222, allocations: 38 kB / 450 MB, free: 26.13 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.857e-05/0.4222, allocations: 20.38 kB / 450 MB, free: 26.12 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001932/0.4224, allocations: 234.9 kB / 450.2 MB, free: 26 MB / 350.1 MB
Notification: Performance of sort global known variables: time 2.4e-07/0.4224, allocations: 4 kB / 450.3 MB, free: 25.99 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0006026/0.423, allocations: 156.1 kB / 450.4 MB, free: 25.97 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 0.0001111/0.4231, allocations: 117.9 kB / 450.5 MB, free: 25.87 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0007441/0.4239, allocations: 0.5981 MB / 451.1 MB, free: 25.64 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.785e-06/0.4239, allocations: 0 / 451.1 MB, free: 25.64 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002784/0.4242, allocations: 255.7 kB / 451.4 MB, free: 25.55 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005071/0.4247, allocations: 74.33 kB / 451.4 MB, free: 25.51 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002981/0.4277, allocations: 2.33 MB / 453.8 MB, free: 23.95 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003354/0.428, allocations: 0.9359 MB / 454.7 MB, free: 23.24 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002851/0.4283, allocations: 73.34 kB / 454.8 MB, free: 23.22 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001324/0.4285, allocations: 43.58 kB / 454.8 MB, free: 23.21 MB / 350.1 MB
Notification: Performance of SimCode: time 4.21e-07/0.4285, allocations: 0.75 kB / 454.8 MB, free: 23.21 MB / 350.1 MB
Notification: Performance of Templates: time 0.008781/0.4373, allocations: 5.045 MB / 459.9 MB, free: 22.91 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)