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 0.001048/0.001048, allocations: 86.8 kB / 15.06 MB, free: 1.09 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001644/0.001645, allocations: 168.7 kB / 15.95 MB, free: 204 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.455/1.455, allocations: 223.3 MB / 240 MB, free: 5.398 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2066/0.2066, allocations: 12.27 MB / 303.3 MB, free: 2.098 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003112/0.0003114, allocations: 8 kB / 366.9 MB, free: 9.773 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1135/0.1138, allocations: 53.08 MB / 420 MB, free: 4.578 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.2782/0.392, allocations: 7.669 MB / 427.7 MB, free: 34.93 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.00206/0.3941, allocations: 0.8203 MB / 428.5 MB, free: 34.75 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003789/0.3945, allocations: 41.72 kB / 428.6 MB, free: 34.75 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002387/0.3948, allocations: 115 kB / 428.7 MB, free: 34.71 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004444/0.3952, allocations: 162.2 kB / 428.8 MB, free: 34.64 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003649/0.3956, allocations: 121.5 kB / 428.9 MB, free: 34.64 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0007403/0.3964, allocations: 0.7641 MB / 429.7 MB, free: 34.45 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006761/0.397, allocations: 411.7 kB / 430.1 MB, free: 34.41 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002087/0.3973, allocations: 251.2 kB / 430.4 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003148/0.3976, allocations: 313.6 kB / 430.7 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 7.526e-05/0.3977, allocations: 41.97 kB / 430.7 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.926e-05/0.3977, allocations: 40 kB / 430.7 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 9.815e-05/0.3979, allocations: 129.8 kB / 430.9 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001365/0.398, allocations: 184.9 kB / 431 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006906/0.3987, allocations: 0.8761 MB / 431.9 MB, free: 34.11 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.747e-06/0.3987, allocations: 0 / 431.9 MB, free: 34.11 MB / 350.1 MB
Notification: Performance of FrontEnd: time 3.196e-06/0.3987, allocations: 1.281 kB / 431.9 MB, free: 34.11 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.241e-05/0.3987, allocations: 0 / 431.9 MB, free: 34.11 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 0.00119/0.3999, allocations: 0.952 MB / 432.9 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.709e-05/0.4, allocations: 11.12 kB / 432.9 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001253/0.4001, allocations: 93.31 kB / 433 MB, free: 33.47 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002173/0.4003, allocations: 296.7 kB / 433.3 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.041e-05/0.4004, allocations: 72.5 kB / 433.3 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001252/0.4005, allocations: 106.3 kB / 433.4 MB, free: 33.19 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00131/0.4018, allocations: 0.8674 MB / 434.3 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.806e-05/0.4019, allocations: 2.438 kB / 434.3 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.112e-05/0.402, allocations: 37.25 kB / 434.3 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.142e-05/0.402, allocations: 29.98 kB / 434.4 MB, free: 33.11 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001035/0.403, allocations: 0.6223 MB / 435 MB, free: 33.1 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003842/0.4069, allocations: 2.842 MB / 437.8 MB, free: 32.07 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008194/0.4077, allocations: 0.5117 MB / 438.4 MB, free: 31.84 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003895/0.4081, allocations: 322 kB / 438.7 MB, free: 31.7 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.149e-05/0.4082, allocations: 3.344 kB / 438.7 MB, free: 31.7 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.457e-05/0.4082, allocations: 40.78 kB / 438.7 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.014e-06/0.4082, allocations: 0 / 438.7 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004271/0.4125, allocations: 2.167 MB / 440.9 MB, free: 30.66 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.579e-05/0.4125, allocations: 94.11 kB / 441 MB, free: 30.56 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003293/0.4129, allocations: 366.3 kB / 441.3 MB, free: 30.37 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.114e-05/0.4129, allocations: 36.86 kB / 441.4 MB, free: 30.33 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001941/0.4131, allocations: 448.2 kB / 441.8 MB, free: 29.98 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001177/0.4132, allocations: 218.9 kB / 442 MB, free: 29.81 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 2.588e-05/0.4132, allocations: 15.16 kB / 442 MB, free: 29.8 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 8.253e-05/0.4133, allocations: 359.5 kB / 442.4 MB, free: 29.47 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003028/0.4136, allocations: 245.3 kB / 442.6 MB, free: 29.37 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003481/0.414, allocations: 483.1 kB / 443.1 MB, free: 28.95 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003673/0.4144, allocations: 307.5 kB / 443.4 MB, free: 28.78 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.988e-06/0.4144, allocations: 6.578 kB / 443.4 MB, free: 28.78 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009823/0.4154, allocations: 0.7926 MB / 444.2 MB, free: 28.41 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.133e-05/0.4154, allocations: 8.812 kB / 444.2 MB, free: 28.41 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.349e-05/0.4154, allocations: 21.2 kB / 444.2 MB, free: 28.41 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.755e-05/0.4155, allocations: 14.97 kB / 444.2 MB, free: 28.41 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005934/0.4161, allocations: 183.4 kB / 444.4 MB, free: 28.39 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.751e-05/0.4161, allocations: 16.62 kB / 444.4 MB, free: 28.38 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003289/0.4164, allocations: 52.69 kB / 444.5 MB, free: 28.36 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.243e-05/0.4165, allocations: 32.28 kB / 444.5 MB, free: 28.36 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 0.0004569/0.4169, allocations: 276.5 kB / 444.8 MB, free: 28.14 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.322e-05/0.417, allocations: 45.75 kB / 444.8 MB, free: 28.12 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001616/0.4172, allocations: 74.44 kB / 444.9 MB, free: 28.06 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.44e-06/0.4172, allocations: 13.25 kB / 444.9 MB, free: 28.05 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.173e-05/0.4172, allocations: 3.312 kB / 444.9 MB, free: 28.05 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.596e-06/0.4172, allocations: 3.938 kB / 444.9 MB, free: 28.05 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009232/0.4182, allocations: 0.7631 MB / 445.7 MB, free: 27.64 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.655e-06/0.4182, allocations: 0 / 445.7 MB, free: 27.64 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004896/0.4187, allocations: 111.7 kB / 445.8 MB, free: 27.63 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.589e-06/0.4187, allocations: 0 / 445.8 MB, free: 27.63 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.703e-05/0.4187, allocations: 21.97 kB / 445.8 MB, free: 27.62 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.286e-06/0.4187, allocations: 3.188 kB / 445.8 MB, free: 27.62 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.054e-06/0.4187, allocations: 0 / 445.8 MB, free: 27.62 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009973/0.4197, allocations: 0.9314 MB / 446.7 MB, free: 27.09 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.256e-05/0.4198, allocations: 113.2 kB / 446.9 MB, free: 26.97 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.749e-05/0.4199, allocations: 19.14 kB / 446.9 MB, free: 26.96 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002739/0.4202, allocations: 32.23 kB / 446.9 MB, free: 26.95 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.709e-05/0.4202, allocations: 34.28 kB / 446.9 MB, free: 26.94 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.505e-05/0.4202, allocations: 17.16 kB / 447 MB, free: 26.94 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001752/0.4204, allocations: 240.4 kB / 447.2 MB, free: 26.8 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.11e-07/0.4204, allocations: 0 / 447.2 MB, free: 26.8 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005664/0.421, allocations: 158.2 kB / 447.3 MB, free: 26.79 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 0.0001211/0.4211, allocations: 110.7 kB / 447.5 MB, free: 26.68 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0007391/0.4219, allocations: 0.5956 MB / 448.1 MB, free: 26.46 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.515e-06/0.4219, allocations: 0 / 448.1 MB, free: 26.46 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002773/0.4222, allocations: 262.7 kB / 448.3 MB, free: 26.36 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004582/0.4226, allocations: 63.84 kB / 448.4 MB, free: 26.33 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002688/0.4253, allocations: 2.247 MB / 450.6 MB, free: 24.84 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003422/0.4257, allocations: 0.9446 MB / 451.6 MB, free: 24.12 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002952/0.426, allocations: 58.5 kB / 451.6 MB, free: 24.11 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000132/0.4261, allocations: 45.52 kB / 451.7 MB, free: 24.11 MB / 350.1 MB
Notification: Performance of SimCode: time 2.2e-07/0.4261, allocations: 0 / 451.7 MB, free: 24.11 MB / 350.1 MB
Notification: Performance of Templates: time 0.009123/0.4353, allocations: 4.901 MB / 456.6 MB, free: 23.79 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)